4M8I | pdb_00004m8i

1.43 Angstrom resolution crystal structure of cell division protein FtsZ (ftsZ) from Staphylococcus epidermidis RP62A in complex with GDP

PDB DOI: https://doi.org/10.2210/pdb4M8I/pdb

Classification: CELL CYCLE
Organism(s): Staphylococcus epidermidis RP62A
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2013-08-13 Released: 2013-09-04
Deposition Author(s): Halavaty, A.S., Minasov, G., Winsor, J., Dubrovska, I., Filippova, E.V., Olsen, D.B., Therien, A., Shuvalova, L., Young, K., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.43 Å
R-Value Free:
0.206 (Depositor), 0.210 (DCC)
R-Value Work:
0.169 (Depositor), 0.176 (DCC)
R-Value Observed:
0.171 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

1.43 Angstrom resolution crystal structure of cell division protein FtsZ (ftsZ) from Staphylococcus epidermidis RP62A in complex with GDP

Halavaty, A.S., Minasov, G., Winsor, J., Dubrovska, I., Filippova, E.V., Olsen, D.B., Therien, A., Shuvalova, L., Young, K., Anderson, W.F.

To be published.

Macromolecule Content

Total Structure Weight: 42.82 kDa
Atom Count: 2,832
Modeled Residue Count: 311
Deposited Residue Count: 400
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cell division protein FtsZ	A	400	Staphylococcus epidermidis RP62A	Mutation(s): 0 Gene Names: ftsZ, SERP0751
UniProt
Find proteins for Q5HQ06 (Staphylococcus epidermidis (strain ATCC 35984 / DSM 28319 / BCRC 17069 / CCUG 31568 / BM 3577 / RP62A)) Explore Q5HQ06 Go to UniProtKB: Q5HQ06
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5HQ06
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GDP Query on GDP Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	GUANOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₁ P₂ QGWNDRXFNXRZMB-UUOKFMHZSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.43 Å
R-Value Free: 0.206 (Depositor), 0.210 (DCC)
R-Value Work: 0.169 (Depositor), 0.176 (DCC)
R-Value Observed: 0.171 (Depositor)

Diffraction Data:

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.335	α = 90
b = 52.063	β = 109.64
c = 87.005	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2013-09-04

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History (Full details and data files)

Version 1.0: 2013-09-04
Type: Initial release
Version 1.1: 2013-09-18
Changes: Advisory
Version 1.2: 2017-11-15
Changes: Refinement description
Version 1.3: 2023-09-20
Changes: Data collection, Database references, Derived calculations, Refinement description