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- PDB-4apv: The Klebsiella pneumoniae primosomal PriB protein: identification... -

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Basic information

Entry
Database: PDB / ID: 4apv
TitleThe Klebsiella pneumoniae primosomal PriB protein: identification, crystal structure, and ssDNA binding mode
ComponentsPRIMOSOMAL REPLICATION PROTEIN N
KeywordsREPLICATION / PRIB PRIMOSOME SSDNA BINDING
Function / homologyNucleic acid-binding proteins / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / Mainly Beta / :
Function and homology information
Biological speciesKLEBSIELLA PNEUMONIAE (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.095 Å
AuthorsLo, Y.H. / Huang, Y.H. / Hsiao, C.D. / Huang, C.Y.
CitationJournal: Genes Cells / Year: 2012
Title: Crystal Structure and DNA-Binding Mode of Klebsiella Pneumoniae Primosomal Prib Protein.
Authors: Huang, Y. / Lo, Y.H. / Huang, W. / Huang, C.Y.
History
DepositionApr 6, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 25, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 23, 2013Group: Database references
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 5-STRANDED BARREL THIS IS REPRESENTED BY A 6-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PRIMOSOMAL REPLICATION PROTEIN N


Theoretical massNumber of molelcules
Total (without water)12,5591
Polymers12,5591
Non-polymers00
Water18010
1
A: PRIMOSOMAL REPLICATION PROTEIN N

A: PRIMOSOMAL REPLICATION PROTEIN N


Theoretical massNumber of molelcules
Total (without water)25,1192
Polymers25,1192
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area3060 Å2
ΔGint-23.9 kcal/mol
Surface area10430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.773, 36.934, 39.451
Angle α, β, γ (deg.)90.00, 113.77, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein PRIMOSOMAL REPLICATION PROTEIN N / PRIMOSOMAL DNA REPLICATION PROTEIN PRIB


Mass: 12559.387 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) KLEBSIELLA PNEUMONIAE (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: G0GH41
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / 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: 10

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Sample preparation

CrystalDensity Matthews: 1.85 Å3/Da / Density % sol: 33.4 % / Description: NONE
Crystal growpH: 5 / Details: 50% ETHANOL, 10 MM SODIUM ACETATE

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 0.97622
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 20, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97622 Å / Relative weight: 1
ReflectionResolution: 2.1→29.4 Å / Num. obs: 5031 / % possible obs: 95.6 % / Observed criterion σ(I): 2 / Redundancy: 3.4 % / Biso Wilson estimate: 34.96 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 40.7
Reflection shellResolution: 2.09→2.1 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.26 / Mean I/σ(I) obs: 6.4 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1V1Q

1v1q


Resolution: 2.095→26.649 Å / SU ML: 0.3 / σ(F): 1.37 / Phase error: 28.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2736 478 9.7 %
Rwork0.1982 --
obs0.2052 4928 96.16 %
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 66.888 Å2 / ksol: 0.389 e/Å3
Displacement parametersBiso mean: 52.9 Å2
Baniso -1Baniso -2Baniso -3
1-2.6389 Å20 Å22.2615 Å2
2--4.2209 Å20 Å2
3----6.8598 Å2
Refinement stepCycle: LAST / Resolution: 2.095→26.649 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms755 0 0 10 765
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007770
X-RAY DIFFRACTIONf_angle_d1.0011039
X-RAY DIFFRACTIONf_dihedral_angle_d14.378282
X-RAY DIFFRACTIONf_chiral_restr0.061121
X-RAY DIFFRACTIONf_plane_restr0.004133
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0945-2.39740.30921710.21921473X-RAY DIFFRACTION98
2.3974-3.01980.30531590.19921520X-RAY DIFFRACTION99
3.0198-26.65070.25331480.19311457X-RAY DIFFRACTION92
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)
13.8729-0.5042-0.74871.5995-0.05965.42520.05580.8803-0.2023-0.1004-0.35610.02940.1939-1.29120.28140.3106-0.0314-0.02610.3248-0.07690.1342-3.0255-0.1049-10.5765
22.25791.59723.28025.40450.33175.8062-0.1258-0.5441-0.0061-0.2095-0.12020.42860.1626-0.38280.29440.3266-0.03370.09480.268-0.07730.2017-2.9355-1.0059-9.6605
36.04942.76652.24642.41740.46743.92460.19840.1139-0.25360.0117-0.2666-0.32120.03540.16260.05770.3657-0.0089-0.01120.2158-0.00260.27826.6319-0.8274-4.6466
46.04232.2433-1.82253.53921.0384.9153-0.18320.7226-0.1201-0.4136-0.06330.34220.0634-0.32060.19310.3477-0.0001-0.04470.33-0.04870.2675-6.97660.584-10.9262
58.18172.7035-2.93782.9976-3.15143.29-0.42670.88150.1079-0.3110.1890.0199-0.5336-0.64950.10740.44560.0631-0.05290.399-0.05140.2509-3.87043.886-9.844
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 2:18)
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 19:39)
3X-RAY DIFFRACTION3CHAIN A AND (RESSEQ 40:55)
4X-RAY DIFFRACTION4CHAIN A AND (RESSEQ 56:88)
5X-RAY DIFFRACTION5CHAIN A AND (RESSEQ 89:102)

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