3IBW | pdb_00003ibw

Crystal Structure of the ACT domain from GTP pyrophosphokinase of Chlorobium tepidum. Northeast Structural Genomics Consortium Target CtR148A

PDB DOI: https://doi.org/10.2210/pdb3IBW/pdb

Classification: TRANSFERASE
Organism(s): Chlorobaculum tepidum
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2009-07-17 Released: 2009-07-28
Deposition Author(s): Vorobiev, S., Su, M., Seetharaman, J., Janjua, J., Xiao, R., Ciccosanti, C., Wang, H., Everett, J.K., Nair, R., Acton, T.B., Rost, B., Montelione, G.T., Tong, L., Hunt, J.F., Northeast Structural Genomics Consortium (NESG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.93 Å
R-Value Free:
0.192 (Depositor), 0.204 (DCC)
R-Value Work:
0.198 (Depositor), 0.211 (DCC)

wwPDB Validation 3D Report Full Report

This is version 1.5 of the entry. See complete history.

Literature

Crystal Structure of the ACT domain from GTP pyrophosphokinase of Chlorobium tepidum.

Vorobiev, S., Su, M., Seetharaman, J., Janjua, J., Xiao, R., Ciccosanti, C., Wang, H., Everett, J.K., Nair, R., Acton, T.B., Rost, B., Montelione, G.T., Tong, L., Hunt, J.F.

To be published.

Macromolecule Content

Total Structure Weight: 20.48 kDa
Atom Count: 1,357
Modeled Residue Count: 156
Deposited Residue Count: 176
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GTP pyrophosphokinase	A, B	88	Chlorobaculum tepidum	Mutation(s): 1 Gene Names: CT1545, relA EC: 2.7.6.5
UniProt
Find proteins for Q8KC80 (Chlorobaculum tepidum (strain ATCC 49652 / DSM 12025 / NBRC 103806 / TLS)) Explore Q8KC80 Go to UniProtKB: Q8KC80
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8KC80
Sequence Annotations Expand
Reference Sequence

Small Molecules

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: 1.93 Å
R-Value Free: 0.192 (Depositor), 0.204 (DCC)
R-Value Work: 0.198 (Depositor), 0.211 (DCC)

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.306	α = 90
b = 64.306	β = 90
c = 93.963	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
SnB	phasing
RESOLVE	phasing
REFMAC	refinement

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2009-07-28

Deposition Author(s):

Northeast Structural Genomics Consortium (NESG)

Revision History (Full details and data files)

Version 1.0: 2009-07-28
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2017-10-25
Changes: Author supporting evidence, Refinement description
Version 1.3: 2019-07-24
Changes: Data collection, Derived calculations, Refinement description
Version 1.4: 2021-10-13
Changes: Database references
Version 1.5: 2024-10-16
Changes: Data collection, Structure summary