6PTV | pdb_00006ptv

Crystal structure of a DnaN sliding clamp (DNA polymerase III subunit beta) from Rickettsia rickettsii bound to griselimycin

PDB DOI: https://doi.org/10.2210/pdb6PTV/pdb

Classification: TRANSFERASE/ANTIBIOTIC
Organism(s): Rickettsia rickettsii str. 'Sheila Smith, Streptomyces griseus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2019-07-16 Released: 2019-08-07
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free:
0.206 (Depositor), 0.205 (DCC)
R-Value Work:
0.169 (Depositor), 0.169 (DCC)
R-Value Observed:
0.169 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.2 of the entry. See complete history.

Literature

Crystal structure of a DnaN sliding clamp (DNA polymerase III subunit beta) from Rickettsia rickettsii bound to griselimycin

Edwards, T.E., Abendroth, J., Horanyi, P.S., Lorimer, D.D., Seattle Structural Genomics Center for Infectious Disease (SSGCID)

To be published.

Macromolecule Content

Total Structure Weight: 175.97 kDa
Atom Count: 13,188
Modeled Residue Count: 1,533
Deposited Residue Count: 1,570
Unique protein chains: 2

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta sliding clamp	A, B, D [auth C], F [auth D]	387	Rickettsia rickettsii str. 'Sheila Smith	Mutation(s): 0 Gene Names: A1G_03290
UniProt
Find proteins for A0A0H3AWV3 (Rickettsia rickettsii (strain Sheila Smith)) Explore A0A0H3AWV3 Go to UniProtKB: A0A0H3AWV3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A0H3AWV3
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
ACE-MVA-MP8-NZC-LEU-MP8-LEU-MVA-PRO-MLU-GLY	C [auth X], E [auth Y]	11	Streptomyces griseus	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MPD Query on MPD Download:Ideal Coordinates CCD File SDF format, chain H [auth D] SDF format, chain G [auth A] MOL2 format, chain H [auth D] MOL2 format, chain G [auth A] mmCIF format, chain H [auth D] mmCIF format, chain G [auth A]	G [auth A], H [auth D]	(4S)-2-METHYL-2,4-PENTANEDIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-YFKPBYRVSA-N		Interactions Focus chain G [auth A] Focus chain H [auth D] Interactions & Density Focus chain G [auth A] Focus chain H [auth D]

Modified Residues 3 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MLU Query on MLU	C [auth X], E [auth Y]	D-PEPTIDE LINKING	C₇ H₁₅ N O₂		--
MP8 Query on MP8	C [auth X], E [auth Y]	L-PEPTIDE LINKING	C₆ H₁₁ N O₂		PRO
MVA Query on MVA	C [auth X], E [auth Y]	L-PEPTIDE LINKING	C₆ H₁₃ N O₂		VAL
NZC Query on NZC	C [auth X], E [auth Y]	L-PEPTIDE LINKING	C₅ H₁₁ N O₃		THR

Biologically Interesting Molecules (External Reference)

1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_002311 Query on PRD_002311	C [auth X], E [auth Y]	ACE-MVA-MP8-NZC-LEU-MP8-LEU-MVA-PRO-MLU-GLY	Peptide-like / Inhibitor		Interactions Focus chain C [auth X] Focus chain E [auth Y] Interactions & Density Focus chain C [auth X] Focus chain E [auth Y]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free: 0.206 (Depositor), 0.205 (DCC)
R-Value Work: 0.169 (Depositor), 0.169 (DCC)
R-Value Observed: 0.169 (Depositor)

Diffraction Data:

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.21	α = 109.38
b = 82.79	β = 89.94
c = 82.86	γ = 106.53

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing
PDB_EXTRACT	data extraction

Structure Validation

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Entry History

Deposition Data

Released Date: 2019-08-07

Deposition Author(s):

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History (Full details and data files)

Version 1.0: 2019-08-07
Type: Initial release
Version 1.1: 2023-10-11
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.2: 2023-11-15
Changes: Data collection, Derived calculations

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.