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- PDB-1pc6: Structural Genomics, NinB -

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Basic information

Entry
Database: PDB / ID: 1pc6
TitleStructural Genomics, NinB
ComponentsProtein ninB
KeywordsStructural genomics / unknown function / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homologyNinB fold / NinB / Recombinase NinB / NinB superfamily / NinB protein / Orthogonal Bundle / Mainly Alpha / BETA-MERCAPTOETHANOL / Protein ninB
Function and homology information
Biological speciesEnterobacteria phage lambda (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.51 Å
AuthorsZhang, R. / Beasley, S. / Maxwell, K.L. / Edwards, A.M. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2005
Title: Functional similarities between phage lambda Orf and Escherichia coli RecFOR in initiation of genetic exchange
Authors: Maxwell, K.L. / Reed, P. / Zhang, R. / Beasley, S. / Walmsley, A.R. / Curtis, F.A. / Joachimiak, A. / Edwards, A.M. / Sharples, G.J.
History
DepositionMay 15, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 20, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Mar 26, 2025Group: 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 / struct_conn / struct_site
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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein ninB
B: Protein ninB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,4984
Polymers33,3422
Non-polymers1562
Water52229
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6080 Å2
ΔGint-42 kcal/mol
Surface area14830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.776, 76.776, 107.390
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
DetailsThe biological assembly is a dimer consists of chain A (Mol. A) and chain B (Mol. B).

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Components

#1: Protein Protein ninB


Mass: 16671.025 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage lambda (virus) / Genus: Lambda-like viruses / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / References: UniProt: P03765
#2: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 29 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.74 Å3/Da / Density % sol: 55.1 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1.4M Na(AC), Sodium cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Temperature: 21 ℃ / pH: 8 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
120 mMTris-HCl1droppH8.0
21 mMEDTA1drop
30.5 mMdithiothreitol1drop
4500 mM1dropKCl
550 %glycerol1drop
61.3 mg/mlprotein1drop
71.4 Msodium acetate1reservoir
80.05 Msodium cacodylate1reservoirpH6.9

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9795,0.9797,0.94656
DetectorType: SBC-2 / Detector: CCD / Date: Jul 2, 2002 / Details: mirrors
RadiationMonochromator: Si 111 channel / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97951
20.97971
30.946561
ReflectionResolution: 2.5→50 Å / Num. all: 13046 / Num. obs: 12916 / % possible obs: 99 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 4 / Redundancy: 7.8 % / Biso Wilson estimate: 33.9 Å2 / Rmerge(I) obs: 0.079 / Net I/σ(I): 29
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 6 % / Rmerge(I) obs: 0.492 / Mean I/σ(I) obs: 2.24 / Num. unique all: 1276 / % possible all: 98.4
Reflection
*PLUS
Num. measured all: 100809

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Processing

Software
NameVersionClassification
CNS0.9refinement
d*TREKdata reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 2.51→36.15 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 589846.35 / Data cutoff high rms absF: 589846.35 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: Freidel pairs were used in the refinement.
RfactorNum. reflection% reflectionSelection details
Rfree0.294 1021 4.8 %RANDOM
Rwork0.234 ---
obs0.234 21398 87.9 %-
all-24343 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 51.9659 Å2 / ksol: 0.333566 e/Å3
Displacement parametersBiso mean: 63.5 Å2
Baniso -1Baniso -2Baniso -3
1-11.76 Å29.91 Å20 Å2
2--11.76 Å20 Å2
3----23.52 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.48 Å0.41 Å
Luzzati d res low-5 Å
Luzzati sigma a0.55 Å0.61 Å
Refinement stepCycle: LAST / Resolution: 2.51→36.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2133 0 0 37 2170
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d21.3
X-RAY DIFFRACTIONc_improper_angle_d0.79
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.038 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.443 133 4.8 %
Rwork0.401 2628 -
obs--67.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM
X-RAY DIFFRACTION3SEO.PARAM
Software
*PLUS
Classification: refinement
Refinement
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 36.2 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.79

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