PDB-4zv9: 2.00 Angstrom resolution crystal structure of an uncharacterized ...

ID or keywords:

Entry

Database: PDB / ID: 4zv9

Title

2.00 Angstrom resolution crystal structure of an uncharacterized protein from Escherichia coli O157:H7 str. Sakai

Components

Uncharacterized protein

Keywords

Structural Genomics / Unknown Function / MCSG /

Human Microbiome / PSI-Biology /

Protein Structure Initiative / Midwest Center for Structural Genomics

Function / homology

Function and homology information

hydrolase activity
Similarity search - Function

Biological species

Escherichia coli O157:H7 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2 Å

Authors

Halavaty, A.S. / Wawrzak, Z. / Filippova, E.V. / Kiryukhina, O. / Endres, M. / Joachimiak, A. / Anderson, W.F. / Midwest Center for Structural Genomics (MCSG)

Citation

Journal: To Be Published
Title: 2.00 Angstrom resolution crystal structure of an uncharacterized protein from Escherichia coli O157:H7 str. Sakai
Authors: Halavaty, A.S. / Wawrzak, Z. / Filippova, E.V. / Kiryukhina, O. / Endres, M. / Joachimiak, A. / Anderson, W.F. / Midwest Center for Structural Genomics (MCSG)

History

Deposition	May 18, 2015	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jun 17, 2015	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4zv9.cif.gz	590.7 KB	Display	PDBx/mmCIF format
PDB format	pdb4zv9.ent.gz	511.6 KB	Display	PDB format
PDBx/mmJSON format	4zv9.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/zv/4zv9 ftp://data.pdbj.org/pub/pdb/validation_reports/zv/4zv9	HTTPS FTP

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Related structure data

Similar structure data	7am5-d 5l9v-1 7am8-d 4aor-1 7am6-3 2sbt-d 2qvp-2 2g7e-d 4dwz-2 7am3-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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	TargetTrack: MCSG-APC113081

Similar structure data

Other databases

TargetTrack: MCSG-APC113081

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Uncharacterized protein

B: Uncharacterized protein

C: Uncharacterized protein

D: Uncharacterized protein

E: Uncharacterized protein

F: Uncharacterized protein

hetero molecules

160 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Uncharacterized protein

hetero molecules

defined by author&software
26.7 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Uncharacterized protein

hetero molecules

defined by author&software
26.6 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

C: Uncharacterized protein

defined by author&software
26.4 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

D: Uncharacterized protein

hetero molecules

defined by author&software
26.5 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

5

E: Uncharacterized protein

hetero molecules

defined by author&software
26.7 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

6

F: Uncharacterized protein

hetero molecules

defined by author&software
26.8 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	70.615, 96.341, 129.617
Angle α, β, γ (deg.)	90.00, 98.22, 90.00
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Dom-ID	Ens-ID	Auth asym-ID	Auth seq-ID
1	1	A	57 - 294
2	1	B	57 - 294
1	2	A	57 - 294
2	2	C	57 - 294
1	3	A	57 - 294
2	3	D	57 - 294
1	4	A	57 - 294
2	4	E	57 - 294
1	5	A	57 - 294
2	5	F	57 - 294
1	6	B	57 - 294
2	6	C	57 - 294
1	7	B	57 - 294
2	7	D	57 - 294
1	8	B	57 - 294
2	8	E	57 - 294
1	9	B	57 - 294
2	9	F	57 - 294
1	10	C	57 - 294
2	10	D	57 - 294
1	11	C	57 - 294
2	11	E	57 - 294
1	12	C	57 - 294
2	12	F	57 - 294
1	13	D	57 - 294
2	13	E	57 - 294
1	14	D	57 - 294
2	14	F	57 - 294
1	15	E	57 - 294
2	15	F	57 - 294

NCS ensembles :

ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15

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Protein , 1 types, 6 molecules ABCDEF

#1: Protein	Uncharacterized protein Mass: 26403.164 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli O157:H7 (bacteria) / Strain: Sakai / Gene: ECs3884 / Plasmid: pMCSG73 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)/pMagic / References: UniProt: Q7AAT4, UniProt: Q8XBV0*PLUS

#1: Protein

Uncharacterized protein

Mass: 26403.164 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Escherichia coli O157:H7 (bacteria) / Strain: Sakai / Gene: ECs3884 / Plasmid: pMCSG73 / Production host:

ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)/pMagic / References: UniProt: Q7AAT4, UniProt: Q8XBV0*PLUS

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Non-polymers , 5 types, 1325 molecules

#2: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol Mass: 92.094 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C₃H₈O₃
#3: Chemical	ChemComp-PO4 / PHOSPHATE ION / Phosphate Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO₄
#4: Chemical	ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₆H₁₄O₄
#5: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#6: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 1312 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION

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Sample preparation

Crystal	Density Matthews: 2.75 Å³/Da / Density % sol: 55.35 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.3 Details: Crystallization: The JCSG+ Suite (D12): 0.04 M Potasium phosphate, 16% (w/v) PEG 8000, 20% (v/v) glycerol Protein: 8.7 mg/ml in 10 mM Tris-HCl pH 8.3, 0.25 M NaCl, 5 mM BME Freezing: crystallization condition

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
Detector	Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 14, 2014
Radiation	Monochromator: Diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97856 Å / Relative weight: 1
Reflection	Resolution: 2→39 Å / Num. obs: 115793 / % possible obs: 100 % / Redundancy: 3.8 % / R_merge(I) obs: 0.052 / Net I/σ(I): 21.7
Reflection shell	Resolution: 2→2.07 Å / Redundancy: 3.8 % / R_merge(I) obs: 0.55 / Mean I/σ(I) obs: 2.5 / % possible all: 100

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Processing

Software

Name	Version	Classification
REFMAC	5.7.0029	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

SAD / Resolution: 2→38.79 Å / Cor.coef. F_o:F_c: 0.96 / Cor.coef. F_o:F_c free: 0.943 / SU B: 6.683 / SU ML: 0.099 / Cross valid method: THROUGHOUT / ESU R: 0.177 / ESU R Free: 0.148 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.199	5263	4.9 %	RANDOM
R_work	0.168	-	-	-
obs	0.169	101473	92 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 39 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.03 Å²	0 Å²	0.29 Å²
2-	-	0.58 Å²	0 Å²
3-	-	-	-0.57 Å²

Refinement step

Cycle: LAST / Resolution: 2→38.79 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	11136	0	82	1312	12530

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.019	11795
X-RAY DIFFRACTION	r_bond_other_d	0.005	0.02	10881
X-RAY DIFFRACTION	r_angle_refined_deg	1.362	1.965	16062
X-RAY DIFFRACTION	r_angle_other_deg	1.123	3	25050
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	3.459	5	1475
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	31.966	24.039	567
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	11.978	15	1665
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	13.661	15	67
X-RAY DIFFRACTION	r_chiral_restr	0.082	0.2	1651
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.021	13780
X-RAY DIFFRACTION	r_gen_planes_other	0.005	0.02	2815
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined
X-RAY DIFFRACTION	r_long_range_B_other
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-ID	Dom-ID	Auth asym-ID	Number	Rms dev position (Å)
1	1	A	14249	0.07
1	2	B	14249	0.07
2	1	A	14227	0.07
2	2	C	14227	0.07
3	1	A	14138	0.07
3	2	D	14138	0.07
4	1	A	14081	0.07
4	2	E	14081	0.07
5	1	A	14255	0.07
5	2	F	14255	0.07
6	1	B	13958	0.08
6	2	C	13958	0.08
7	1	B	14165	0.07
7	2	D	14165	0.07
8	1	B	13967	0.08
8	2	E	13967	0.08
9	1	B	14276	0.06
9	2	F	14276	0.06
10	1	C	13766	0.09
10	2	D	13766	0.09
11	1	C	13797	0.09
11	2	E	13797	0.09
12	1	C	14032	0.08
12	2	F	14032	0.08
13	1	D	14123	0.08
13	2	E	14123	0.08
14	1	D	14177	0.08
14	2	F	14177	0.08
15	1	E	14084	0.08
15	2	F	14084	0.08

LS refinement shell

Resolution: 2→2.05 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.237	270	-
R_work	0.207	5024	-
obs	-	-	62.06 %

