6PTR | pdb_00006ptr

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

PDB DOI: https://doi.org/10.2210/pdb6PTR/pdb

Classification: TRANSFERASE/ANTIBIOTIC
Organism(s): Bartonella birtlesii LL-WM9, 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: 1.75 Å
R-Value Free:
0.206 (Depositor), 0.206 (DCC)
R-Value Work:
0.178 (Depositor), 0.178 (DCC)
R-Value Observed:
0.178 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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 Bartonella birtlesii 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: 88.68 kDa
Atom Count: 6,620
Modeled Residue Count: 764
Deposited Residue Count: 784
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta sliding clamp	A, C [auth B]	381	Bartonella birtlesii LL-WM9	Mutation(s): 0 Gene Names: ME7_01154
UniProt
Find proteins for J1IY24 (Bartonella birtlesii LL-WM9) Explore J1IY24 Go to UniProtKB: J1IY24
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	J1IY24
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	B [auth X], D [auth Y]	11	Streptomyces griseus	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
IOD Query on IOD Download:Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain N [auth A] SDF format, chain U [auth B] SDF format, chain T [auth B] SDF format, chain S [auth B] SDF format, chain R [auth B] SDF format, chain P [auth A] SDF format, chain O [auth A] SDF format, chain M [auth A] SDF format, chain L [auth A] SDF format, chain K [auth A] MOL2 format, chain J [auth A] MOL2 format, chain N [auth A] MOL2 format, chain U [auth B] MOL2 format, chain T [auth B] MOL2 format, chain S [auth B] MOL2 format, chain R [auth B] MOL2 format, chain P [auth A] MOL2 format, chain O [auth A] MOL2 format, chain M [auth A] MOL2 format, chain L [auth A] MOL2 format, chain K [auth A] mmCIF format, chain J [auth A] mmCIF format, chain N [auth A] mmCIF format, chain U [auth B] mmCIF format, chain T [auth B] mmCIF format, chain S [auth B] mmCIF format, chain R [auth B] mmCIF format, chain P [auth A] mmCIF format, chain O [auth A] mmCIF format, chain M [auth A] mmCIF format, chain L [auth A] mmCIF format, chain K [auth A]	J [auth A] K [auth A] L [auth A] M [auth A] N [auth A] J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], P [auth A], R [auth B], S [auth B], T [auth B], U [auth B]	IODIDE ION I XMBWDFGMSWQBCA-UHFFFAOYSA-M		Interactions Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Interactions & Density Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain Q [auth B] SDF format, chain I [auth A] SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain Q [auth B] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A]	E [auth A] F [auth A] G [auth A] H [auth A] I [auth A] E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], Q [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain Q [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain Q [auth B]

Modified Residues 3 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MLU Query on MLU	B [auth X], D [auth Y]	D-PEPTIDE LINKING	C₇ H₁₅ N O₂		--
MP8 Query on MP8	B [auth X], D [auth Y]	L-PEPTIDE LINKING	C₆ H₁₁ N O₂		PRO
MVA Query on MVA	B [auth X], D [auth Y]	L-PEPTIDE LINKING	C₆ H₁₃ N O₂		VAL
NZC Query on NZC	B [auth X], D [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	B [auth X], D [auth Y]	ACE-MVA-MP8-NZC-LEU-MP8-LEU-MVA-PRO-MLU-GLY	Peptide-like / Inhibitor		Interactions Focus chain B [auth X] Focus chain D [auth Y] Interactions & Density Focus chain B [auth X] Focus chain D [auth Y]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free: 0.206 (Depositor), 0.206 (DCC)
R-Value Work: 0.178 (Depositor), 0.178 (DCC)
R-Value Observed: 0.178 (Depositor)

Diffraction Data:

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 91.95	α = 90
b = 93.13	β = 90
c = 110.74	γ = 90

Software Package:

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