2P12

Crystal structure of protein of unknown function DUF402 from Rhodococcus sp. RHA1

PDB DOI: https://doi.org/10.2210/pdb2P12/pdb

Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
Organism(s): Rhodococcus jostii RHA1
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2007-03-01 Released: 2007-04-03
Deposition Author(s): Kim, Y., Evdokimova, E., Kudritska, M., Edwards, A., Savchenko, A., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.63 Å
R-Value Free: 0.216
R-Value Work: 0.171
R-Value Observed: 0.175

wwPDB Validation 3D Report Full Report

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

Literature

The crystal structure of the protein of uncharacterized function, DUF402 from Rhodococcus sp. RHA1

Kim, Y., Evdokimova, E., Kudritska, M., Edwards, A., Savchenko, A., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 40.92 kDa
Atom Count: 3,493
Modelled Residue Count: 331
Deposited Residue Count: 352
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hypothetical protein DUF402	A, B	176	Rhodococcus jostii RHA1	Mutation(s): 4 Gene Names: RHA1_ro00977
UniProt
Find proteins for Q0SI31 (Rhodococcus jostii (strain RHA1)) Explore Q0SI31 Go to UniProtKB: Q0SI31
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q0SI31
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A]	D [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
ACY Query on ACY Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain E [auth B] MOL2 format, chain C [auth A] MOL2 format, chain E [auth B]	C [auth A], E [auth B]	ACETIC ACID C₂ H₄ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain E [auth B] Interactions & Density Focus chain C [auth A] Focus chain E [auth B]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.63 Å
R-Value Free: 0.216
R-Value Work: 0.171
R-Value Observed: 0.175
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 132.203	α = 90
b = 38.98	β = 107.69
c = 70.721	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SBC-Collect	data collection
HKL-3000	data collection
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing
SHELXCD	phasing
SHELXD	phasing
MLPHARE	phasing
RESOLVE	phasing
ARP/wARP	model building

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2007-04-03

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2007-04-03
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Advisory, Source and taxonomy, Version format compliance
Version 1.3: 2017-10-18
Changes: Refinement description

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Help and Resources

2P12

Crystal structure of protein of unknown function DUF402 from Rhodococcus sp. RHA1

The crystal structure of the protein of uncharacterized function, DUF402 from Rhodococcus sp. RHA1

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)