PDB-3eer: High resolution structure of putative organic hydroperoxide resis...

ID or keywords:

Entry

Database: PDB / ID: 3eer

Title

High resolution structure of putative organic hydroperoxide resistance protein from Vibrio cholerae O1 biovar eltor str. N16961

Components

Organic hydroperoxide resistance protein, putative

Keywords

OXIDOREDUCTASE / CSGID / organic hydroperoxide resistance protein / ORHC / Structural Genomics / Center for Structural Genomics of Infectious Diseases

Function / homology

Function and homology information

response to oxidative stress / metal ion binding
Similarity search - Function

Biological species

Vibrio cholerae O1 biovar El Tor (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.45 Å

Authors

Nocek, B. / Maltseva, N. / Kwon, K. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)

Citation

Journal: To be Published
Title: High resolution crystal structure of the organic hydroperoxide resistance protein from Vibrio cholerae O1 biovar eltor str. N16961
Authors: Nocek, B. / Mulligan, R. / Kwon, K. / Anderson, W.F. / Joachimiak, A.

History

Deposition	Sep 5, 2008	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 21, 2008	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Version format compliance

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3eer.cif.gz	44 KB	Display	PDBx/mmCIF format
PDB format	pdb3eer.ent.gz	34.6 KB	Display	PDB format
PDBx/mmJSON format	3eer.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	3eer_validation.pdf.gz	441.8 KB	Display	wwPDB validaton report
Full document	3eer_full_validation.pdf.gz	441.9 KB	Display
Data in XML	3eer_validation.xml.gz	9.9 KB	Display
Data in CIF	3eer_validation.cif.gz	14.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ee/3eer ftp://data.pdbj.org/pub/pdb/validation_reports/ee/3eer	HTTPS FTP

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Related structure data

Similar structure data	6d9n-d 2dda-4 5hw3-d 2dda-1 6eb4-2 4htp-1 6ebd-2 3fvh-d 6eci-6 2dda-2 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	TargetDB: IDP001325

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#134 - Feb 2011 Integrin similarity (1) #172 - Apr 2014 RecA and Rad51 similarity (1) #194 - Feb 2016 Designer Insulins similarity (1) #234 - Jun 2019 MDM2 and Cancer similarity (1) #259 - Jul 2021 Designed Proteins and Citizen Science similarity (1)

Deposited unit

A: Organic hydroperoxide resistance protein, putative

hetero molecules

16.3 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Organic hydroperoxide resistance protein, putative

hetero molecules

A: Organic hydroperoxide resistance protein, putative

hetero molecules

defined by author&software
32.6 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	59.649, 71.127, 71.629
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	24
Space group name H-M	I2₁2₁2₁

Components on special symmetry positions

ID	Model	Components
1	1	A-2005- ZN
2	1	A-3007- HOH
3	1	A-3021- HOH

#1: Protein	Organic hydroperoxide resistance protein, putative Mass: 15436.041 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio cholerae O1 biovar El Tor (bacteria) Strain: N16961 / Gene: VC_A1006 / Production host: Escherichia coli (E. coli) / Strain (production host): BLD21(DE3) / References: UniProt: Q9KKU4
#2: Chemical	ChemComp-ACT / ACETATE ION Mass: 59.044 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C₂H₃O₂
#3: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#4: Chemical	ChemComp-IMD / IMIDAZOLE Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₅N₂
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 182 / Source method: isolated from a natural source / Formula: H₂O
Sequence details	TARGET ID DOES NOT EXIST IN TARGETDB A THE TIME OF PROCESSING.

