2BE3

Structure of a GTP Pyrophosphokinase Family Protein from Streptococcus pneumoniae

PDB DOI: https://doi.org/10.2210/pdb2BE3/pdb

Classification: TRANSFERASE
Organism(s): Streptococcus pneumoniae TIGR4
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2005-10-21 Released: 2005-12-06
Deposition Author(s): Cuff, M.E., Hatzos, C., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.234
R-Value Work: 0.182
R-Value Observed: 0.185

wwPDB Validation 3D Report Full Report

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

Literature

Structure of a GTP Pyrophosphokinase Family Protein from Streptococcus pneumoniae

Cuff, M.E., Hatzos, C., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 53.88 kDa
Atom Count: 3,557
Modelled Residue Count: 392
Deposited Residue Count: 452
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GTP pyrophosphokinase	A, B	226	Streptococcus pneumoniae TIGR4	Mutation(s): 6 Gene Names: SP1097 EC: 2.7.6.5
UniProt
Find proteins for A0A0H2UPY1 (Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4)) Explore A0A0H2UPY1 Go to UniProtKB: A0A0H2UPY1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A0H2UPY1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PG4 Query on PG4 Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A]	D [auth A]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A]	E [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A]	C [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

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: 2.40 Å
R-Value Free: 0.234
R-Value Work: 0.182
R-Value Observed: 0.185
Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 104.843	α = 90
b = 104.843	β = 90
c = 170.562	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
MAR345	data collection
HKL-2000	data scaling
HKL-3000	phasing
SHELXD	phasing
MLPHARE	phasing
DM	phasing
CCP4	phasing
RESOLVE	phasing
Coot	model building
O	model building
ARP/wARP	model building

Structure Validation

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Entry History

Deposition Data

Released Date: 2005-12-06

Deposition Author(s):

Cuff, M.E.

Hatzos, C.

Joachimiak, A.

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2005-12-06
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Advisory, Source and taxonomy, Version format compliance
Version 1.3: 2017-10-18
Changes: Refinement description

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2BE3

Structure of a GTP Pyrophosphokinase Family Protein from Streptococcus pneumoniae

Structure of a GTP Pyrophosphokinase Family Protein from Streptococcus pneumoniae

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)