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- PDB-2q82: Crystal structure of core protein P7 from Pseudomonas phage phi12... -

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Basic information

Entry
Database: PDB / ID: 2q82
TitleCrystal structure of core protein P7 from Pseudomonas phage phi12. Northeast Structural Genomics Target OC1
ComponentsCore protein P7
KeywordsSTRUCTURAL PROTEIN / P7 / core protein / NESG / OC1 / structural genomics / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium
Function / homologyOxidized Rhodanese; domain 1 - #20 / Core protein P7, N-terminal core domain / Oxidized Rhodanese; domain 1 / 3-Layer(aba) Sandwich / Alpha Beta / Core protein P7
Function and homology information
Biological speciesPseudomonas phage phi12 (bacteriophage)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.83 Å
AuthorsBenach, J. / Eryilmaz, E. / Su, M. / Seetharaman, J. / Wei, H. / Gottlieb, P. / Hunt, J.F. / Ghose, R. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Structure and dynamics of the P7 protein from the bacteriophage phi 12.
Authors: Eryilmaz, E. / Benach, J. / Su, M. / Seetharaman, J. / Dutta, K. / Wei, H. / Gottlieb, P. / Hunt, J.F. / Ghose, R.
History
DepositionJun 8, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 7, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 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 1.3Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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

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Assembly

Deposited unit
A: Core protein P7


Theoretical massNumber of molelcules
Total (without water)14,4501
Polymers14,4501
Non-polymers00
Water3,387188
1
A: Core protein P7

A: Core protein P7


Theoretical massNumber of molelcules
Total (without water)28,9012
Polymers28,9012
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_765-x+2,-x+y+1,-z+2/31
Buried area1350/11910
MethodPISA
Unit cell
Length a, b, c (Å)75.499, 75.499, 46.486
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
DetailsThe putative biological unit is a dimer, created by -x, -x+y, -z+2/3 + (1 1 0) symmetry operation

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Components

#1: Protein Core protein P7


Mass: 14450.371 Da / Num. of mol.: 1 / Fragment: Residues 1-129
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas phage phi12 (bacteriophage)
Genus: Cystovirus / Plasmid: pET21D / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: Q94M07
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 188 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.65 Å3/Da / Density % sol: 53.56 %
Description: THE STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 23% PEG10000, 100mM Sodium acetate, 10% n-Hexyl-D-glucoside, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12B / Wavelength: 0.97947 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: May 8, 2007 / Details: mirrors
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97947 Å / Relative weight: 1
ReflectionRedundancy: 10.5 % / Av σ(I) over netI: 12 / Number: 305699 / Rmerge(I) obs: 0.05 / Χ2: 0.78 / D res high: 1.7 Å / D res low: 50 Å / Num. obs: 29155 / % possible obs: 89.4
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
3.665098.410.0310.92111.6
2.913.6610010.0350.88611.6
2.542.9110010.0560.84711.6
2.312.5410010.090.80811.5
2.142.3110010.1250.77911.4
2.022.1499.810.190.71111.1
1.912.0295.710.2880.67910.3
1.831.9182.810.3880.6319.2
1.761.836910.4720.6047.5
1.71.7648.610.6740.6455.7
ReflectionResolution: 1.7→50 Å / Num. obs: 29155 / % possible obs: 89.4 % / Observed criterion σ(I): -3 / Redundancy: 10.5 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 12
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obs% possible all
1.7-1.765.70.67448.6
1.76-1.837.50.47269
1.83-1.919.20.38882.8
1.91-2.0210.30.28895.7
2.02-2.1411.10.1999.8
2.14-2.3111.40.125100
2.31-2.5411.50.09100
2.54-2.9111.60.056100
2.91-3.6611.60.035100
3.66-5011.60.03198.4

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Phasing

PhasingMethod: SAD
Phasing MADD res high: 1.88 Å / D res low: 5.83 Å / FOM : 0.295 / Reflection: 9638
Phasing MAD setR kraut acentric: 0.037 / Highest resolution: 5.83 Å / Lowest resolution: 1.88 Å / FOM : 0.297 / Power: 0.71 kW
Phasing dmFOM : 0.52 / FOM acentric: 0.52 / FOM centric: 0.5 / Reflection: 12613 / Reflection acentric: 11383 / Reflection centric: 1230
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
5.1-37.8890.920.950.84661494167
3.2-5.10.90.910.7919681697271
2.6-3.20.720.730.5823342108226
2.2-2.60.520.530.3622762090186
1.9-2.20.280.290.237983519279
1.8-1.90.130.130.0815761475101

