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- PDB-6d9n: Crystal structure of an organic hydroperoxide resistance protein ... -

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Basic information

Entry
Database: PDB / ID: 6d9n
TitleCrystal structure of an organic hydroperoxide resistance protein from Elizabethkingia anophelis with crystallant-derived thiocyanate bound
ComponentsOrganic hydroperoxide resistance protein
KeywordsOXIDOREDUCTASE / OPR1 / thiocyanate / disulfide / SSGCID / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
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
THIOCYANATE ION / Organic hydroperoxide resistance protein
Similarity search - Component
Biological speciesElizabethkingia anophelis NUHP1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.2 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To be Published
Title: Crystal structure of an organic hydroperoxide resistance protein from Elizabethkingia anophelis with crystallant-derived thiocyanate bound
Authors: Mayclin, S.J. / Delker, S.L. / Horanyi, P.S. / Lorimer, D.D. / Edwards, T.E.
History
DepositionApr 30, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 6, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 15, 2020Group: Data collection / Category: reflns_shell / Item: _reflns_shell.percent_possible_all
Revision 1.2Oct 4, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)31,9106
Polymers31,6692
Non-polymers2404
Water7,638424
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7100 Å2
ΔGint-55 kcal/mol
Surface area12610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.390, 50.030, 57.980
Angle α, β, γ (deg.)90.00, 102.63, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Organic hydroperoxide resistance protein


Mass: 15834.734 Da / Num. of mol.: 2 / Fragment: ElanA.00074.a.B1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Elizabethkingia anophelis NUHP1 (bacteria)
Gene: BD94_1921 / Plasmid: ElanA.00074.a.B1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A077EDR1
#2: Chemical ChemComp-SCN / THIOCYANATE ION / Thiocyanate


Mass: 58.082 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CNS
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 424 / 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: 2.12 Å3/Da / Density % sol: 41.92 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6.9
Details: 26.04 mg/mL ElanA.00074.a.B1.PW38309 + MCSG1 D4 (294273d4) (200 mM sodium thiocyanate, pH 6.9, 20% w/v PEG3350), cryoprotectant: 15% ethylene glycol, puck id hay3-7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Oct 18, 2017 / Details: mirrors
RadiationMonochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.2→50 Å / Num. obs: 82449 / % possible obs: 99.6 % / Redundancy: 4.076 % / Biso Wilson estimate: 10.43 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.047 / Rrim(I) all: 0.054 / Χ2: 1.045 / Net I/σ(I): 15.13
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.2-1.234.020.5722.4560710.8610.6699.1
1.23-1.264.020.4872.8758370.8930.56299.3
1.26-1.34.0470.4023.4957810.9270.46499.3
1.3-1.344.0520.344.0355820.9330.39299.7
1.34-1.394.0570.2794.954320.9520.32199.5
1.39-1.434.0850.2295.952520.9660.26499.8
1.43-1.494.0840.177.7650600.9860.19699.7
1.49-1.554.0910.1429.4648360.9860.16499.7
1.55-1.624.1170.10612.2847090.9910.12299.6
1.62-1.74.1240.0871544900.9930.199.7
1.7-1.794.1180.07317.7442650.9950.08399.8
1.79-1.94.1160.05821.2340350.9970.06799.8
1.9-2.034.0930.04726.0437970.9970.05499.5
2.03-2.194.090.03830.4935350.9980.04499.7
2.19-2.44.090.03434.2532630.9980.03999.5
2.4-2.684.1020.03136.3129490.9990.03599.8
2.68-3.14.1110.02739.5826190.9990.031100
3.1-3.794.0880.02442.8222200.9990.02899.6
3.79-5.374.0820.02344.3517400.9990.02699.8
5.37-503.9010.02643.579760.9980.0399.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX(dev_3092: ???)refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
PDB_EXTRACT3.24data extraction
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1N2F

1n2f


Resolution: 1.2→40.394 Å / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 15.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1575 2069 2.51 %
Rwork0.1406 --
obs0.141 82422 99.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.2→40.394 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2087 0 14 424 2525
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112354
X-RAY DIFFRACTIONf_angle_d1.2873244
X-RAY DIFFRACTIONf_dihedral_angle_d19.353881
X-RAY DIFFRACTIONf_chiral_restr0.101380
X-RAY DIFFRACTIONf_plane_restr0.009437
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2-1.22790.20021410.19345297X-RAY DIFFRACTION99
1.2279-1.25860.21761390.1845332X-RAY DIFFRACTION99
1.2586-1.29270.19251560.17015251X-RAY DIFFRACTION99
1.2927-1.33070.19481320.16525342X-RAY DIFFRACTION100
1.3307-1.37360.22881300.1555332X-RAY DIFFRACTION100
1.3736-1.42270.16791440.14465334X-RAY DIFFRACTION100
1.4227-1.47970.17021270.13425375X-RAY DIFFRACTION100
1.4797-1.54710.15431390.1275304X-RAY DIFFRACTION100
1.5471-1.62860.14251390.11555375X-RAY DIFFRACTION100
1.6286-1.73070.13621320.1215380X-RAY DIFFRACTION100
1.7307-1.86430.16621310.13115372X-RAY DIFFRACTION100
1.8643-2.05190.1561450.13215350X-RAY DIFFRACTION100
2.0519-2.34880.1611450.13165374X-RAY DIFFRACTION100
2.3488-2.95910.14771310.14895432X-RAY DIFFRACTION100
2.9591-40.4170.13981380.14125503X-RAY DIFFRACTION100

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