1ZIS | pdb_00001zis

Recombinant Lumazine synthase (hexagonal form)

PDB DOI: https://doi.org/10.2210/pdb1ZIS/pdb

Classification: TRANSFERASE
Organism(s): Bacillus subtilis
Expression System: Bacillus subtilis
Mutation(s): No

Deposited: 2005-04-27 Released: 2006-10-03
Deposition Author(s): Lopez-Jaramillo, F.J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free:
0.240 (Depositor), 0.230 (DCC)
R-Value Work:
0.206 (Depositor), 0.190 (DCC)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal structure of recombinant Lumazine synthase (hexagonal form)

Lopez-Jaramillo, F.J.

To be published.

Macromolecule Content

Total Structure Weight: 167.04 kDa
Atom Count: 11,700
Modeled Residue Count: 1,540
Deposited Residue Count: 1,540
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
6,7-dimethyl-8-ribityllumazine synthase	A, B, C, D, E A, B, C, D, E, F, G, H, I, J	154	Bacillus subtilis	Mutation(s): 0 Gene Names: ribH EC: 2.5.1.78
UniProt
Find proteins for P11998 (Bacillus subtilis (strain 168)) Explore P11998 Go to UniProtKB: P11998
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P11998
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
INI Query on INI Download Ideal Coordinates CCD File SDF format, chain BA [auth I] SDF format, chain DA [auth J] SDF format, chain L [auth A] SDF format, chain N [auth B] SDF format, chain P [auth C] SDF format, chain V [auth F] SDF format, chain Z [auth H] SDF format, chain X [auth G] SDF format, chain T [auth E] SDF format, chain S [auth D] MOL2 format, chain BA [auth I] MOL2 format, chain DA [auth J] MOL2 format, chain L [auth A] MOL2 format, chain N [auth B] MOL2 format, chain P [auth C] MOL2 format, chain V [auth F] MOL2 format, chain Z [auth H] MOL2 format, chain X [auth G] MOL2 format, chain T [auth E] MOL2 format, chain S [auth D] mmCIF format, chain BA [auth I] mmCIF format, chain DA [auth J] mmCIF format, chain L [auth A] mmCIF format, chain N [auth B] mmCIF format, chain P [auth C] mmCIF format, chain V [auth F] mmCIF format, chain Z [auth H] mmCIF format, chain X [auth G] mmCIF format, chain T [auth E] mmCIF format, chain S [auth D]	BA [auth I] DA [auth J] L [auth A] N [auth B] P [auth C] BA [auth I], DA [auth J], L [auth A], N [auth B], P [auth C], S [auth D], T [auth E], V [auth F], X [auth G], Z [auth H]	5-NITRO-6-RIBITYL-AMINO-2,4(1H,3H)-PYRIMIDINEDIONE C₉ H₁₄ N₄ O₈ KSKGHNZSCSCHEQ-RPDRRWSUSA-N		Interactions Focus chain BA [auth I] Focus chain DA [auth J] Focus chain L [auth A] Focus chain N [auth B] Focus chain P [auth C] Focus chain S [auth D] Focus chain T [auth E] Focus chain V [auth F] Focus chain X [auth G] Focus chain Z [auth H] Interactions & Density Focus chain BA [auth I] Focus chain DA [auth J] Focus chain L [auth A] Focus chain N [auth B] Focus chain P [auth C] Focus chain S [auth D] Focus chain T [auth E] Focus chain V [auth F] Focus chain X [auth G] Focus chain Z [auth H]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain AA [auth I] SDF format, chain CA [auth J] SDF format, chain K [auth A] SDF format, chain R [auth D] SDF format, chain W [auth G] SDF format, chain Y [auth H] SDF format, chain U [auth F] SDF format, chain Q [auth D] SDF format, chain O [auth C] SDF format, chain M [auth B] MOL2 format, chain AA [auth I] MOL2 format, chain CA [auth J] MOL2 format, chain K [auth A] MOL2 format, chain R [auth D] MOL2 format, chain W [auth G] MOL2 format, chain Y [auth H] MOL2 format, chain U [auth F] MOL2 format, chain Q [auth D] MOL2 format, chain O [auth C] MOL2 format, chain M [auth B] mmCIF format, chain AA [auth I] mmCIF format, chain CA [auth J] mmCIF format, chain K [auth A] mmCIF format, chain R [auth D] mmCIF format, chain W [auth G] mmCIF format, chain Y [auth H] mmCIF format, chain U [auth F] mmCIF format, chain Q [auth D] mmCIF format, chain O [auth C] mmCIF format, chain M [auth B]	AA [auth I] CA [auth J] K [auth A] M [auth B] O [auth C] AA [auth I], CA [auth J], K [auth A], M [auth B], O [auth C], Q [auth D], R [auth D], U [auth F], W [auth G], Y [auth H]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain AA [auth I] Focus chain CA [auth J] Focus chain K [auth A] Focus chain M [auth B] Focus chain O [auth C] Focus chain Q [auth D] Focus chain R [auth D] Focus chain U [auth F] Focus chain W [auth G] Focus chain Y [auth H] Interactions & Density Focus chain AA [auth I] Focus chain CA [auth J] Focus chain K [auth A] Focus chain M [auth B] Focus chain O [auth C] Focus chain Q [auth D] Focus chain R [auth D] Focus chain U [auth F] Focus chain W [auth G] Focus chain Y [auth H]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free: 0.240 (Depositor), 0.230 (DCC)
R-Value Work: 0.206 (Depositor), 0.190 (DCC)

Space Group: P 6₃ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 153.69	α = 90
b = 153.69	β = 90
c = 296.3	γ = 120

Software Package:

Software Name	Purpose
CNS	refinement
XDS	data reduction
XDS	data scaling
AMoRE	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2006-10-03

Deposition Author(s):

Lopez-Jaramillo, F.J.

Revision History (Full details and data files)

Version 1.0: 2006-10-03
Type: Initial release
Version 1.1: 2008-04-30
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2013-01-16
Changes: Other
Version 1.4: 2018-01-24
Changes: Database references
Version 1.5: 2023-08-23
Changes: Data collection, Database references, Derived calculations, Refinement description