4LKB | pdb_00004lkb

Crystal structure of a putative 4-Oxalocrotonate Tautomerase from Nostoc sp. PCC 7120

PDB DOI: https://doi.org/10.2210/pdb4LKB/pdb

Classification: ISOMERASE
Organism(s): Nostoc sp. PCC 7120 = FACHB-418
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2013-07-07 Released: 2013-07-24
Deposition Author(s): Kumaran, D., Chamala, S., Evans, B., Foti, R., Gizzi, A., Hillerich, B., Kar, A., Lafleur, J., Seidel, R., Villigas, G., Zencheck, W., Al Obaidi, N., Almo, S.C., Swaminathan, S., New York Structural Genomics Research Consortium (NYSGRC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.16 Å
R-Value Free:
0.221 (Depositor), 0.229 (DCC)
R-Value Work:
0.176 (Depositor), 0.186 (DCC)
R-Value Observed:
0.178 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Crystal structure of a putative 4-Oxalocrotonate Tautomerase from Nostoc sp. PCC 7120

Kumaran, D., Almo, S.C., Swaminathan, S.

To be published.

Macromolecule Content

Total Structure Weight: 108.33 kDa
Atom Count: 6,348
Modeled Residue Count: 726
Deposited Residue Count: 906
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
hypothetical protein alr4568/putative 4-Oxalocrotonate Tautomerase	A [auth F] B C D E A [auth F], B, C, D, E, F [auth A]	151	Nostoc sp. PCC 7120 = FACHB-418	Mutation(s): 0 Gene Names: alr4568
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain O [auth E] SDF format, chain M [auth D] SDF format, chain L [auth D] SDF format, chain I [auth B] SDF format, chain H [auth F] MOL2 format, chain O [auth E] MOL2 format, chain M [auth D] MOL2 format, chain L [auth D] MOL2 format, chain I [auth B] MOL2 format, chain H [auth F] mmCIF format, chain O [auth E] mmCIF format, chain M [auth D] mmCIF format, chain L [auth D] mmCIF format, chain I [auth B] mmCIF format, chain H [auth F]	H [auth F], I [auth B], L [auth D], M [auth D], O [auth E]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain H [auth F] Focus chain I [auth B] Focus chain L [auth D] Focus chain M [auth D] Focus chain O [auth E] Interactions & Density Focus chain H [auth F] Focus chain I [auth B] Focus chain L [auth D] Focus chain M [auth D] Focus chain O [auth E]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain N [auth E] SDF format, chain K [auth D] SDF format, chain J [auth C] SDF format, chain G [auth F] MOL2 format, chain N [auth E] MOL2 format, chain K [auth D] MOL2 format, chain J [auth C] MOL2 format, chain G [auth F] mmCIF format, chain N [auth E] mmCIF format, chain K [auth D] mmCIF format, chain J [auth C] mmCIF format, chain G [auth F]	G [auth F], J [auth C], K [auth D], N [auth E]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain G [auth F] Focus chain J [auth C] Focus chain K [auth D] Focus chain N [auth E] Interactions & Density Focus chain G [auth F] Focus chain J [auth C] Focus chain K [auth D] Focus chain N [auth E]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A [auth F] B C D E A [auth F], B, C, D, E, F [auth A]	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.16 Å
R-Value Free: 0.221 (Depositor), 0.229 (DCC)
R-Value Work: 0.176 (Depositor), 0.186 (DCC)
R-Value Observed: 0.178 (Depositor)

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 111.022	α = 90
b = 132.926	β = 90
c = 133.121	γ = 90

Software Package:

Software Name	Purpose
CBASS	data collection
SHELXD	phasing
SHELXE	model building
ARP/wARP	model building
Coot	model building
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2013-07-24

Deposition Author(s):

New York Structural Genomics Research Consortium (NYSGRC)

Revision History (Full details and data files)

Version 1.0: 2013-07-24
Type: Initial release
Version 1.1: 2024-11-06
Changes: Data collection, Database references, Derived calculations, Structure summary