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- PDB-3lus: Crystal structure of a putative organic hydroperoxide resistance ... -

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Basic information

Entry
Database: PDB / ID: 3lus
TitleCrystal structure of a putative organic hydroperoxide resistance protein with molecule of captopril bound in one of the active sites from Vibrio cholerae O1 biovar eltor str. N16961
ComponentsOrganic hydroperoxide resistance protein
KeywordsOXIDOREDUCTASE / ORGANIC HYDROPEROXIDE RESISTANCE PROTEIN / ORHC / CAPTOPRIL-BOUND / CSGID / NIAID / 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
Organic hydroperoxide resistance protein famiy / OsmC/Ohr family / OsmC/Ohr superfamily / OsmC-like protein / K homology (KH) domain / N-terminal domain of TfIIb - #10 / N-terminal domain of TfIIb / GMP Synthetase; Chain A, domain 3 / Single Sheet / K homology domain-like, alpha/beta ...Organic hydroperoxide resistance protein famiy / OsmC/Ohr family / OsmC/Ohr superfamily / OsmC-like protein / K homology (KH) domain / N-terminal domain of TfIIb - #10 / N-terminal domain of TfIIb / GMP Synthetase; Chain A, domain 3 / Single Sheet / K homology domain-like, alpha/beta / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
L-CAPTOPRIL / Organic hydroperoxide resistance protein, putative
Similarity search - Component
Biological speciesVibrio cholerae O1 biovar El Tor (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 Å
AuthorsNocek, B. / Maltseva, N. / Makowska-Grzyska, M. / Anderson, W. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: TO BE PUBLISHED
Title: Crystal structure of a putative organic hydroperoxide resistance protein with molecule of captopril bound in one of the active sites from Vibrio cholerae O1 biovar eltor str. N16961
Authors: Nocek, B. / Maltseva, N. / Makowska-Grzyska, N. / Kwon, K. / Anderson, W. / Joachimiak, A. / NIAID
History
DepositionFeb 18, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 21, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2May 1, 2013Group: Non-polymer description
Revision 1.3Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 22, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Organic hydroperoxide resistance protein
B: Organic hydroperoxide resistance protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,1833
Polymers30,9662
Non-polymers2171
Water1,62190
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7440 Å2
ΔGint-44 kcal/mol
Surface area12400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.203, 76.198, 79.396
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Organic hydroperoxide resistance protein


Mass: 15482.936 Da / Num. of mol.: 2
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): BL21DE3 / References: UniProt: Q9KKU4
#2: Chemical ChemComp-X8Z / L-CAPTOPRIL / Captopril


Mass: 217.285 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H15NO3S / Comment: inhibitor, medication*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 90 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.87 Å3/Da / Density % sol: 34.08 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M sodium Acetate 0.1 M MES 30% Peg 2000MME 30mM captopril 5mM DTT, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 25, 2009 / Details: mirrors
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.96→40 Å / Num. all: 17357 / Num. obs: 17357 / % possible obs: 100 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 6.8 % / Rmerge(I) obs: 0.87 / Net I/σ(I): 30
Reflection shellResolution: 1.96→1.99 Å / Redundancy: 5 % / Rmerge(I) obs: 0.435 / Mean I/σ(I) obs: 3.5 / % possible all: 99.8

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
MOLREPphasing
Cootmodel building
REFMAC5.5.0102refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3EER

3eer


Resolution: 1.96→40 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.936 / SU B: 9.038 / SU ML: 0.115 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.182 / ESU R Free: 0.165 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22697 873 5.1 %RANDOM
Rwork0.1708 ---
obs0.17349 16382 99.92 %-
all-17225 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.992 Å2
Baniso -1Baniso -2Baniso -3
1-2.69 Å20 Å20 Å2
2---2.27 Å20 Å2
3----0.42 Å2
Refinement stepCycle: LAST / Resolution: 1.96→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2113 0 14 90 2217
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0222126
X-RAY DIFFRACTIONr_bond_other_d0.0010.021334
X-RAY DIFFRACTIONr_angle_refined_deg1.7581.9622895
X-RAY DIFFRACTIONr_angle_other_deg0.98833298
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8635286
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.98425.71484
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.63515326
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.534158
X-RAY DIFFRACTIONr_chiral_restr0.1120.2348
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022438
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02382
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0251.51427
X-RAY DIFFRACTIONr_mcbond_other0.3381.5590
X-RAY DIFFRACTIONr_mcangle_it1.73922271
X-RAY DIFFRACTIONr_scbond_it3.0733699
X-RAY DIFFRACTIONr_scangle_it4.8654.5624
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.96→2.011 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.28 62 -
Rwork0.208 1185 -
obs--99.52 %
Refinement TLS params.

