3C1L

Crystal structure of an antioxidant defense protein (mlr4105) from mesorhizobium loti maff303099 at 2.00 A resolution

PDB DOI: https://doi.org/10.2210/pdb3C1L/pdb

Classification: OXIDOREDUCTASE
Organism(s): Mesorhizobium japonicum MAFF 303099
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2008-01-23 Released: 2008-02-05
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.225
R-Value Work: 0.171
R-Value Observed: 0.174

wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

Literature

Crystal structure of putative antioxidant defense protein (NP_105057.1) from Mesorhizobium loti at 2.00 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content

Total Structure Weight: 255.15 kDa
Atom Count: 17,569
Modelled Residue Count: 2,183
Deposited Residue Count: 2,256
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative antioxidant defense protein Mlr4105	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	188	Mesorhizobium japonicum MAFF 303099	Mutation(s): 0 Gene Names: NP_105057.1, mlr4105
UniProt
Find proteins for Q98ES4 (Mesorhizobium japonicum (strain LMG 29417 / CECT 9101 / MAFF 303099)) Explore Q98ES4 Go to UniProtKB: Q98ES4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q98ES4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain AA [auth E] SDF format, chain BA [auth E] SDF format, chain CA [auth G] SDF format, chain DA [auth H] SDF format, chain EA [auth H] SDF format, chain FA [auth I] SDF format, chain GA [auth I] SDF format, chain HA [auth I] SDF format, chain JA [auth J] SDF format, chain KA [auth J] SDF format, chain LA [auth J] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain S [auth B] SDF format, chain T [auth B] SDF format, chain U [auth C] SDF format, chain V [auth C] SDF format, chain W [auth C] SDF format, chain X [auth D] SDF format, chain Y [auth D] SDF format, chain Z [auth D] MOL2 format, chain AA [auth E] MOL2 format, chain BA [auth E] MOL2 format, chain CA [auth G] MOL2 format, chain DA [auth H] MOL2 format, chain EA [auth H] MOL2 format, chain FA [auth I] MOL2 format, chain GA [auth I] MOL2 format, chain HA [auth I] MOL2 format, chain JA [auth J] MOL2 format, chain KA [auth J] MOL2 format, chain LA [auth J] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B] MOL2 format, chain U [auth C] MOL2 format, chain V [auth C] MOL2 format, chain W [auth C] MOL2 format, chain X [auth D] MOL2 format, chain Y [auth D] MOL2 format, chain Z [auth D]	AA [auth E] BA [auth E] CA [auth G] DA [auth H] EA [auth H] AA [auth E], BA [auth E], CA [auth G], DA [auth H], EA [auth H], FA [auth I], GA [auth I], HA [auth I], JA [auth J], KA [auth J], LA [auth J], M [auth A], N [auth A], O [auth A], P [auth A], Q [auth B], R [auth B], S [auth B], T [auth B], U [auth C], V [auth C], W [auth C], X [auth D], Y [auth D], Z [auth D]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain AA [auth E] Focus chain BA [auth E] Focus chain CA [auth G] Focus chain DA [auth H] Focus chain EA [auth H] Focus chain FA [auth I] Focus chain GA [auth I] Focus chain HA [auth I] Focus chain JA [auth J] Focus chain KA [auth J] Focus chain LA [auth J] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth C] Focus chain V [auth C] Focus chain W [auth C] Focus chain X [auth D] Focus chain Y [auth D] Focus chain Z [auth D] Interactions & Density Focus chain AA [auth E] Focus chain BA [auth E] Focus chain CA [auth G] Focus chain DA [auth H] Focus chain EA [auth H] Focus chain FA [auth I] Focus chain GA [auth I] Focus chain HA [auth I] Focus chain JA [auth J] Focus chain KA [auth J] Focus chain LA [auth J] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth C] Focus chain V [auth C] Focus chain W [auth C] Focus chain X [auth D] Focus chain Y [auth D] Focus chain Z [auth D]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain IA [auth J] MOL2 format, chain IA [auth J]	IA [auth J]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain IA [auth J] Interactions & Density Focus chain IA [auth J]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.225
R-Value Work: 0.171
R-Value Observed: 0.174
Space Group: P 1 2₁ 1
Diffraction Data: https://doi.org/10.18430/M33C1L

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.69	α = 90
b = 68.06	β = 95.94
c = 266.83	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
MolProbity	model building
PDB_EXTRACT	data extraction
MAR345	data collection
XDS	data reduction
MOSFLM	data reduction
XSCALE	data scaling
SCALA	data scaling
SHARP	phasing
MOLREP	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2008-02-05

Deposition Author(s):

Joint Center for Structural Genomics (JCSG)

Revision History (Full details and data files)

Version 1.0: 2008-02-05
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Source and taxonomy, Version format compliance
Version 1.2: 2017-10-25
Changes: Refinement description
Version 1.3: 2019-07-24
Changes: Data collection, Derived calculations, Refinement description
Version 1.4: 2023-02-01
Changes: Database references, Derived calculations