3NQ4 | pdb_00003nq4

30mer structure of Lumazine synthase from Salmonella typhimurium LT2

PDB DOI: https://doi.org/10.2210/pdb3NQ4/pdb

Classification: TRANSFERASE
Organism(s): Salmonella enterica subsp. enterica serovar Typhimurium str. LT2
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2010-06-29 Released: 2011-06-08
Deposition Author(s): Kumar, P., Singh, M., Karthikeyan, S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.50 Å
R-Value Free:
0.299 (Depositor), 0.307 (DCC)
R-Value Work:
0.255 (Depositor), 0.266 (DCC)
R-Value Observed:
0.256 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Crystal structure of Lumazine synthase from Salmonella typhimurium LT2

Kumar, P., Singh, M., Karthikeyan, S.

To be published.

Macromolecule Content

Total Structure Weight: 484.51 kDa
Atom Count: 33,262
Modeled Residue Count: 4,620
Deposited Residue Count: 4,680
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
6,7-dimethyl-8-ribityllumazine synthase	A AA [auth 1] B BA [auth 2] C A, AA [auth 1], B, BA [auth 2], C, CA [auth 3], D, DA [auth 4], E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X, Y, Z	156	Salmonella enterica subsp. enterica serovar Typhimurium str. LT2	Mutation(s): 0 Gene Names: ribH, STM0417 EC: 2.5.1.78
UniProt
Find proteins for P66038 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)) Explore P66038 Go to UniProtKB: P66038
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P66038
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain ZA [auth P] SDF format, chain YA [auth N] SDF format, chain XA [auth M] SDF format, chain WA [auth M] SDF format, chain VA [auth M] SDF format, chain UA [auth L] SDF format, chain TA [auth L] SDF format, chain SA [auth K] SDF format, chain RB [auth 3] SDF format, chain RA [auth J] SDF format, chain QB [auth 2] SDF format, chain QA [auth H] SDF format, chain PB [auth 2] SDF format, chain PA [auth H] SDF format, chain OB [auth 2] SDF format, chain OA [auth H] SDF format, chain NB [auth 1] SDF format, chain NA [auth G] SDF format, chain MB [auth 1] SDF format, chain MA [auth F] SDF format, chain LB [auth Z] SDF format, chain LA [auth F] SDF format, chain KB [auth Z] SDF format, chain KA [auth E] SDF format, chain JB [auth X] SDF format, chain JA [auth D] SDF format, chain IB [auth X] SDF format, chain IA [auth D] SDF format, chain HB [auth V] SDF format, chain HA [auth C] SDF format, chain GB [auth V] SDF format, chain GA [auth C] SDF format, chain FB [auth U] SDF format, chain FA [auth B] SDF format, chain EB [auth S] SDF format, chain EA [auth A] SDF format, chain DB [auth R] SDF format, chain CB [auth Q] SDF format, chain BB [auth Q] SDF format, chain AB [auth Q] MOL2 format, chain ZA [auth P] MOL2 format, chain YA [auth N] MOL2 format, chain XA [auth M] MOL2 format, chain WA [auth M] MOL2 format, chain VA [auth M] MOL2 format, chain UA [auth L] MOL2 format, chain TA [auth L] MOL2 format, chain SA [auth K] MOL2 format, chain RB [auth 3] MOL2 format, chain RA [auth J] MOL2 format, chain QB [auth 2] MOL2 format, chain QA [auth H] MOL2 format, chain PB [auth 2] MOL2 format, chain PA [auth H] MOL2 format, chain OB [auth 2] MOL2 format, chain OA [auth H] MOL2 format, chain NB [auth 1] MOL2 format, chain NA [auth G] MOL2 format, chain MB [auth 1] MOL2 format, chain MA [auth F] MOL2 format, chain LB [auth Z] MOL2 format, chain LA [auth F] MOL2 format, chain KB [auth Z] MOL2 format, chain KA [auth E] MOL2 format, chain JB [auth X] MOL2 format, chain JA [auth D] MOL2 format, chain IB [auth X] MOL2 format, chain IA [auth D] MOL2 format, chain HB [auth V] MOL2 format, chain HA [auth C] MOL2 format, chain GB [auth V] MOL2 format, chain GA [auth C] MOL2 format, chain FB [auth U] MOL2 format, chain FA [auth B] MOL2 format, chain EB [auth S] MOL2 format, chain EA [auth A] MOL2 format, chain DB [auth R] MOL2 format, chain CB [auth Q] MOL2 format, chain BB [auth Q] MOL2 format, chain AB [auth Q] mmCIF format, chain ZA [auth P] mmCIF format, chain YA [auth N] mmCIF format, chain XA [auth M] mmCIF format, chain WA [auth M] mmCIF format, chain VA [auth M] mmCIF format, chain UA [auth L] mmCIF format, chain TA [auth L] mmCIF format, chain SA [auth K] mmCIF format, chain RB [auth 3] mmCIF format, chain RA [auth J] mmCIF format, chain QB [auth 2] mmCIF format, chain QA [auth H] mmCIF format, chain PB [auth 2] mmCIF format, chain PA [auth H] mmCIF format, chain OB [auth 2] mmCIF format, chain OA [auth H] mmCIF format, chain NB [auth 1] mmCIF format, chain NA [auth G] mmCIF format, chain MB [auth 1] mmCIF format, chain MA [auth F] mmCIF format, chain LB [auth Z] mmCIF format, chain LA [auth F] mmCIF format, chain KB [auth Z] mmCIF format, chain KA [auth E] mmCIF format, chain JB [auth X] mmCIF format, chain JA [auth D] mmCIF format, chain IB [auth X] mmCIF format, chain IA [auth D] mmCIF format, chain HB [auth V] mmCIF format, chain HA [auth C] mmCIF format, chain GB [auth V] mmCIF format, chain GA [auth C] mmCIF format, chain FB [auth U] mmCIF format, chain FA [auth B] mmCIF format, chain EB [auth S] mmCIF format, chain EA [auth A] mmCIF format, chain DB [auth R] mmCIF format, chain CB [auth Q] mmCIF format, chain BB [auth Q] mmCIF format, chain AB [auth Q]	AB [auth Q] BB [auth Q] CB [auth Q] DB [auth R] EA [auth A] AB [auth Q], BB [auth Q], CB [auth Q], DB [auth R], EA [auth A], EB [auth S], FA [auth B], FB [auth U], GA [auth C], GB [auth V], HA [auth C], HB [auth V], IA [auth D], IB [auth X], JA [auth D], JB [auth X], KA [auth E], KB [auth Z], LA [auth F], LB [auth Z], MA [auth F], MB [auth 1], NA [auth G], NB [auth 1], OA [auth H], OB [auth 2], PA [auth H], PB [auth 2], QA [auth H], QB [auth 2], RA [auth J], RB [auth 3], SA [auth K], TA [auth L], UA [auth L], VA [auth M], WA [auth M], XA [auth M], YA [auth N], ZA [auth P]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain AB [auth Q] Focus chain BB [auth Q] Focus chain CB [auth Q] Focus chain DB [auth R] Focus chain EA [auth A] Focus chain EB [auth S] Focus chain FA [auth B] Focus chain FB [auth U] Focus chain GA [auth C] Focus chain GB [auth V] Focus chain HA [auth C] Focus chain HB [auth V] Focus chain IA [auth D] Focus chain IB [auth X] Focus chain JA [auth D] Focus chain JB [auth X] Focus chain KA [auth E] Focus chain KB [auth Z] Focus chain LA [auth F] Focus chain LB [auth Z] Focus chain MA [auth F] Focus chain MB [auth 1] Focus chain NA [auth G] Focus chain NB [auth 1] Focus chain OA [auth H] Focus chain OB [auth 2] Focus chain PA [auth H] Focus chain PB [auth 2] Focus chain QA [auth H] Focus chain QB [auth 2] Focus chain RA [auth J] Focus chain RB [auth 3] Focus chain SA [auth K] Focus chain TA [auth L] Focus chain UA [auth L] Focus chain VA [auth M] Focus chain WA [auth M] Focus chain XA [auth M] Focus chain YA [auth N] Focus chain ZA [auth P] Interactions & Density Focus chain AB [auth Q] Focus chain BB [auth Q] Focus chain CB [auth Q] Focus chain DB [auth R] Focus chain EA [auth A] Focus chain EB [auth S] Focus chain FA [auth B] Focus chain FB [auth U] Focus chain GA [auth C] Focus chain GB [auth V] Focus chain HA [auth C] Focus chain HB [auth V] Focus chain IA [auth D] Focus chain IB [auth X] Focus chain JA [auth D] Focus chain JB [auth X] Focus chain KA [auth E] Focus chain KB [auth Z] Focus chain LA [auth F] Focus chain LB [auth Z] Focus chain MA [auth F] Focus chain MB [auth 1] Focus chain NA [auth G] Focus chain NB [auth 1] Focus chain OA [auth H] Focus chain OB [auth 2] Focus chain PA [auth H] Focus chain PB [auth 2] Focus chain QA [auth H] Focus chain QB [auth 2] Focus chain RA [auth J] Focus chain RB [auth 3] Focus chain SA [auth K] Focus chain TA [auth L] Focus chain UA [auth L] Focus chain VA [auth M] Focus chain WA [auth M] Focus chain XA [auth M] Focus chain YA [auth N] Focus chain ZA [auth P]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.50 Å
R-Value Free: 0.299 (Depositor), 0.307 (DCC)
R-Value Work: 0.255 (Depositor), 0.266 (DCC)
R-Value Observed: 0.256 (Depositor)

Space Group: I 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 174.43	α = 90
b = 157.49	β = 91.58
c = 202.788	γ = 90

Software Package:

Software Name	Purpose
MAR345dtb	data collection
PHASER	phasing
CCP4	model building
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling
CCP4	phasing

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2011-06-08

Deposition Author(s):

Kumar, P.

Singh, M.

Karthikeyan, S.

Revision History (Full details and data files)

Version 1.0: 2011-06-08
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2013-01-23
Changes: Structure summary
Version 1.3: 2023-11-01
Changes: Data collection, Database references, Derived calculations, Refinement description