3C1L | pdb_00003c1l

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 (Depositor), 0.227 (DCC)
R-Value Work:
0.171 (Depositor), 0.176 (DCC)
R-Value Observed:
0.174 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.5 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
Modeled Residue Count: 2,183
Deposited Residue Count: 2,256
Unique protein chains: 1

Macromolecules

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| 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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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 BA [auth E] SDF format, chain DA [auth H] SDF format, chain GA [auth I] SDF format, chain JA [auth J] SDF format, chain KA [auth J] SDF format, chain O [auth A] SDF format, chain R [auth B] SDF format, chain V [auth C] SDF format, chain Y [auth D] SDF format, chain Z [auth D] SDF format, chain X [auth D] SDF format, chain W [auth C] SDF format, chain U [auth C] SDF format, chain T [auth B] SDF format, chain S [auth B] SDF format, chain Q [auth B] SDF format, chain P [auth A] SDF format, chain N [auth A] SDF format, chain M [auth A] SDF format, chain LA [auth J] SDF format, chain HA [auth I] SDF format, chain FA [auth I] SDF format, chain EA [auth H] SDF format, chain CA [auth G] SDF format, chain AA [auth E] MOL2 format, chain BA [auth E] MOL2 format, chain DA [auth H] MOL2 format, chain GA [auth I] MOL2 format, chain JA [auth J] MOL2 format, chain KA [auth J] MOL2 format, chain O [auth A] MOL2 format, chain R [auth B] MOL2 format, chain V [auth C] MOL2 format, chain Y [auth D] MOL2 format, chain Z [auth D] MOL2 format, chain X [auth D] MOL2 format, chain W [auth C] MOL2 format, chain U [auth C] MOL2 format, chain T [auth B] MOL2 format, chain S [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain P [auth A] MOL2 format, chain N [auth A] MOL2 format, chain M [auth A] MOL2 format, chain LA [auth J] MOL2 format, chain HA [auth I] MOL2 format, chain FA [auth I] MOL2 format, chain EA [auth H] MOL2 format, chain CA [auth G] MOL2 format, chain AA [auth E] mmCIF format, chain BA [auth E] mmCIF format, chain DA [auth H] mmCIF format, chain GA [auth I] mmCIF format, chain JA [auth J] mmCIF format, chain KA [auth J] mmCIF format, chain O [auth A] mmCIF format, chain R [auth B] mmCIF format, chain V [auth C] mmCIF format, chain Y [auth D] mmCIF format, chain Z [auth D] mmCIF format, chain X [auth D] mmCIF format, chain W [auth C] mmCIF format, chain U [auth C] mmCIF format, chain T [auth B] mmCIF format, chain S [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain P [auth A] mmCIF format, chain N [auth A] mmCIF format, chain M [auth A] mmCIF format, chain LA [auth J] mmCIF format, chain HA [auth I] mmCIF format, chain FA [auth I] mmCIF format, chain EA [auth H] mmCIF format, chain CA [auth G] mmCIF format, chain AA [auth E]	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] mmCIF 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 (Depositor), 0.227 (DCC)
R-Value Work: 0.171 (Depositor), 0.176 (DCC)
R-Value Observed: 0.174 (Depositor)

Diffraction Data:

Space Group: P 1 2₁ 1

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

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View more in-depth experimental data

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
Version 1.5: 2024-11-20
Changes: Data collection, Refinement description, Structure summary