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SnBphasing
RESOLVE2.08phasing
CNS1.1refinement
PDB_EXTRACT2data extraction
CBASSdata collection
HKL-2000data reduction
RefinementMethod to determine structure: SAD / Resolution: 1.83→20 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber / Details: THE FRIEDEL PAIRS WERE USED FOR PHASING
RfactorNum. reflection% reflection
Rfree0.226 2070 7.9 %
Rwork0.21 --
obs0.21 21894 83.6 %
Solvent computationBsol: 52.745 Å2
Displacement parametersBiso mean: 39.389 Å2
Baniso -1Baniso -2Baniso -3
1-6.207 Å22.497 Å20 Å2
2--6.913 Å20 Å2
3----13.12 Å2
Refinement stepCycle: LAST / Resolution: 1.83→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms856 0 0 188 1044
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-IDTotal num. of bins used
1.83-1.850.214320.255270X-RAY DIFFRACTION41
1.85-1.860.32140.269254X-RAY DIFFRACTION41
1.86-1.880.359320.287280X-RAY DIFFRACTION41
1.88-1.890.278300.24308X-RAY DIFFRACTION41
1.89-1.910.236320.267310X-RAY DIFFRACTION41
1.91-1.930.235400.255374X-RAY DIFFRACTION41
1.93-1.950.318330.246342X-RAY DIFFRACTION41
1.95-1.970.314480.268395X-RAY DIFFRACTION41
1.97-1.990.198390.246404X-RAY DIFFRACTION41
1.99-2.010.312420.266387X-RAY DIFFRACTION41
2.01-2.030.252540.273456X-RAY DIFFRACTION41
2.03-2.050.296500.251464X-RAY DIFFRACTION41
2.05-2.080.298630.281474X-RAY DIFFRACTION41
2.08-2.10.253560.256490X-RAY DIFFRACTION41
2.1-2.130.279400.249464X-RAY DIFFRACTION41
2.13-2.160.195600.244526X-RAY DIFFRACTION41
2.16-2.190.309550.257479X-RAY DIFFRACTION41
2.19-2.220.191560.217569X-RAY DIFFRACTION41
2.22-2.250.242490.21500X-RAY DIFFRACTION41
2.25-2.290.227550.224525X-RAY DIFFRACTION41
2.29-2.320.286420.229502X-RAY DIFFRACTION41
2.32-2.360.213490.223518X-RAY DIFFRACTION41
2.36-2.410.243640.202520X-RAY DIFFRACTION41
2.41-2.450.314540.23540X-RAY DIFFRACTION41
2.45-2.50.336580.241532X-RAY DIFFRACTION41
2.5-2.560.278580.25507X-RAY DIFFRACTION41
2.56-2.620.199560.211563X-RAY DIFFRACTION41
2.62-2.680.226470.223547X-RAY DIFFRACTION41
2.68-2.750.278530.207532X-RAY DIFFRACTION41
2.75-2.840.284680.203545X-RAY DIFFRACTION41
2.84-2.930.203720.216534X-RAY DIFFRACTION41
2.93-3.030.237760.224555X-RAY DIFFRACTION41
3.03-3.150.28530.219580X-RAY DIFFRACTION41
3.15-3.290.238560.213578X-RAY DIFFRACTION41
3.29-3.470.184470.193558X-RAY DIFFRACTION41
3.47-3.680.147700.195570X-RAY DIFFRACTION41
3.68-3.970.18520.182592X-RAY DIFFRACTION41
3.97-4.360.19620.176562X-RAY DIFFRACTION41
4.36-4.980.172460.164585X-RAY DIFFRACTION41
4.98-6.250.26580.237570X-RAY DIFFRACTION41
6.25-200.211490.223563X-RAY DIFFRACTION41
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.par
X-RAY DIFFRACTION2water_rep.param

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