4RRP

Crystal Structure of the Fab complexed with antigen Asf1p, Northeast Structural Genomics Consortium (NESG) Target PdR16

PDB DOI: https://doi.org/10.2210/pdb4RRP/pdb

Classification: IMMUNE SYSTEM
Organism(s): Homo sapiens, Saccharomyces cerevisiae AWRI796
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2014-11-06 Released: 2014-12-31
Deposition Author(s): Kuzin, A., Lew, S., Seetharaman, J., Mao, L., Xiao, R., Oconnell, P.T., Maglaqui, M., Bailey, L., Everett, J.K., Acton, T.B., Montelione, G.T., Hunt, J.F., Tong, L., Chaperone-Enabled Studies of Epigenetic Regulation Enzymes (CEBS), Northeast Structural Genomics Consortium (NESG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.79 Å
R-Value Free: 0.253
R-Value Work: 0.183
R-Value Observed: 0.185

wwPDB Validation 3D Report Full Report

This is version 1.5 of the entry. See complete history.

Literature

Crystal Structure of the Fab complexed with antigen Asf1p, Northeast Structural Genomics Consortium (NESG) Target PdR16

Kuzin, A., Lew, S., Seetharaman, J., Mao, L., Xiao, R., Oconnell, P.T., Maglaqui, M., Bailey, L., Everett, J.K., Acton, T.B., Montelione, G.T., Hunt, J.F., Tong, L.

To be published.

Macromolecule Content

Total Structure Weight: 402.46 kDa
Atom Count: 27,161
Modelled Residue Count: 3,503
Deposited Residue Count: 3,684
Unique protein chains: 3

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab antibody, light chain	A C [auth B] E [auth C] G [auth D] I [auth E] A, C [auth B], E [auth C], G [auth D], I [auth E], K [auth F]	216	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab antibody, heavy chain	B [auth G] D [auth H] F [auth I] H [auth J] J [auth K] B [auth G], D [auth H], F [auth I], H [auth J], J [auth K], L	238	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Antigen Asf1p	M, N, O, P, Q M, N, O, P, Q, R	160	Saccharomyces cerevisiae AWRI796	Mutation(s): 0 Gene Names: AWRI796_2536
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain S [auth A] MOL2 format, chain S [auth A]	S [auth A]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain S [auth A] Interactions & Density Focus chain S [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.79 Å
R-Value Free: 0.253
R-Value Work: 0.183
R-Value Observed: 0.185
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 92.725	α = 90
b = 181.309	β = 90
c = 259.286	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
SCALEPACK	data scaling
BALBES	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2014-12-31

Deposition Author(s):

Chaperone-Enabled Studies of Epigenetic Regulation Enzymes (CEBS)

Northeast Structural Genomics Consortium (NESG)

Revision History (Full details and data files)

Version 1.0: 2014-12-31
Type: Initial release
Version 1.1: 2015-01-07
Changes: Structure summary
Version 1.2: 2015-01-14
Changes: Derived calculations, Structure summary
Version 1.3: 2015-02-25
Changes: Structure summary
Version 1.4: 2015-07-22
Changes: Source and taxonomy
Version 1.5: 2023-09-20
Changes: Data collection, Database references, Derived calculations, Refinement description