PDB-3ci6: Crystal structure of the GAF domain from Acinetobacter phosphoeno...

ID or keywords:

Entry

Database: PDB / ID: 3ci6

Title

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

Components

Phosphoenolpyruvate-protein phosphotransferase

Keywords

TRANSFERASE / PEP-phosphotransferase / GAF domain / Acinetobacter / Structural Genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG / Kinase / Magnesium / Metal-binding / Phosphotransferase system / Pyruvate / Sugar transport / Transport

Function / homology

Function and homology information

phosphoenolpyruvate-protein phosphotransferase / phosphoenolpyruvate-protein phosphotransferase activity / phosphoenolpyruvate-dependent sugar phosphotransferase system / kinase activity / metal ion binding / cytoplasm
Similarity search - Function

Biological species

Acinetobacter sp. (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MAD / Resolution: 1.55 Å

Authors

Cuff, M.E. / Shackelford, G. / Kim, Y. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)

Citation

Journal: TO BE PUBLISHED
Title: Crystal structure of the GAF domain from Acinetobacter phosphoenolpyruvate-protein phosphotransferase.
Authors: Cuff, M.E. / Shackelford, G. / Kim, Y. / Joachimiak, A.

History

Deposition	Mar 10, 2008	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 13, 2008	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.2	Oct 25, 2017	Group: Refinement description / Category: software

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3ci6.cif.gz	88 KB	Display	PDBx/mmCIF format
PDB format	pdb3ci6.ent.gz	72.4 KB	Display	PDB format
PDBx/mmJSON format	3ci6.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ci/3ci6 ftp://data.pdbj.org/pub/pdb/validation_reports/ci/3ci6	HTTPS FTP

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Related structure data

Similar structure data	4bv0-1 2dul-d 1l9h-2 4pcb-2 4hs4-2 6c6b-3 5dhg-1 3drm-d 3s2y-2 4hs4-5 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search
Other databases	TargetDB: APC87504.2

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#183 - Mar 2015 Phototropin similarity (4) #50 - Feb 2004 Glycolytic Enzymes similarity (2) #152 - Aug 2012 cAMP-dependent Protein Kinase similarity (4)

Deposited unit

A: Phosphoenolpyruvate-protein phosphotransferase

B: Phosphoenolpyruvate-protein phosphotransferase

hetero molecules

39.3 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by software

Unit cell

Length a, b, c (Å)	39.081, 54.992, 124.118
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Details

AUTHORS STATE THAT THE BIOLOGICAL UNIT OF THIS POLYPEPTIDE IS UNKNOWN

#1: Protein	Phosphoenolpyruvate-protein phosphotransferase Mass: 19264.807 Da / Num. of mol.: 2 / Fragment: GAF domain: Residues 1-168 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Acinetobacter sp. (bacteria) / Strain: ADP1 / Gene: ptsP, ACIAD0454 / Plasmid: pMCSG19b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: Q6FEW8, phosphoenolpyruvate-protein phosphotransferase
#2: Chemical	ChemComp-P4G / 1-ETHOXY-2-(2-ETHOXYETHOXY)ETHANE Mass: 162.227 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₈H₁₈O₃
#3: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#4: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃H₈O₃
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 285 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 1.73 Å³/Da / Density % sol: 28.9 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.1M Tris-HCl pH 8.5, 0.2M MgCl2, 30% PEG 400, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 19-ID / Wavelength: 0.97931, 0.97945

Detector

Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 2, 2008

Radiation

Monochromator: SAGITALLY FOCUSED Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	0.97931	1
2	0.97945	1

Reflection

Redundancy: 10.3 % / Av σ(I) over netI: 9 / Number: 407628 / R_merge(I) obs: 0.095 / Χ²: 2.44 / D res high: 1.55 Å / D res low: 50 Å / Num. obs: 39536 / % possible obs: 99.2

