3RLF

Crystal structure of the maltose-binding protein/maltose transporter complex in an outward-facing conformation bound to MgAMPPNP

PDB DOI: https://doi.org/10.2210/pdb3RLF/pdb

Classification: HYDROLASE/TRANSPORT PROTEIN
Organism(s): Escherichia coli K-12
Expression System: Escherichia coli
Mutation(s): No
Membrane Protein: Yes PDBTMMemProtMDmpstruc

Deposited: 2011-04-19 Released: 2011-08-10
Deposition Author(s): Oldham, M.L., Chen, J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.254
R-Value Work: 0.223
R-Value Observed: 0.225

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.1 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 220.46 kDa
Atom Count: 15,268
Modelled Residue Count: 1,892
Deposited Residue Count: 1,952
Unique protein chains: 4

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Maltose-binding periplasmic protein	A [auth E]	380	Escherichia coli K-12	Mutation(s): 0 Gene Names: malE, b4034, JW3994 Membrane Entity: Yes
UniProt
Find proteins for P0AEX9 (Escherichia coli (strain K12)) Explore P0AEX9 Go to UniProtKB: P0AEX9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0AEX9
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Maltose transport system permease protein malF	B [auth F]	514	Escherichia coli K-12	Mutation(s): 0 Gene Names: malF, b4033, JW3993 Membrane Entity: Yes
UniProt
Find proteins for P02916 (Escherichia coli (strain K12)) Explore P02916 Go to UniProtKB: P02916
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P02916
Sequence Annotations Expand
Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Maltose transport system permease protein malG	C [auth G]	296	Escherichia coli K-12	Mutation(s): 0 Gene Names: malG, b4032, JW3992 Membrane Entity: Yes
UniProt
Find proteins for P68183 (Escherichia coli (strain K12)) Explore P68183 Go to UniProtKB: P68183
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P68183
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Maltose/maltodextrin import ATP-binding protein MalK	D [auth A], E [auth B]	381	Escherichia coli K-12	Mutation(s): 0 Gene Names: malK, b4035, JW3995 EC: 3.6.3.19 Membrane Entity: Yes
UniProt
Find proteins for P68187 (Escherichia coli (strain K12)) Explore P68187 Go to UniProtKB: P68187
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P68187
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose	F [auth C]	2		N/A	Interactions Focus chain F [auth C] Interactions & Density Focus chain F [auth C]
Glycosylation Resources
GlyTouCan: G07411ON GlyCosmos: G07411ON

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PGV Query on PGV Download Ideal Coordinates CCD File SDF format, chain H [auth F] SDF format, chain I [auth F] SDF format, chain J [auth G] SDF format, chain K [auth G] MOL2 format, chain H [auth F] MOL2 format, chain I [auth F] MOL2 format, chain J [auth G] MOL2 format, chain K [auth G]	H [auth F], I [auth F], J [auth G], K [auth G]	(1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE C₄₀ H₇₇ O₁₀ P ADYWCMPUNIVOEA-GPJPVTGXSA-N		Interactions Focus chain H [auth F] Focus chain I [auth F] Focus chain J [auth G] Focus chain K [auth G] Interactions & Density Focus chain H [auth F] Focus chain I [auth F] Focus chain J [auth G] Focus chain K [auth G]
ANP Query on ANP Download Ideal Coordinates CCD File SDF format, chain M [auth A] SDF format, chain O [auth B] MOL2 format, chain M [auth A] MOL2 format, chain O [auth B]	M [auth A], O [auth B]	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER C₁₀ H₁₇ N₆ O₁₂ P₃ PVKSNHVPLWYQGJ-KQYNXXCUSA-N		Interactions Focus chain M [auth A] Focus chain O [auth B] Interactions & Density Focus chain M [auth A] Focus chain O [auth B]
UMQ Query on UMQ Download Ideal Coordinates CCD File SDF format, chain G [auth E] MOL2 format, chain G [auth E]	G [auth E]	UNDECYL-MALTOSIDE C₂₃ H₄₄ O₁₁ UYEMNFYVTFDKRG-ZNGNCRBCSA-N		Interactions Focus chain G [auth E] Interactions & Density Focus chain G [auth E]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain L [auth A] SDF format, chain N [auth B] MOL2 format, chain L [auth A] MOL2 format, chain N [auth B]	L [auth A], N [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain L [auth A] Focus chain N [auth B] Interactions & Density Focus chain L [auth A] Focus chain N [auth B]

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 5
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900001 Query on PRD_900001	F [auth C]	alpha-maltose	Oligosaccharide / Nutrient		Interactions Focus chain F [auth C] Interactions & Density Focus chain F [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.254
R-Value Work: 0.223
R-Value Observed: 0.225
Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.098	α = 86.7
b = 95.812	β = 82.68
c = 109.983	γ = 76.4

Software Package:

Software Name	Purpose
Blu-Ice	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2011-08-10

Deposition Author(s):

Oldham, M.L.

Chen, J.

Revision History (Full details and data files)

Version 1.0: 2011-08-10
Type: Initial release
Version 1.1: 2011-08-24
Changes: Database references
Version 1.2: 2011-09-28
Changes: Database references
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary
Version 2.1: 2023-09-13
Changes: Data collection, Database references, Refinement description, Structure summary