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- PDB-3pvs: Structure and biochemical activities of Escherichia coli MgsA -

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Basic information

Entry
Database: PDB / ID: 3pvs
TitleStructure and biochemical activities of Escherichia coli MgsA
ComponentsReplication-associated recombination protein A
KeywordsRECOMBINATION / Recombination protein A / Maintenance of genome stability protein A
Function / homology
Function and homology information


post-AAA+ oligomerization domain-like / DNA polymerase III clamp loader subunits, C-terminal domain / Zinc Finger, Delta Prime; domain 3 - #10 / Zinc Finger, Delta Prime; domain 3 / Helicase, Ruva Protein; domain 3 - #60 / Helicase, Ruva Protein; domain 3 / P-loop containing nucleotide triphosphate hydrolases / Up-down Bundle / Rossmann fold / Orthogonal Bundle ...post-AAA+ oligomerization domain-like / DNA polymerase III clamp loader subunits, C-terminal domain / Zinc Finger, Delta Prime; domain 3 - #10 / Zinc Finger, Delta Prime; domain 3 / Helicase, Ruva Protein; domain 3 - #60 / Helicase, Ruva Protein; domain 3 / P-loop containing nucleotide triphosphate hydrolases / Up-down Bundle / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 Å
AuthorsPage, A.N. / George, N.P. / Marceau, A.H. / Cox, M.M. / Keck, J.L.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Structure and Biochemical Activities of Escherichia coli MgsA.
Authors: Page, A.N. / George, N.P. / Marceau, A.H. / Cox, M.M. / Keck, J.L.
History
DepositionDec 7, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 2, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Replication-associated recombination protein A
B: Replication-associated recombination protein A
C: Replication-associated recombination protein A
D: Replication-associated recombination protein A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)199,1368
Polymers198,7564
Non-polymers3804
Water8,215456
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area25760 Å2
ΔGint-124 kcal/mol
Surface area71270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.946, 143.689, 163.186
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Replication-associated recombination protein A


Mass: 49689.000 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: C5W2B1
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 456 / 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: 2.95 Å3/Da / Density % sol: 58.27 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.6
Details: 10 mM MES, pH 6.6, 38% Ethylene Glycol, 16% Glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 24, 2009
RadiationMonochromator: 0.99 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.35→30 Å / Num. all: 98365 / Num. obs: 89807 / % possible obs: 91.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.8 % / Rmerge(I) obs: 0.068 / Χ2: 0.91 / Net I/σ(I): 8.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.35-2.393.60.49426760.79154.5
2.39-2.434.10.48529790.76961.1
2.43-2.484.50.47832980.79768.4
2.48-2.534.80.40736140.78575
2.53-2.5950.35840200.79882.1
2.59-2.655.20.3543690.77790.1
2.65-2.715.50.33147080.79896.4
2.71-2.795.90.29748290.81598.9
2.79-2.876.20.25248600.81399.6
2.87-2.966.40.2248550.83899.9
2.96-3.076.40.18448810.82899.8
3.07-3.196.40.13849140.79999.9
3.19-3.336.40.10348700.84799.9
3.33-3.516.40.08249031.03100
3.51-3.736.40.06649140.996100
3.73-4.026.30.05649420.997100
4.02-4.426.30.04749501.125100
4.42-5.066.30.03749811.08499.9
5.06-6.366.20.03350271.017100
6.36-3060.02552171.07899.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→30 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.905 / WRfactor Rfree: 0.2623 / WRfactor Rwork: 0.1907 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8177 / SU B: 20.373 / SU ML: 0.205 / SU R Cruickshank DPI: 0.3999 / SU Rfree: 0.2895 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.289 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U
RfactorNum. reflection% reflectionSelection details
Rfree0.266 3990 5 %RANDOM
Rwork0.1949 ---
all0.1984 81808 --
obs0.1984 79468 97.14 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 104.64 Å2 / Biso mean: 52.708 Å2 / Biso min: 15.46 Å2
Baniso -1Baniso -2Baniso -3
1-3.73 Å20 Å20 Å2
2---0.45 Å20 Å2
3----3.28 Å2
Refinement stepCycle: LAST / Resolution: 2.5→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13071 0 20 456 13547
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.02213342
X-RAY DIFFRACTIONr_angle_refined_deg1.6081.96318090
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.30651663
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.17123.031650
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.595152193
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.3115145
X-RAY DIFFRACTIONr_chiral_restr0.1040.21978
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02110328
X-RAY DIFFRACTIONr_mcbond_it0.8151.58342
X-RAY DIFFRACTIONr_mcangle_it1.577213324
X-RAY DIFFRACTIONr_scbond_it2.48535000
X-RAY DIFFRACTIONr_scangle_it4.274.54766
LS refinement shellResolution: 2.5→2.564 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.322 257 -
Rwork0.255 4429 -
all-4686 -
obs--78.86 %
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)
10.0947-0.0380.06890.30890.00230.3341-0.0151-0.0220.0064-0.1314-0.0028-0.01490.03270.060.01790.07590.02170.00840.030.00290.0022-29.238-11.731-52.503
20.14190.00430.03550.39340.00320.25550.0202-0.04480.0120.0973-0.0428-0.02160.0354-0.05040.02250.0584-0.01570.00360.052-0.01090.0067-38.26-11.72-18.47
30.2178-0.0336-0.03980.32330.11340.25510.0380.0012-0.0037-0.0151-0.07020.1108-0.0533-0.00520.03230.02630.0073-0.0080.0268-0.02130.0612-45.8820.157-39.041
40.13510.07050.03690.23590.06820.2901-0.0139-0.0299-0.06790.02740.0183-0.09550.0530.0481-0.00450.01680.021200.0370.00260.0587-22.199-23.538-30.994
50.1839-0.0577-0.18570.50740.54610.6743-0.0294-0.0342-0.0729-0.0099-0.10780.08020.0197-0.09030.13720.05010.00410.01540.1275-0.05320.0661-45.663-23.935-38.562
60.134-0.0436-0.01180.1036-0.01330.1672-0.01270.01390.00650.0044-0.0016-0.014-0.02320.03210.01420.0274-0.0048-0.00510.0682-0.01320.078-28.845-4.729-34.185
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A14 - 446
2X-RAY DIFFRACTION2B14 - 446
3X-RAY DIFFRACTION3C14 - 447
4X-RAY DIFFRACTION4D14 - 447
5X-RAY DIFFRACTION5A448
6X-RAY DIFFRACTION5B448
7X-RAY DIFFRACTION5C448
8X-RAY DIFFRACTION5D448
9X-RAY DIFFRACTION6A449 - 561
10X-RAY DIFFRACTION6B449 - 578
11X-RAY DIFFRACTION6C449 - 537
12X-RAY DIFFRACTION6D449 - 573

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