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- PDB-1gpc: CORE GP32, DNA-BINDING PROTEIN -

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Basic information

Entry
Database: PDB / ID: 1gpc
TitleCORE GP32, DNA-BINDING PROTEIN
ComponentsPROTEIN (CORE GP32)
KeywordsDNA BINDING PROTEIN/DNA / SSB / SINGLE-STRANDED DNA-BINDING / ZINC BINDING DOMAIN / DNA BINDING PROTEIN-DNA COMPLEX
Function / homology
Function and homology information


bidirectional double-stranded viral DNA replication / single-stranded DNA binding / DNA recombination / DNA replication / DNA repair / metal ion binding
Similarity search - Function
Replication Fork Single-Stranded DNA Binding Protein / Replication Fork Single-Stranded Dna Binding Protein / Bacteriophage T4, Gp32, single-stranded DNA-binding domain / Bacteriophage T4, Gp32, single-stranded DNA-binding superfamily / Bacteriophage T4, Gp32, single-stranded DNA-binding / gp32 DNA binding protein like / Nucleic acid-binding, OB-fold / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Single-stranded DNA-binding protein
Similarity search - Component
Biological speciesEnterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.2 Å
AuthorsShamoo, Y. / Friedman, A.M. / Parsons, M.R. / Konigsberg, W.H. / Steitz, T.A.
CitationJournal: Nature / Year: 1995
Title: Crystal structure of a replication fork single-stranded DNA binding protein (T4 gp32) complexed to DNA.
Authors: Shamoo, Y. / Friedman, A.M. / Parsons, M.R. / Konigsberg, W.H. / Steitz, T.A.
History
DepositionJun 1, 1995Processing site: NDB
Revision 1.0Oct 15, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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 (CORE GP32)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9782
Polymers24,9131
Non-polymers651
Water1,838102
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.500, 66.500, 235.400
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 PROTEIN (CORE GP32) / GP32*III


Mass: 24913.020 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage T4 (virus) / Genus: T4-like viruses / Species: Enterobacteria phage T4 sensu lato / Gene: GENE 32 / Variant: T4D / Plasmid: PYS55 / Gene (production host): GENE 32 / Production host: Escherichia coli (E. coli) / References: UniProt: P03695
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 102 / Source method: isolated from a natural source / Formula: H2O
Source detailsMOLECULE_NAME: CORE GP32. PYS55 ENCODES RESIDUES 18 - 254 OF BACTERIOPHAGE T4 GENE 32.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.01 Å3/Da / Density % sol: 59.2 %
Crystal growDetails: MOLECULE: CORE GP32. CRYSTALLIZED IN PRESENCE OF P(DT6).
Crystal grow
*PLUS
pH: 8.4 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 %PEG800011
2100 mMammonium sulfate11
350 mMsodium chloride11
45 %ethylene glycol11
520 mMEPPS11

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.908
DetectorDetector: CCD / Date: Jan 15, 1994
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.908 Å / Relative weight: 1
ReflectionNum. obs: 16406 / % possible obs: 91.7 % / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.058
Reflection
*PLUS
Highest resolution: 2.2 Å / % possible obs: 91.7 % / Observed criterion σ(I): 0 / Num. measured all: 33415 / Rmerge(I) obs: 0.058

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Processing

Software
NameClassification
X-PLORrefinement
DENZOdata reduction
RefinementResolution: 2.2→8 Å / σ(F): 2 /
RfactorNum. reflection
Rwork0.236 -
obs0.236 14867
Displacement parametersBiso mean: 29.15 Å2
Refinement stepCycle: LAST / Resolution: 2.2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2144 0 1 306 2451
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 8 Å / σ(F): 2
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 0.016

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