Diffraction reflection shell

Highest resolution (Å)	Lowest resolution (Å)	% possible obs (%)	ID	R_merge(I) obs	Chi squared	Redundancy
3.82	50	94.8	1	0.07	9.922	10
3.03	3.82	98	1	0.072	5.952	10
2.65	3.03	98.4	1	0.097	4.869	10.3
2.41	2.65	98.9	1	0.102	3.614	10.4
2.24	2.41	99.5	1	0.098	2.598	10.4
2.1	2.24	99.6	1	0.105	2.147	10.5
2	2.1	99.6	1	0.119	1.578	10.4
1.91	2	99.9	1	0.144	1.223	10.5
1.84	1.91	99.9	1	0.179	0.95	10.4
1.77	1.84	99.9	1	0.223	0.754	10.4
1.72	1.77	100	1	0.276	0.68	10.4
1.67	1.72	100	1	0.335	0.605	10.4
1.63	1.67	100	1	0.376	0.544	10.4
1.59	1.63	100	1	0.434	0.532	10.2
1.55	1.59	100	1	0.501	0.532	9.9

Reflection

Resolution: 1.55→50 Å / Num. all: 39536 / Num. obs: 39536 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Redundancy: 10.3 % / B_iso Wilson estimate: 17.2 Å² / R_merge(I) obs: 0.095 / Χ²: 2.438 / Net I/σ(I): 9

Reflection shell

Resolution: 1.55→1.59 Å / Redundancy: 9.9 % / R_merge(I) obs: 0.501 / Mean I/σ(I) obs: 3.9 / Num. unique all: 2589 / Χ²: 0.532 / % possible all: 100

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Phasing

Phasing

Method:

MAD

Phasing MAD

D res high: 1.55 Å / D res low: 50 Å / FOM : 0.331 / FOM acentric: 0.371 / FOM centric: 0 / Reflection: 39428 / Reflection acentric: 35223 / Reflection centric: 4205

Phasing MAD set

R cullis acentric: 1.75 / R cullis centric: 1 / Highest resolution: 1.55 Å / Lowest resolution: 50 Å / Loc acentric: 0.2 / Loc centric: 0.1 / Power acentric: 0 / Power centric: 0 / Reflection acentric: 35223 / Reflection centric: 4205

Phasing MAD set shell

ID: 1 / R cullis centric: 1 / Power acentric: 0 / Power centric: 0

Resolution (Å)	R cullis acentric	Loc acentric	Loc centric	Reflection acentric	Reflection centric
10.19-50	1.31	0.5	0.3	83	66
5.67-10.19	1.42	0.5	0.3	509	185
3.93-5.67	1.25	0.5	0.4	1346	306
3.01-3.93	1.33	0.4	0.2	2578	444
2.43-3.01	1.87	0.3	0.2	4219	574
2.05-2.43	1.68	0.2	0.1	6255	725
1.76-2.05	2.1	0.2	0.1	8694	886
1.55-1.76	2.57	0.1	0	11539	1019

Phasing MAD set site

ID	Atom type symbol	B iso	Fract x	Fract y	Fract z
1	Se	15.43339	0.802	0.045	0.17
2	Se	20.72184	1.048	-0.09	0.017
3	Se	18.51715	1.325	0.097	0.016
4	Se	16.72565	0.308	0.121	0.2
5	Se	15.87277	0.324	-0.05	0.135
6	Se	36.91026	0.823	-0.056	-0.025
7	Se	20.92768	1.386	-0.086	-0.047
8	Se	15.83245	0.173	-0.156	0.151
9	Se	35.79361	1.154	0.181	-0.011
10	Se	27.28678	0.604	-0.143	0.05
11	Se	23.59939	1.083	0.333	-0.059
12	Se	18.65728	0.407	-0.102	0.107
13	Se	10.71119	1.012	0.087	0.153
14	Se	23.93945	0.17	-0.188	0.125

Phasing MAD shell

Resolution (Å)	FOM	FOM acentric	Reflection	Reflection acentric	Reflection centric
10.19-50	0.236	0.424	149	83	66
5.67-10.19	0.355	0.484	694	509	185
3.93-5.67	0.437	0.536	1652	1346	306
3.01-3.93	0.455	0.534	3022	2578	444
2.43-3.01	0.47	0.535	4793	4219	574
2.05-2.43	0.438	0.488	6980	6255	725
1.76-2.05	0.327	0.36	9580	8694	886
1.55-1.76	0.178	0.194	12558	11539	1019

