2RDM | pdb_00002rdm

Crystal structure of response regulator receiver protein from Sinorhizobium medicae WSM419

PDB DOI: https://doi.org/10.2210/pdb2RDM/pdb

Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
Organism(s): Sinorhizobium medicae WSM419
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2007-09-24 Released: 2007-10-09
Deposition Author(s): Patskovsky, Y., Yan, Q., Zhan, C., Toro, R., Meyer, A.J., Gilmore, M., Hu, S., Groshong, C., Rodgers, L., Sauder, J.M., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.76 Å
R-Value Free:
0.220 (Depositor), 0.220 (DCC)
R-Value Work:
0.188 (Depositor), 0.188 (DCC)
R-Value Observed:
0.189 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.6 of the entry. See complete history.

Literature

Crystal structure of response regulator receiver protein from Sinorhizobium medicae WSM419.

Patskovsky, Y., Yan, Q., Zhan, C., Toro, R., Meyer, A.J., Gilmore, M., Hu, S., Groshong, C., Rodgers, L., Sauder, J.M., Burley, S.K., Almo, S.C.

To be published.

Macromolecule Content

Total Structure Weight: 43.27 kDa
Atom Count: 3,071
Modeled Residue Count: 369
Deposited Residue Count: 396
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Response regulator receiver protein	A, B, C	132	Sinorhizobium medicae WSM419	Mutation(s): 1 Gene Names: Smed_4830
UniProt
Find proteins for A6UIY7 (Sinorhizobium medicae (strain WSM419)) Explore A6UIY7 Go to UniProtKB: A6UIY7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A6UIY7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 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] SDF format, chain F [auth C] SDF format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain F [auth C] MOL2 format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain F [auth C] mmCIF format, chain E [auth A]	D [auth A], E [auth A], F [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth C] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth C]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.76 Å
R-Value Free: 0.220 (Depositor), 0.220 (DCC)
R-Value Work: 0.188 (Depositor), 0.188 (DCC)
R-Value Observed: 0.189 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 122.593	α = 90
b = 58.657	β = 117.96
c = 60.301	γ = 90

Software Package:

Software Name	Purpose
SHELXD	phasing
SHELXE	model building
REFMAC	refinement
ADSC	data collection
HKL-2000	data reduction
SCALEPACK	data scaling

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2007-10-09

Deposition Author(s):

New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History (Full details and data files)

Version 1.0: 2007-10-09
Type: Initial release
Version 1.1: 2011-07-13
Changes: Source and taxonomy, Version format compliance
Version 1.2: 2017-10-25
Changes: Refinement description
Version 1.3: 2018-11-14
Changes: Data collection, Structure summary
Version 1.4: 2021-02-03
Changes: Database references, Derived calculations, Structure summary
Version 1.5: 2021-10-20
Changes: Database references
Version 1.6: 2024-10-16
Changes: Data collection, Refinement description, Structure summary