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	3.366	-0.6882	0.1818	2.3821	-1.0987	2.3202	0.226	-0.0072	0.2235	-0.2424	-0.2063	-0.1262	-0.0233	0.1884	-0.0197	0.0615	-0.0256	0.008	0.1287	-0.0167	0.1207	63.9883	57.4593	85.7259
2	2.947	-0.2241	-0.1438	0.4235	-0.2191	1.2976	0.0625	-0.5685	0.1674	0.1123	-0.0145	-0.0339	-0.0655	0.2843	-0.048	0.0371	-0.0412	-0.0035	0.2521	-0.0521	0.0716	71.4544	58.2393	99.9434
3	1.225	0.448	0.3064	1.1986	0.8873	2.0268	0.1327	-0.2597	-0.1393	0.2138	-0.1003	-0.0094	0.3394	0.0607	-0.0324	0.0718	0.0009	-0.0211	0.0933	-0.0031	0.0998	18.7221	8.5808	87.6796
4	1.5006	-0.063	0.227	0.1857	0.0609	1.2336	0.0393	-0.0546	-0.0476	0.0123	-0.0442	-0.0023	0.1203	-0.081	0.0049	0.017	-0.0023	-0.0189	0.029	-0.0283	0.0746	9.7384	12.107	74.7709
5	2.7527	1.7792	-0.0773	5.4563	-0.8693	2.3584	0.0915	0.2344	-0.5276	0.0209	-0.2559	-1.5871	0.3938	0.4625	0.1644	0.3387	0.1871	-0.111	0.1708	0.0271	0.6139	71.5236	19.2725	126.2282
6	3.7398	1.3194	-0.5197	5.0708	-0.6013	2.5751	0.4012	-0.1789	-0.4011	1.0936	-0.6548	-2.0608	-0.0697	0.6882	0.2536	0.5394	0.0048	-0.5032	0.339	0.2211	0.963	80.3984	27.9845	136.5857
7	2.8058	0.4054	-1.0722	4.8847	2.0357	2.9266	0.4117	-0.3086	-0.2946	0.6181	-0.3187	-0.4027	0.381	0.1251	-0.093	0.5762	0.0921	-0.2106	0.1575	0.0709	0.1879	56.4452	5.8638	130.5288
8	2.0061	0.2992	0.3049	2.201	-0.3363	0.7679	0.2694	0.0275	-0.1788	0.285	-0.0543	-0.0413	0.2803	-0.0737	-0.2152	0.4405	0.1105	-0.097	0.1027	0.0284	0.0695	44.2173	8.402	119.6988
9	3.8032	-1.739	0.9453	3.4653	-1.4978	2.7519	0.0974	0.2757	0.0725	-0.169	-0.0749	0.0262	0.1779	-0.0285	-0.0225	0.0196	-0.0084	-0.0133	0.1078	-0.0163	0.0481	38.8242	13.1074	76.2319
10	1.4785	-0.0511	-0.0767	0.6403	0.2239	1.2132	-0.0228	0.0374	0.0133	0.1094	0.1143	-0.0904	0.0091	0.1995	-0.0915	0.0301	0.0119	-0.0312	0.0668	-0.0073	0.0513	46.7562	18.1632	89.7741
11	1.4246	0.0996	-0.4266	2.4246	2.1039	2.2361	0.0618	-0.4108	0.0518	0.1623	-0.0741	0.1176	0.0836	0.0181	0.0122	0.0506	-0.0117	0.0129	0.1585	0.0183	0.0656	43.4893	50.1863	95.5994
12	1.652	-0.0109	-0.0794	0.4374	-0.0674	0.8126	0.0678	-0.132	0.1302	-0.0065	-0.0196	0.0164	-0.0524	-0.1017	-0.0482	0.0178	0.0075	0.0263	0.0324	0.0003	0.046	34.6087	56.6529	83.6926

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	57 - 94
2	X-RAY DIFFRACTION	2	A	95 - 294
3	X-RAY DIFFRACTION	3	B	57 - 94
4	X-RAY DIFFRACTION	4	B	95 - 294
5	X-RAY DIFFRACTION	5	C	57 - 157
6	X-RAY DIFFRACTION	6	C	158 - 294
7	X-RAY DIFFRACTION	7	D	57 - 95
8	X-RAY DIFFRACTION	8	D	96 - 294
9	X-RAY DIFFRACTION	9	E	57 - 95
10	X-RAY DIFFRACTION	10	E	96 - 294
11	X-RAY DIFFRACTION	11	F	57 - 95
12	X-RAY DIFFRACTION	12	F	96 - 294

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