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

IDL11 (°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)
11.47840.99-0.3274.2750.13461.17520.2824-0.21780.12430.1878-0.2467-0.0368-0.21640.0532-0.03570.1446-0.0019-0.01310.10280.01360.0945-8.7263-3.366726.6956
24.4624-0.29330.77234.5881-0.63351.53330.0236-0.0564-0.34340.1276-0.1960.55480.2711-0.37050.17240.1713-0.06770.05120.2058-0.05280.2037-19.3332-18.327224.04
32.2237-1.7943-1.17087.00553.2633.7507-0.1423-0.01240.0059-0.07190.04830.32490.0911-0.31260.0940.0866-0.031-0.0460.12390.01180.1433-19.7303-20.447817.3191
40.91531.2548-0.73394.8822-1.91981.16470.01620.0618-0.0410.0197-0.00210.113-0.0558-0.1273-0.01410.1239-0.0119-0.01110.1144-0.01410.1133-10.9806-10.078911.8024
56.18021.25244.047411.34640.21622.68810.0124-0.23370.29080.2436-0.17090.22690.0264-0.1590.15840.1556-0.0051-0.01690.12050.00780.105-5.85999.61335.2828
60.6547-1.37661.11625.6341-3.46863.40280.05640.0588-0.0824-0.17950.04770.26340.0905-0.0503-0.10410.1218-0.0007-0.01970.0971-0.0090.1099-6.8693-13.35577.7924
70.3084-1.50390.82348.7478-5.62065.245-0.06980.0279-0.0023-0.02750.0216-0.23520.2189-0.09460.04830.1353-0.01140.01990.1088-0.01240.146-1.6209-19.063213.0935
88.19480.5862.43494.7875-2.09527.60190.02890.07360.0142-0.4175-0.093-0.3508-0.0542-0.11560.06410.22870.05970.03190.06270.02490.0439-0.14491.3263-1.8697
90.96661.1207-1.99061.6956-2.75144.59950.00120.0555-0.02870.11-0.0856-0.0766-0.14910.03020.08440.1514-0.0003-0.00480.11410.01250.1336-0.2204-2.909113.0025
101.1174-0.48060.72360.7146-1.71625.7940.07710.12840.0928-0.1834-0.146-0.11940.10510.51860.06890.1792-0.00460.02610.11460.01220.14192.2845-9.77117.1186
111.3123-1.76070.27774.9542-1.02031.64050.163-0.0310.0548-0.1454-0.1793-0.14520.26370.14270.01630.13420.00760.01930.10220.00970.1024-3.8563-21.599810.6144
125.37591.0328-0.247217.79650.08953.8409-0.06440.04890.2785-0.80930.20410.4187-0.3151-0.2067-0.13970.1120.0308-0.04670.12520.0160.1291-17.4193-4.94756.9349
132.3361-1.709-1.715513.72827.99028.0035-0.12180.1562-0.0696-0.09640.01360.4042-0.1632-0.40310.10830.09940.0495-0.02070.10770.03990.07-18.8801-5.246713.0036
140.7897-0.49790.31482.2713-0.97361.39350.0030.05110.003-0.1353-0.04050.0531-0.029-0.0870.03740.10550.0151-0.01290.1281-0.00740.1164-13.3195-13.304922.568
1516.3167-9.3396-0.83666.231-0.86672.09940.01440.2877-0.6721-0.161900.42570.2701-0.2813-0.01440.175-0.0779-0.01480.0801-0.01650.1865-12.9574-32.221332.7194
161.52583.151-2.0777.465-3.89483.03480.0011-0.06060.0117-0.0872-0.02870.0038-0.06370.0770.02760.1110.0082-0.00780.0948-0.00970.1209-6.5985-5.903826.0733
1721.5798-1.83833.699515.7117-5.935710.2716-0.0635-0.5612-0.6135-0.919-0.2622-0.16961.213-0.23990.32560.1942-0.06230.06360.20910.04680.0626-12.6456-23.488239.9663
184.9911-1.4374-3.39851.9016-3.606216.4475-0.383-0.2974-0.22150.12790.30960.09420.2654-0.43090.07340.3824-0.0841-0.10550.14680.04280.0759-3.8962-25.367339.8634
190.84690.74610.29351.5548-1.50173.5844-0.0012-0.0814-0.0995-0.0091-0.1201-0.19290.06680.00270.12130.1155-0.0029-0.00710.11980.0160.1364-2.4224-20.678525.5283
203.7891.5975-5.47610.8012-2.20618.66390.0039-0.371-0.10460.0975-0.1449-0.0771-0.1010.51340.1410.1215-0.0024-0.01590.13320.01260.1244-2.9598-13.781532.6744
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 17
2X-RAY DIFFRACTION2A18 - 27
3X-RAY DIFFRACTION3A28 - 44
4X-RAY DIFFRACTION4A45 - 68
5X-RAY DIFFRACTION5A69 - 77
6X-RAY DIFFRACTION6A78 - 92
7X-RAY DIFFRACTION7A93 - 104
8X-RAY DIFFRACTION8A105 - 117
9X-RAY DIFFRACTION9A118 - 128
10X-RAY DIFFRACTION10A129 - 145
11X-RAY DIFFRACTION11B2 - 16
12X-RAY DIFFRACTION12B17 - 27
13X-RAY DIFFRACTION13B28 - 41
14X-RAY DIFFRACTION14B42 - 69
15X-RAY DIFFRACTION15B70 - 79
16X-RAY DIFFRACTION16B80 - 104
17X-RAY DIFFRACTION17B105 - 109
18X-RAY DIFFRACTION18B110 - 117
19X-RAY DIFFRACTION19B118 - 129
20X-RAY DIFFRACTION20B130 - 145

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