Phasing dm

Method: Solvent flattening and Histogram matching / Reflection: 39428

Phasing dm shell

Resolution (Å)	Delta phi final	FOM	Reflection
6.73-100	67.5	0.32	513
5.25-6.73	67	0.836	556
4.45-5.25	60.8	0.896	666
3.94-4.45	57.5	0.904	754
3.56-3.94	60	0.892	848
3.28-3.56	59.3	0.891	932
3.06-3.28	60.3	0.877	994
2.87-3.06	58.5	0.886	1068
2.72-2.87	60.3	0.87	1119
2.59-2.72	57.1	0.863	1175
2.47-2.59	62.3	0.862	1246
2.37-2.47	60.3	0.867	1298
2.28-2.37	58.2	0.885	1338
2.2-2.28	57.2	0.873	1393
2.13-2.2	57.6	0.868	1448
2.06-2.13	60.7	0.852	1478
2.01-2.06	62.5	0.845	1550
1.95-2.01	62.7	0.833	1545
1.9-1.95	65.3	0.819	1647
1.85-1.9	66.6	0.814	1644
1.81-1.85	67.1	0.814	1697
1.77-1.81	68.9	0.829	1714
1.73-1.77	69.3	0.802	1792
1.7-1.73	71	0.781	1797
1.66-1.7	73.5	0.776	1847
1.63-1.66	74	0.767	1872
1.6-1.63	75.8	0.764	1929
1.55-1.6	75.8	0.74	3568

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
MLPHARE		phasing
DM	5	phasing
REFMAC		refinement
PDB_EXTRACT	3.004	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

Refinement

Method to determine structure:

MAD / Resolution: 1.55→41.17 Å / Cor.coef. F_o:F_c: 0.965 / Cor.coef. F_o:F_c free: 0.951 / SU B: 3.016 / SU ML: 0.055 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.094 / ESU R Free: 0.09
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.196	1983	5 %	RANDOM
R_work	0.168	-	-	-
all	0.17	39430	-	-
obs	0.17	39430	99.24 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 11.117 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.43 Å²	0 Å²	0 Å²
2-	-	1.14 Å²	0 Å²
3-	-	-	-0.71 Å²

Refinement step

Cycle: LAST / Resolution: 1.55→41.17 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2515	0	48	285	2848

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.015	0.022	2881
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	1926
X-RAY DIFFRACTION	r_angle_refined_deg	1.538	1.98	3908
X-RAY DIFFRACTION	r_angle_other_deg	0.924	3.002	4717
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.916	5	380
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	37.111	25.224	134
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.83	15	533
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	20.745	15	18
X-RAY DIFFRACTION	r_chiral_restr	0.094	0.2	440
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	3308
X-RAY DIFFRACTION	r_gen_planes_other	0.003	0.02	542
X-RAY DIFFRACTION	r_nbd_refined	0.241	0.2	609
X-RAY DIFFRACTION	r_nbd_other	0.189	0.2	2097
X-RAY DIFFRACTION	r_nbtor_refined	0.175	0.2	1445
X-RAY DIFFRACTION	r_nbtor_other	0.088	0.2	1672
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.149	0.2	188
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.178	0.2	46
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.251	0.2	106
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.191	0.2	50
X-RAY DIFFRACTION	r_mcbond_it	1.311	1.5	2148
X-RAY DIFFRACTION	r_mcbond_other	0.256	1.5	721
X-RAY DIFFRACTION	r_mcangle_it	1.495	2	2927
X-RAY DIFFRACTION	r_scbond_it	3.003	3	1161
X-RAY DIFFRACTION	r_scangle_it	4.03	4.5	981

LS refinement shell

Resolution: 1.55→1.59 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.219	157	-
R_work	0.171	2709	-
all	-	2866	-
obs	-	-	99.86 %

