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- PDB-2ojl: Crystal structure of Q7WAF1_BORPA from Bordetella parapertussis. ... -

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Basic information

Entry
Database: PDB / ID: 2ojl
TitleCrystal structure of Q7WAF1_BORPA from Bordetella parapertussis. Northeast Structural Genomics target BpR68.
ComponentsHypothetical protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / bpr68 / nesg / Q7WAF1 / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium
Function / homologySelenoprotein, Rdx-type / Rdx family / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta / Uncharacterized protein
Function and homology information
Biological speciesBordetella parapertussis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å
AuthorsBenach, J. / Neely, H. / Seetharaman, J. / Wang, H. / Fang, Y. / Cunningham, K. / Ma, L.C. / Xiao, R. / Liu, J. / Baran, M.C. ...Benach, J. / Neely, H. / Seetharaman, J. / Wang, H. / Fang, Y. / Cunningham, K. / Ma, L.C. / Xiao, R. / Liu, J. / Baran, M.C. / Acton, T.B. / Rost, B. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Crystal structure of Q7WAF1_BORPA from Bordetella parapertussis
Authors: Benach, J. / Neely, H. / Seetharaman, J. / Wang, H. / Fang, Y. / Cunningham, K. / Ma, L.C. / Xiao, R. / Liu, J. / Baran, M.C. / Acton, T.B. / Rost, B. / Montelione, G.T. / Hunt, J.F. / Tong, L.
History
DepositionJan 12, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 23, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_ref_seq_dif
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hypothetical protein
B: Hypothetical protein


Theoretical massNumber of molelcules
Total (without water)24,6012
Polymers24,6012
Non-polymers00
Water2,306128
1
A: Hypothetical protein
B: Hypothetical protein

A: Hypothetical protein
B: Hypothetical protein


Theoretical massNumber of molelcules
Total (without water)49,2034
Polymers49,2034
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_666-y+1,-x+1,-z+11
Unit cell
Length a, b, c (Å)65.671, 65.671, 76.783
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number94
Space group name H-MP42212

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Components

#1: Protein Hypothetical protein /


Mass: 12300.726 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bordetella parapertussis (bacteria) / Strain: 12822 / Gene: BPP1426 / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+Magic / References: UniProt: Q7WAF1
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 128 / 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: 1.68 Å3/Da / Density % sol: 26.83 %
Description: THE STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS
Crystal growTemperature: 293 K / Method: microbatch under oil
Details: 0.1M NH4NO3, 0.1M Na citrate pH 4.0, 20% PEG 1000. Drops: 0.5 microliter protein plus 1 microliter mother liquid, mineral oil, MICROBATCH UNDER OIL, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97917 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 12, 2006
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97917 Å / Relative weight: 1
ReflectionRedundancy: 10.7 % / Av σ(I) over netI: 12.8 / Number: 198632 / Rmerge(I) obs: 0.09 / Χ2: 1.81 / D res high: 2.1 Å / D res low: 40 Å / Num. obs: 18616 / % possible obs: 99
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
4.524099.610.0562.4310.8
3.594.5298.410.0682.75910.1
3.143.5999.910.0772.22411.1
2.853.1499.910.0922.09111.2
2.652.8599.810.1171.69111.2
2.492.6599.910.1431.53211.1
2.372.4999.710.1761.39711.1
2.262.3799.710.2341.25210.9
2.182.2693.110.2921.5559.1
2.12.1899.610.3481.18310.1
ReflectionResolution: 2.1→40 Å / Num. obs: 18616 / % possible obs: 99 % / Redundancy: 10.7 % / Rmerge(I) obs: 0.09 / Χ2: 1.814 / Net I/σ(I): 12.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.1-2.1810.10.34818601.183199.6
2.18-2.269.10.29217861.555193.1
2.26-2.3710.90.23418501.252199.7
2.37-2.4911.10.17618751.397199.7
2.49-2.6511.10.14318691.532199.9
2.65-2.8511.20.11718761.691199.8
2.85-3.1411.20.09218732.091199.9
3.14-3.5911.10.07718862.224199.9
3.59-4.5210.10.06818532.759198.4
4.52-4010.80.05618882.43199.6

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNS1.1refinement
PDB_EXTRACT2data extraction
ADSCQUANTUMdata collection
HKL-2000data reduction
SHELXSphasing
RefinementMethod to determine structure: SAD / Resolution: 2.1→20 Å / FOM work R set: 0.884 / σ(F): 2 / Stereochemistry target values: Engh & Huber / Details: THE FRIEDEL PAIRS WERE USED FOR PHASING
RfactorNum. reflection% reflection
Rfree0.218 1670 8.9 %
Rwork0.198 --
obs0.198 17367 92.8 %
Solvent computationBsol: 44.783 Å2
Displacement parametersBiso mean: 26.655 Å2
Baniso -1Baniso -2Baniso -3
1--3.872 Å20 Å20 Å2
2---1.261 Å20 Å2
3---5.133 Å2
Refinement stepCycle: LAST / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1235 0 0 128 1363
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.7451.5
X-RAY DIFFRACTIONc_scbond_it3.3392
X-RAY DIFFRACTIONc_mcangle_it2.752
X-RAY DIFFRACTIONc_scangle_it5.282.5
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 33

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs
2.1-2.120.192420.224397439
2.12-2.140.218630.206404467
2.14-2.170.218490.174419468
2.17-2.190.209500.226425475
2.19-2.220.24450.229403448
2.22-2.250.276410.268369410
2.25-2.270.315310.266372403
2.27-2.30.309500.221465515
2.3-2.330.305380.214493531
2.33-2.370.232420.189471513
2.37-2.40.274530.219473526
2.4-2.440.228270.173513540
2.44-2.480.191660.196461527
2.48-2.520.24510.219510561
2.52-2.570.242530.189474527
2.57-2.620.271550.228488543
2.62-2.670.22580.199488546
2.67-2.730.143470.191515562
2.73-2.790.286670.22452519
2.79-2.860.201380.198529567
2.86-2.940.248430.207512555
2.94-3.030.266490.209496545
3.03-3.120.254560.201522578
3.12-3.230.196520.183495547
3.23-3.360.293490.211517566
3.36-3.520.173460.184518564
3.52-3.70.186570.165479536
3.7-3.930.179530.175505558
3.93-4.230.209550.165511566
4.23-4.650.16620.152509571
4.65-5.310.157650.181495560
5.31-6.650.255650.27508573
6.65-200.2520.221509561
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.par
X-RAY DIFFRACTION2water_rep.param

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