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- PDB-3dm3: Crystal structure of a domain of a Replication factor A protein, ... -

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Basic information

Entry
Database: PDB / ID: 3dm3
TitleCrystal structure of a domain of a Replication factor A protein, from Methanocaldococcus jannaschii. NorthEast Structural Genomics target MjR118E
ComponentsReplication factor A
KeywordsREPLICATION / Replication factor A Synonyms RP-A RF-A Replication factor A protein 1 Single-stranded DNA-binding protein / Probably plays an essential for replication of the chromosome / DNA recombination and repair / Structural Genomics / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG / DNA damage / DNA repair / DNA replication / DNA-binding / Metal-binding / Zinc / Zinc-finger
Function / homology
Function and homology information


response to ionizing radiation / double-strand break repair via homologous recombination / DNA replication / DNA binding / metal ion binding
Similarity search - Function
: / Replication factor A, C-terminal / Replication factor-A C terminal domain / OB-fold nucleic acid binding domain, AA-tRNA synthetase-type / OB-fold nucleic acid binding domain / Nucleic acid-binding proteins / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleic acid-binding, OB-fold / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Replication factor A
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 Å
AuthorsSeetharaman, J. / Su, M. / Maglaqui, M. / Janjua, H. / Ciccosanti, C. / Xiao, R. / Nair, R. / Everett, J.K. / Acton, T.B. / Rost, B. ...Seetharaman, J. / Su, M. / Maglaqui, M. / Janjua, H. / Ciccosanti, C. / Xiao, R. / Nair, R. / Everett, J.K. / Acton, T.B. / Rost, B. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Crystal structure of a domain of a Replication factor A protein, from Methanocaldococcus jannaschii. NorthEast Structural Genomics target MjR118E
Authors: Seetharaman, J. / Su, M. / Maglaqui, M. / Janjua, H. / Ciccosanti, C. / Xiao, R. / Nair, R. / Everett, J.K. / Acton, T.B. / Rost, B. / Montelione, G.T. / Tong, L. / Hunt, J.F.
History
DepositionJun 30, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 26, 2008Provider: 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

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Assembly

Deposited unit
A: Replication factor A
B: Replication factor A
C: Replication factor A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,2966
Polymers35,2273
Non-polymers693
Water3,387188
1
A: Replication factor A
B: Replication factor A
hetero molecules

A: Replication factor A
B: Replication factor A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,10710
Polymers46,9694
Non-polymers1386
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/61
Buried area8030 Å2
ΔGint-115 kcal/mol
Surface area17400 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)76.001, 76.001, 249.479
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein Replication factor A / RP-A / RF-A / Replication factor A protein 1 / Single-stranded DNA-binding protein / mjaSSB


Mass: 11742.265 Da / Num. of mol.: 3 / Fragment: residues 170-274
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (archaea)
Gene: rpa, MJ1159 / Plasmid: PET 21 / Production host: Escherichia coli (E. coli) / References: UniProt: Q58559
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 188 / 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: 58.34 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 100 mM Sodium Citrate, 100mM NaCL, pH 5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSLS X4A10.979
SYNCHROTRONSSRL BL9-220.979
Detector
TypeIDDetectorDate
ADSC QUANTUM 2101CCDJun 2, 2008
2CCDMay 21, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. all: 35883 / Num. obs: 35883 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.7 % / Biso Wilson estimate: 17.4 Å2 / Rmerge(I) obs: 0.102 / Rsym value: 0.075 / Net I/σ(I): 10
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.383 / Mean I/σ(I) obs: 10 / Num. unique all: 3575 / Rsym value: 0.339 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
SHELXSphasing
RefinementMethod to determine structure: SAD / Resolution: 2.4→39.76 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 54241 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.274 1481 5.1 %RANDOM
Rwork0.225 ---
obs0.225 35883 91.6 %-
all-35883 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 42.5599 Å2 / ksol: 0.413729 e/Å3
Displacement parametersBiso mean: 26.3 Å2
Baniso -1Baniso -2Baniso -3
1-3.01 Å25.06 Å20 Å2
2--3.01 Å20 Å2
3----6.02 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.38 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.38 Å0.24 Å
Refinement stepCycle: LAST / Resolution: 2.4→39.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2301 0 3 188 2492
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d25.3
X-RAY DIFFRACTIONc_improper_angle_d0.7
X-RAY DIFFRACTIONc_mcbond_it1.331.5
X-RAY DIFFRACTIONc_mcangle_it2.162
X-RAY DIFFRACTIONc_scbond_it2.092
X-RAY DIFFRACTIONc_scangle_it3.162.5
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.326 220 5.1 %
Rwork0.244 4083 -
obs--81.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top

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