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	4.2413	2.0581	0.4123	1.9564	0.1063	1.0478	-0.0519	0.0121	0.181	-0.0057	0.0608	0.1584	-0.0805	-0.0955	-0.0089	0.0555	-0.0041	0.0071	0.0586	-0.0169	0.0448	18.5802	35.7389	-8.0588
2	2.2585	-0.6967	-1.0027	1.379	0.2981	2.275	-0.1744	-0.1038	-0.0714	0.1231	0.0949	-0.1126	0.0385	0.2639	0.0795	0.0839	0.0194	0.0088	0.0439	-0.0177	0.0416	26.7402	31.2706	5.7322
3	3.6171	-0.3905	-1.1048	5.8182	0.1344	4.3523	0.0837	-0.5501	0.0133	0.6449	-0.0528	-0.6834	-0.1287	0.5834	-0.0309	0.1086	-0.0216	-0.0631	0.1331	-0.0087	0.0099	28.5156	29.1693	13.5495
4	1.9885	-0.5523	-1.7504	0.9361	0.7517	4.7738	-0.1262	-0.0636	-0.1786	0.2095	0.0542	0.0298	0.2323	-0.0988	0.072	0.0858	0.0122	0.0403	0.0322	0.0122	0.0565	18.2254	23.7132	10.3824
5	10.9201	-0.0133	-2.6392	0.1536	-0.2396	1.5816	0.0632	-0.2919	-0.0473	0.0514	-0.0327	-0.0443	0.0022	0.1038	-0.0305	0.0403	-0.0064	0.008	0.0623	-0.0358	0.0385	24.7751	26.4857	-2.563
6	2.0694	-0.2973	0.2249	0.4811	-0.1726	0.9578	-0.0803	-0.0055	-0.0836	0.0309	0.0526	0.0101	0.1183	-0.0071	0.0277	0.0657	-0.011	-0.0033	0.0512	-0.0064	0.0816	16.4353	18.5559	-13.5276
7	0.9566	-0.0611	-0.3321	1.0837	-0.1049	0.6737	0.0221	0.0577	-0.0185	-0.1094	-0.0238	-0.0753	-0.0179	0.0312	0.0018	0.0683	-0.0067	-0.0082	0.068	-0.0122	0.0547	25.3445	28.1031	-28.6329
8	6.5085	-1.501	-5.5892	7.9755	1.186	11.4979	-0.4327	0.0074	-0.6869	-0.0138	-0.2251	0.3246	0.8322	-0.1688	0.6578	0.1973	0.0113	0.0727	0.0539	0.0247	0.1426	18.3969	30.8818	-39.1995
9	2.4217	0.8333	1.8191	0.7754	0.9203	3.2861	0.0169	0.1018	-0.0134	-0.0722	0.0381	0.0215	-0.0444	0.0292	-0.055	0.0742	-0.0011	-0.0193	0.0478	-0.0039	0.0657	19.4888	30.0508	-24.6409
10	2.4935	-0.6698	0.3238	0.3981	-0.2817	0.9074	-0.0728	0.0206	-0.0014	-0.0201	0.0584	-0.0377	0.0108	0.036	0.0145	0.061	-0.0091	-0.0061	0.0591	-0.0147	0.0603	24.0995	27.147	-15.9894

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	X-RAY DIFFRACTION	1	A	A	1 - 24	4 - 27
2	X-RAY DIFFRACTION	2	A	A	25 - 59	28 - 62
3	X-RAY DIFFRACTION	3	A	A	60 - 83	63 - 86
4	X-RAY DIFFRACTION	4	A	A	84 - 139	87 - 142
5	X-RAY DIFFRACTION	5	A	A	140 - 167	143 - 170
6	X-RAY DIFFRACTION	6	B	B	1 - 39	4 - 42
7	X-RAY DIFFRACTION	7	B	B	40 - 95	43 - 98
8	X-RAY DIFFRACTION	8	B	B	96 - 109	99 - 112
9	X-RAY DIFFRACTION	9	B	B	110 - 137	113 - 140
10	X-RAY DIFFRACTION	10	B	B	138 - 168	141 - 171

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