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- PDB-3nct: X-ray crystal structure of the bacterial conjugation factor PsiB,... -

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Basic information

Entry
Database: PDB / ID: 3nct
TitleX-ray crystal structure of the bacterial conjugation factor PsiB, a negative regulator of reca
ComponentsProtein psiB
KeywordsDNA BINDING PROTEIN / CHAPERONE
Function / homologyPlasmid SOS inhibition protein / Protein PsiB / Protein PsiB-like superfamily / Plasmid SOS inhibition protein (PsiB) / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / Protein PsiB
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å
AuthorsPetrova, V. / Satyshur, K.A. / George, N.P. / McCaslin, D. / Cox, M.M. / Keck, J.L.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: X-ray crystal structure of the bacterial conjugation factor PsiB, a negative regulator of RecA.
Authors: Petrova, V. / Satyshur, K.A. / George, N.P. / McCaslin, D. / Cox, M.M. / Keck, J.L.
History
DepositionJun 5, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 21, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 27, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein psiB
B: Protein psiB
C: Protein psiB
D: Protein psiB


Theoretical massNumber of molelcules
Total (without water)64,5094
Polymers64,5094
Non-polymers00
Water4,648258
1
A: Protein psiB
C: Protein psiB


Theoretical massNumber of molelcules
Total (without water)32,2542
Polymers32,2542
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1920 Å2
ΔGint-10 kcal/mol
Surface area12060 Å2
MethodPISA
2
B: Protein psiB
D: Protein psiB


Theoretical massNumber of molelcules
Total (without water)32,2542
Polymers32,2542
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1960 Å2
ΔGint-10 kcal/mol
Surface area12120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.815, 93.815, 164.827
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein
Protein psiB


Mass: 16127.248 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: ECOK12F063, psiB / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P10031
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 258 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE AUTHORS CLAIM THAT THE UNIPROT ENTRY P10031 CONTAINS AN INCORRECT AMINOACID AT POSITION 137. ...THE AUTHORS CLAIM THAT THE UNIPROT ENTRY P10031 CONTAINS AN INCORRECT AMINOACID AT POSITION 137. THE CORRECT FULL SEQUENCE IS REPORTED IN THE PAPER BY DUTREIX M. ET AL. (NUCLEIC ACIDS RESEARCH 1988, V. 16, PAGES:10669-10679). SEE ALSO REMARK SEQADV.

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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: 2.81 Å3/Da / Density % sol: 56.24 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.2
Details: 136 mM sodium acetate, pH 5.2, 1.4% PEG 4000, 20% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.97919 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 16, 2008
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97919 Å / Relative weight: 1
ReflectionResolution: 2.2→30 Å / Num. obs: 71325 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6 % / Rmerge(I) obs: 0.059 / Net I/σ(I): 22
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 5.9 % / Rsym value: 0.269 / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SOLVEphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.2→30 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.943 / SU B: 9.442 / SU ML: 0.111 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.169 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.21029 1909 5 %RANDOM
Rwork0.18491 ---
all0.18619 ---
obs0.18619 36000 99.48 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 47.049 Å2
Baniso -1Baniso -2Baniso -3
1-0.64 Å20 Å20 Å2
2--0.64 Å20 Å2
3----1.28 Å2
Refinement stepCycle: LAST / Resolution: 2.2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4298 0 0 258 4556
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0214449
X-RAY DIFFRACTIONr_angle_refined_deg1.0831.9286060
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6075565
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.55124.255235
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.44515680
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.851532
X-RAY DIFFRACTIONr_chiral_restr0.0710.2665
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213518
X-RAY DIFFRACTIONr_mcbond_it0.4151.52771
X-RAY DIFFRACTIONr_mcangle_it0.81924438
X-RAY DIFFRACTIONr_scbond_it1.58331678
X-RAY DIFFRACTIONr_scangle_it2.6114.51616
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.263 135 -
Rwork0.196 2602 -
obs--99.42 %
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)
11.44160.820.11082.4654-0.24953.28550.00270.10090.2915-0.0040.07740.1769-0.4140.1242-0.08010.1183-0.0497-0.03430.02630.03970.0997-21.821-8.721-39.382
21.57330.5881-0.55713.0411-0.98132.9324-0.10770.0461-0.2613-0.07650.1431-0.07570.3770.1122-0.03540.13570.0209-0.01470.0171-0.02190.0628-26.767-39.543-38.296
33.43980.53130.79512.09790.50132.96270.02930.0648-0.47670.0691-0.0217-0.53860.0870.7168-0.00760.0264-0.0053-0.0550.24160.05580.2492-4.564-22.527-32.625
43.00990.522-0.72592.8841-0.79293.7266-0.03330.11540.50060.13230.26640.8244-0.0083-0.3723-0.23310.00740.00790.02630.04670.08090.3136-44.148-25.446-33.641
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-10 - 9999
2X-RAY DIFFRACTION2B-10 - 9999
3X-RAY DIFFRACTION3C-10 - 9999
4X-RAY DIFFRACTION4D-10 - 9999

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