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- PDB-4noz: Crystal Structure of an Organic Hydroperoxide Resistance Protein ... -

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Basic information

Entry
Database: PDB / ID: 4noz
TitleCrystal Structure of an Organic Hydroperoxide Resistance Protein from Burkholderia cenocepacia
ComponentsOrganic hydroperoxide resistance protein
KeywordsPROTEIN BINDING / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Seattle Structural Genomics Center for Infectious Disease / SSGCID / OsmC-like protein / Organic hydroperoxide resistance
Function / homology
Function and homology information


response to oxidative stress
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
Organic hydroperoxide resistance protein
Similarity search - Component
Biological speciesBurkholderia cenocepacia (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.22 Å
AuthorsDranow, D.M. / Lukacs, C.M. / Edwards, T.E. / Lorimer, D. / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: TO BE PUBLISHED
Title: Crystal Structure of an Organic Hydroperoxide Resistance Protein from Burkholderia cenocepacia
Authors: Dranow, D.M. / Lukacs, C.M. / Edwards, T.E. / Lorimer, D.
History
DepositionNov 20, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 4, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 11, 2013Group: Other
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software
Revision 1.3Sep 20, 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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)31,5969
Polymers31,1622
Non-polymers4347
Water4,270237
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7970 Å2
ΔGint-33 kcal/mol
Surface area12780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.190, 121.190, 64.140
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number90
Space group name H-MP4212
Components on special symmetry positions
IDModelComponents
11B-418-

HOH

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Components

#1: Protein Organic hydroperoxide resistance protein


Mass: 15580.785 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia cenocepacia (bacteria)
Strain: ATCC BAA-245 / DSM 16553 / LMG 16656 / NCTC 13227 / J2315 / CF5610
Gene: ohR, BceJ2315_63600, BCAS0085 / Production host: Escherichia coli (E. coli) / References: UniProt: B4EPK2
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 237 / 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: 3.78 Å3/Da / Density % sol: 67.45 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: MCSG1(d2): 0.2M NaCl, 0.1M Bis-Tris:HCl, pH=6.5, 25% PEG-3350, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97857 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 16, 2013 / Details: Beryllium Lenses
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2.22→99.6114 Å / Num. all: 24188 / Num. obs: 24096 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 9 % / Biso Wilson estimate: 36.86 Å2 / Rmerge(I) obs: 0.063 / Net I/σ(I): 32.67
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.22-2.280.4665.7165081753100
2.28-2.340.4076.3816114169899.7
2.34-2.410.3178.1315853167799.9
2.41-2.480.3018.715140160699.8
2.48-2.560.23111.3714825156399.8
2.56-2.650.18214.1114185151399.8
2.65-2.750.14517.2213816147899.9
2.75-2.870.11321.17131631415100
2.87-2.990.09524.86126851374100
2.99-3.140.07231.3911765129199.8
3.14-3.310.05440.4910992124299.9
3.31-3.510.04247.3910369119099.8
3.51-3.750.03457.459595111799.8
3.75-4.050.02966.488751104899.8
4.05-4.440.02671.9793395999.6
4.44-4.960.02280.61718087799.1
4.96-5.730.02475.32629978799.2
5.73-7.020.02274.65529966699
7.02-9.930.01891.67418253498.3
9.930.016102.18225930891.1

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.5.5phasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1ZB8

1zb8


Resolution: 2.22→85.69 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.945 / WRfactor Rfree: 0.1732 / WRfactor Rwork: 0.1456 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8841 / SU B: 6.568 / SU ML: 0.088 / SU R Cruickshank DPI: 0.1539 / SU Rfree: 0.1422 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.154 / ESU R Free: 0.142 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.1951 1226 5.1 %RANDOM
Rwork0.1616 ---
all0.1633 25322 --
obs0.1633 24096 99.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 78.97 Å2 / Biso mean: 33.583 Å2 / Biso min: 10.14 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å20 Å2-0 Å2
2--0.07 Å20 Å2
3----0.14 Å2
Refinement stepCycle: LAST / Resolution: 2.22→85.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2092 0 28 237 2357
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0192167
X-RAY DIFFRACTIONr_bond_other_d0.0010.022132
X-RAY DIFFRACTIONr_angle_refined_deg1.4811.9742929
X-RAY DIFFRACTIONr_angle_other_deg0.71934886
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5855292
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.24223.08681
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.90415332
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7051516
X-RAY DIFFRACTIONr_chiral_restr0.080.2338
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212484
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02468
X-RAY DIFFRACTIONr_mcbond_it1.2191.7951162
X-RAY DIFFRACTIONr_mcbond_other1.2061.7931161
X-RAY DIFFRACTIONr_mcangle_it1.9672.6811450
LS refinement shellResolution: 2.22→2.278 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.245 103 -
Rwork0.19 1649 -
all-1752 -
obs--99.83 %
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)
11.9629-0.4779-0.78464.19531.22821.26350.04580.32870.0185-0.2983-0.038-0.2097-0.0555-0.004-0.00790.08290.01890.0320.14810.00850.111546.44519.649812.1151
20.85730.78360.42522.8021.87872.0593-0.0053-0.038-0.081-0.03370.0855-0.17810.01810.0905-0.08020.08020.0349-0.01240.0944-0.00130.15339.638514.805624.5566
32.70080.79942.91521.49751.25285.59940.0337-0.1416-0.25450.14780.0436-0.02890.2172-0.0872-0.07730.06320.0521-0.00060.08960.02830.109134.62915.897232.0792
41.4634-0.14650.36471.16350.31992.05180.0039-0.08210.00610.01510.02-0.0566-0.0031-0.0095-0.02390.07590.0281-0.01210.09580.00120.125233.482523.655331.3156
51.9535-0.44580.09511.670.08910.9511-0.0455-0.0371-0.27620.02190.0695-0.0504-0.00680.0139-0.0240.05190.0175-0.00320.04150.00430.0835.783813.237324.9468
64.25471.43922.26930.92021.15592.68560.11840.2247-0.1681-0.1392-0.0599-0.18030.0169-0.1419-0.05850.13770.03680.00460.1773-0.01110.145540.32617.140312.2307
71.33640.36110.31792.64263.50316.88940.07160.45190.094-0.20830.0275-0.1839-0.05440.013-0.09910.11740.03270.04280.23230.04180.092939.436422.59546.8247
83.2735-0.0399-0.70261.74280.90621.55090.14150.60560.0784-0.2752-0.05310.0099-0.1675-0.2597-0.08840.15130.0525-0.04640.24730.02210.07931.095521.75297.0782
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 32
2X-RAY DIFFRACTION2A33 - 74
3X-RAY DIFFRACTION3A75 - 112
4X-RAY DIFFRACTION4A113 - 141
5X-RAY DIFFRACTION5B-6 - 34
6X-RAY DIFFRACTION6B35 - 75
7X-RAY DIFFRACTION7B76 - 111
8X-RAY DIFFRACTION8B112 - 141

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