3CI6

Crystal structure of the GAF domain from Acinetobacter phosphoenolpyruvate-protein phosphotransferase

PDB DOI: https://doi.org/10.2210/pdb3CI6/pdb

Classification: TRANSFERASE
Organism(s): Acinetobacter baylyi ADP1
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2008-03-10 Released: 2008-05-13
Deposition Author(s): Cuff, M.E., Shackelford, G., Kim, Y., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.55 Å
R-Value Free: 0.196
R-Value Work: 0.168
R-Value Observed: 0.170

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal structure of the GAF domain from Acinetobacter phosphoenolpyruvate-protein phosphotransferase.

Cuff, M.E., Shackelford, G., Kim, Y., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 39.25 kDa
Atom Count: 3,113
Modelled Residue Count: 324
Deposited Residue Count: 342
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphoenolpyruvate-protein phosphotransferase	A, B	171	Acinetobacter baylyi ADP1	Mutation(s): 0 Gene Names: ptsP, ACIAD0454 EC: 2.7.3.9
UniProt
Find proteins for Q6FEW8 (Acinetobacter baylyi (strain ATCC 33305 / BD413 / ADP1)) Explore Q6FEW8 Go to UniProtKB: Q6FEW8
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q6FEW8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
P4G Query on P4G Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain F [auth B] MOL2 format, chain C [auth A] MOL2 format, chain F [auth B]	C [auth A], F [auth B]	1-ETHOXY-2-(2-ETHOXYETHOXY)ETHANE C₈ H₁₈ O₃ RRQYJINTUHWNHW-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain F [auth B] Interactions & Density Focus chain C [auth A] Focus chain F [auth B]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain G [auth B] MOL2 format, chain D [auth A] MOL2 format, chain G [auth B]	D [auth A], G [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain G [auth B] Interactions & Density Focus chain D [auth A] Focus chain G [auth B]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain H [auth B] MOL2 format, chain E [auth A] MOL2 format, chain H [auth B]	E [auth A], H [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain H [auth B] Interactions & Density Focus chain E [auth A] Focus chain H [auth B]

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: 1.55 Å
R-Value Free: 0.196
R-Value Work: 0.168
R-Value Observed: 0.170
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.081	α = 90
b = 54.992	β = 90
c = 124.118	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MLPHARE	phasing
DM	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing
SHELXD	phasing
SHELXE	model building
SOLVE	phasing
RESOLVE	phasing
ARP/wARP	model building
CCP4	phasing
O	model building
Coot	model building

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2008-05-13

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2008-05-13
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Source and taxonomy, Version format compliance
Version 1.2: 2017-10-25
Changes: Refinement description

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Help and Resources

3CI6

Crystal structure of the GAF domain from Acinetobacter phosphoenolpyruvate-protein phosphotransferase

Crystal structure of the GAF domain from Acinetobacter phosphoenolpyruvate-protein phosphotransferase.

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)