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- PDB-2a1k: RB69 single-stranded DNA binding protein core domain -

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Basic information

Entry
Database: PDB / ID: 2a1k
TitleRB69 single-stranded DNA binding protein core domain
Componentsgp32 single stranded DNA binding protein
KeywordsDNA BINDING PROTEIN / Zn2+ binding subdomain / 5-stranded beta-sheet / OB fold / single-stranded DNA binding
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 RB69 (virus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsSun, S. / Geng, L. / Shamoo, Y.
CitationJournal: Proteins / Year: 2006
Title: Structure and enzymatic properties of a chimeric bacteriophage RB69 DNA polymerase and single-stranded DNA binding protein with increased processivity.
Authors: Sun, S. / Geng, L. / Shamoo, Y.
History
DepositionJun 20, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 9, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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: gp32 single stranded DNA binding protein
B: gp32 single stranded DNA binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,3254
Polymers52,1952
Non-polymers1312
Water7,855436
1
A: gp32 single stranded DNA binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,1632
Polymers26,0971
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: gp32 single stranded DNA binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,1632
Polymers26,0971
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.700, 67.700, 123.750
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

#1: Protein gp32 single stranded DNA binding protein


Mass: 26097.328 Da / Num. of mol.: 2 / Fragment: Core domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage RB69 (virus) / Genus: T4-like viruses / Gene: 32 / Plasmid: pKC30 / Production host: Escherichia coli (E. coli) / Strain (production host): AR120 / References: UniProt: Q7Y265
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 436 / 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: 57.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: PEG200, MES, magnesium chloride, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Dec 7, 2003 / Details: osmic mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→47.87 Å / Num. all: 49458 / Num. obs: 49458 / % possible obs: 96.295 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Biso Wilson estimate: 31.1 Å2 / Rmerge(I) obs: 0.091 / Net I/σ(I): 5 / Scaling rejects: 1324
Reflection shellResolution: 2→2.09 Å / % possible obs: 6.1 % / Rmerge(I) obs: 0.344 / Mean I/σ(I) obs: 1.3 / Num. measured obs: 784 / % possible all: 96.3

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Phasing

Phasing MRCor.coef. Fo:Fc: 0.764 / Packing: 0.53
Highest resolutionLowest resolutionMethodReflection percentσ(F)
Rotation4 Å15 Åfast direct99.4 0
Translation4 Å15 Ågeneral99.4 0

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Processing

Software
NameVersionClassificationNB
d*TREK7.1SSIdata scaling
CNSrefinement
PDB_EXTRACT1.601data extraction
CrystalClear(MSC/RIGAKU)data reduction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GPC

1gpc


Resolution: 2→47.87 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.259 1719 4.6 %RANDOM
Rwork0.236 ---
all0.243 37572 --
obs0.243 36718 97.7 %-
Solvent computationBsol: 55.561 Å2
Displacement parametersBiso mean: 31.3 Å2
Baniso -1Baniso -2Baniso -3
1--2.489 Å20 Å20 Å2
2---2.489 Å20 Å2
3---4.978 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.35 Å0.31 Å
Refinement stepCycle: LAST / Resolution: 2→47.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3434 0 2 436 3872
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.23321
X-RAY DIFFRACTIONc_bond_d0.008093
X-RAY DIFFRACTIONc_dihedral_angle_d23.8
X-RAY DIFFRACTIONc_improper_angle_d0.74
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkRefine-IDNum. reflection obs
2-2.150.34953230.3096X-RAY DIFFRACTION7520
2.15-2.370.31673310.275X-RAY DIFFRACTION7269
2.37-2.710.27893410.2505X-RAY DIFFRACTION7358
2.71-3.420.25973660.2386X-RAY DIFFRACTION7416
3.42-5000.21343580.2134X-RAY DIFFRACTION7155
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2ion.param
X-RAY DIFFRACTION3water.param

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