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.46 Å³/Da / Density % sol: 50.02 %
Crystal grow	Temperature: 291 K / pH: 8 Details: 0.2 M ZnAcetate, 0.1 M Imidazole, 20% Peg 3000, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9794
Detector	Type: SBC-3 / Detector: CCD / Date: Aug 16, 2008 / Details: MIRRORS
Radiation	Monochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9794 Å / Relative weight: 1
Reflection	Resolution: 1.45→40 Å / Num. obs: 27234 / % possible obs: 99.1 % / Observed criterion σ(I): 0 / Redundancy: 6.4 % / R_merge(I) obs: 0.106 / Net I/σ(I): 19.7
Reflection shell	Resolution: 1.45→1.48 Å / Redundancy: 2.8 % / R_merge(I) obs: 0.464 / Mean I/σ(I) obs: 2.34 / % possible all: 90.9

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Processing

Software

Name	Version	Classification
SBC-Collect		data collection
MOLREP		phasing
CCP4		model building
REFMAC	5.5.0054	refinement
HKL-3000		data reduction
HKL-3000		data scaling
HKL-3000		phasing
DM		phasing
ARP/wARP		model building
CCP4		phasing
Coot		model building

Refinement

Method to determine structure:

SAD / Resolution: 1.45→40 Å / Cor.coef. F_o:F_c: 0.969 / Cor.coef. F_o:F_c free: 0.963 / SU B: 1.36 / SU ML: 0.031 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.051 / ESU R Free: 0.053 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.164	1358	5 %	RANDOM
R_work	0.139	-	-	-
obs	0.141	25858	99 %	-
all	-	27216	-	-

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: 5.82 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.47 Å²	0 Å²	0 Å²
2-	-	-0.08 Å²	0 Å²
3-	-	-	-0.4 Å²

Refinement step

Cycle: LAST / Resolution: 1.45→40 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1009	0	39	182	1230

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.015	0.022	1075
X-RAY DIFFRACTION	r_bond_other_d	0.003	0.02	660
X-RAY DIFFRACTION	r_angle_refined_deg	1.508	1.975	1465
X-RAY DIFFRACTION	r_angle_other_deg	0.986	3	1637
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.635	5	149
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	41.118	25.61	41
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	10.36	15	161
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	21.242	15	4
X-RAY DIFFRACTION	r_chiral_restr	0.097	0.2	176
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	1249
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	197
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	0.843	1.5	728
X-RAY DIFFRACTION	r_mcbond_other	0.255	1.5	292
X-RAY DIFFRACTION	r_mcangle_it	1.377	2	1147
X-RAY DIFFRACTION	r_scbond_it	2.156	3	347
X-RAY DIFFRACTION	r_scangle_it	3.316	4.5	313
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 1.45→1.49 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.271	103	-
R_work	0.215	1717	-
obs	-	-	90.64 %

