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- PDB-1d0q: STRUCTURE OF THE ZINC-BINDING DOMAIN OF BACILLUS STEAROTHERMOPHIL... -

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Basic information

Entry
Database: PDB / ID: 1d0q
TitleSTRUCTURE OF THE ZINC-BINDING DOMAIN OF BACILLUS STEAROTHERMOPHILUS DNA PRIMASE
ComponentsDNA PRIMASEPrimase
KeywordsTRANSFERASE / DNA PRIMASE / ZINC-BINDING MOTIF / PROTEIN
Function / homology
Function and homology information


DNA primase DnaG / primosome complex / DNA primase activity / DNA helicase activity / DNA-directed RNA polymerase complex / DNA binding / zinc ion binding / ATP binding
Similarity search - Function
DNA Primase; Chain A / Zinc finger, CHC2-type domain / DNA primase, DnaB-helicase binding domain / DnaB-helicase binding domain of primase / Zinc finger, CHC2-type / DNA primase, DnaG / DNA primase, catalytic core, N-terminal / DNA primase DnaG, bacteria / Bacterial DnaG primase, TOPRIM domain / DNA Primase, CHC2-type zinc finger ...DNA Primase; Chain A / Zinc finger, CHC2-type domain / DNA primase, DnaB-helicase binding domain / DnaB-helicase binding domain of primase / Zinc finger, CHC2-type / DNA primase, DnaG / DNA primase, catalytic core, N-terminal / DNA primase DnaG, bacteria / Bacterial DnaG primase, TOPRIM domain / DNA Primase, CHC2-type zinc finger / DNA primase, catalytic core, N-terminal domain superfamily / CHC2 zinc finger / DNA primase catalytic core, N-terminal domain / zinc finger / Toprim-like / DNA helicase, DnaB-like, N-terminal domain superfamily / DNA helicase DnaB, N-terminal/DNA primase DnaG, C-terminal / TOPRIM / Toprim domain profile. / TOPRIM domain / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.71 Å
AuthorsPan, H. / Wigley, D.B.
CitationJournal: Structure Fold.Des. / Year: 2000
Title: Structure of the zinc-binding domain of Bacillus stearothermophilus DNA primase.
Authors: Pan, H. / Wigley, D.B.
History
DepositionSep 14, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 29, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 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.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_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: DNA PRIMASE
B: DNA PRIMASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,8874
Polymers22,7562
Non-polymers1312
Water2,918162
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)36.170, 58.745, 45.750
Angle α, β, γ (deg.)90.00, 91.73, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein DNA PRIMASE / Primase


Mass: 11378.001 Da / Num. of mol.: 2 / Fragment: ZINC-BINDING DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Plasmid: PET21D / Production host: Geobacillus stearothermophilus (bacteria)
References: UniProt: Q9X4D0, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases
#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 / Water


Mass: 18.015 Da / Num. of mol.: 162 / 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: 2.13 Å3/Da / Density % sol: 42.36 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.1
Details: LITHIUM SULFATE, SODIUM CITRATE, ZINC ACETATE, pH 6.1, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal
*PLUS
Density % sol: 35 %
Crystal grow
*PLUS
pH: 7.5 / Details: used microseeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
15 mg/mlprotein1drop
225 mMTris-HCl1drop
32 mMEDTA1drop
460 %sat1reservoirLi2SO4
51 mMzinc acetate1reservoir
6100 mMsodium citrate1reservoir

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineTypeIDWavelength
SYNCHROTRONSRS PX9.510.88
ROTATING ANODERIGAKU21.5418
Detector
TypeIDDetectorDate
MARRESEARCH1IMAGE PLATEAug 8, 1998
MARRESEARCH2IMAGE PLATEFeb 13, 1998
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.881
21.54181
ReflectionResolution: 1.71→15 Å / Num. all: 22075 / Num. obs: 22075 / % possible obs: 95.9 % / Redundancy: 1.78 % / Biso Wilson estimate: 10.96 Å2 / Rmerge(I) obs: 0.047 / Net I/σ(I): 14.95
Reflection shellResolution: 1.7→1.78 Å / Redundancy: 1.65 % / Rmerge(I) obs: 0.227 / % possible all: 94.7
Reflection
*PLUS

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Processing

Software
NameClassification
MLPHAREphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 1.71→15 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflectionSelection details
Rfree0.225 1103 RANDOM
Rwork0.204 --
all-22075 -
obs-22075 -
Refinement stepCycle: LAST / Resolution: 1.71→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1582 0 2 162 1746
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.196
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.01
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg2.6

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