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	8.199	5.0793	3.9086	4.5944	1.3011	7.9632	-0.0699	0.0041	-0.1503	0.0739	0.0037	-0.1587	-0.2187	0.4068	0.0663	0.0517	0.0005	0.0146	0.0609	-0.0072	0.0287	17.2509	7.7785	32.3302
2	0.3398	0.2739	0.1588	1.0063	-0.2532	1.0208	0.0219	0.021	0.0577	0.0593	0.0282	0.0203	0.0872	-0.064	-0.0502	0.0284	-0.0012	-0.0035	0.0552	0.0029	0.0487	10.3898	-8.6693	24.6132
3	1.3263	0.2732	-1.3608	8.9638	7.2157	7.8679	0.0363	-0.0281	0.0983	0.253	-0.0829	0.2601	0.2415	-0.1307	0.0466	0.0529	-0.01	-0.0146	0.0821	0.0215	0.0567	5.5006	-6.3435	25.1144
4	1.1712	-0.0964	-1.1516	7.5806	8.1822	9.7752	-0.0367	-0.0296	0.1467	0.0915	-0.1445	0.2938	0.1275	-0.1591	0.1812	0.0556	0.0371	-0.0169	0.1409	0.0163	0.0861	2.6408	-3.7487	22.3853
5	3.0422	0.6646	-0.9513	3.0014	1.308	5.8083	0.0284	0.0889	-0.3012	-0.068	-0.0257	0.2171	0.3805	-0.3383	-0.0027	0.0797	-0.025	-0.0211	0.0582	-0.0001	0.0744	7.7003	-13.1635	7.1855
6	0.5621	0.641	0.1108	2.7268	0.1692	0.8014	0.0215	-0.0348	0.0158	0.0095	-0.0549	0.0283	-0.014	-0.0611	0.0334	0.0233	-0.0014	-0.0022	0.0501	0.0007	0.0219	13.6661	5.9328	14.0906
7	5.5731	2.4779	1.6517	10.248	-1.0161	3.1536	-0.0513	-0.1043	0.191	0.4679	-0.0864	-0.1084	-0.5851	0.1403	0.1377	0.1525	-0.0173	-0.0251	0.0371	-0.0345	0.0937	18.6073	26.3739	17.1219
8	0.8676	-0.9297	0.0261	7.7209	0.2238	0.6317	-0.0188	-0.0467	-0.015	0.03	0.0361	0.0915	-0.1067	-0.0466	-0.0172	0.036	0.0051	0.0001	0.0467	0.0017	0.0245	12.7483	13.2058	8.1942
9	4.7816	-1.7081	1.1161	6.5008	-1.888	5.3623	0.0014	0.092	-0.1047	-0.0472	-0.1732	-0.1675	0.3751	0.4174	0.1718	0.058	0.0278	0.0075	0.044	0.0125	0.0196	23.7863	-11.1682	9.9073
10	0.8784	-0.3554	0.2207	2.9102	-0.4735	0.9192	0.0386	-0.0129	0.0335	-0.0172	-0.0786	-0.0116	-0.0945	0.0238	0.04	0.0292	-0.0071	0.0069	0.0487	0.0067	0.0298	18.4076	13.9508	5.1407
11	3.4397	-1.2845	0.1506	4.4693	-1.393	4.0945	0.0316	0.0737	0.1122	0.062	-0.0016	0.0282	-0.1892	0.0341	-0.03	0.033	-0.0127	-0.0121	0.0439	-0.0011	0.0283	24.4159	20.8106	5.614
12	1.5583	1.7312	-1.9661	2.969	-2.5638	2.9263	0.0086	-0.0325	-0.0036	0.1149	-0.0457	-0.0923	-0.0809	0.0929	0.0371	0.0374	-0.0103	-0.0091	0.0539	0.008	0.0381	23.9001	11.6616	15.9681
13	4.2253	-2.5118	-0.5518	4.5821	0.4658	1.9506	0.0394	0.0349	0.073	-0.1428	0.0163	-0.2078	-0.0201	0.177	-0.0557	0.0314	0.0005	0.0045	0.0575	0.0111	0.0437	27.396	3.8388	16.3814
14	1.6394	-4.0378	3.1066	10.36	-7.0074	6.8923	0.1121	0.0995	0.0852	-0.1976	-0.1672	-0.2759	0.3138	0.3173	0.055	0.0509	-0.0033	-0.0017	0.072	-0.0134	0.1043	25.0598	4.9844	6.6824
15	9.5899	-4.1405	4.9155	2.7435	-2.1613	2.5718	-0.0248	0.296	0.1199	0.0653	-0.0684	-0.1617	-0.0662	0.1982	0.0932	0.0729	-0.0316	-0.0111	0.0859	0.024	0.0604	22.4187	14.6234	0.7112

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	6 - 11
2	X-RAY DIFFRACTION	2	A	12 - 20
3	X-RAY DIFFRACTION	3	A	21 - 28
4	X-RAY DIFFRACTION	4	A	29 - 35
5	X-RAY DIFFRACTION	5	A	36 - 45
6	X-RAY DIFFRACTION	6	A	46 - 70
7	X-RAY DIFFRACTION	7	A	71 - 76
8	X-RAY DIFFRACTION	8	A	77 - 86
9	X-RAY DIFFRACTION	9	A	87 - 98
10	X-RAY DIFFRACTION	10	A	99 - 109
11	X-RAY DIFFRACTION	11	A	110 - 117
12	X-RAY DIFFRACTION	12	A	118 - 126
13	X-RAY DIFFRACTION	13	A	127 - 133
14	X-RAY DIFFRACTION	14	A	134 - 139
15	X-RAY DIFFRACTION	15	A	140 - 145

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