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- PDB-1xhx: Phi29 DNA Polymerase, orthorhombic crystal form -

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Basic information

Entry
Database: PDB / ID: 1xhx
TitlePhi29 DNA Polymerase, orthorhombic crystal form
ComponentsDNA polymerase
KeywordsTRANSFERASE / DNA polymerase / protein-primed / strand displacement / processivity / replication
Function / homology
Function and homology information


nucleoside binding / viral DNA genome replication / exonuclease activity / Hydrolases; Acting on ester bonds; Exodeoxyribonucleases producing 5'-phosphomonoesters / DNA replication / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / nucleotide binding / DNA binding / metal ion binding
Similarity search - Function
TPR 1 domain of DNA polymerase / TPR 1 domain of DNA polymerase / DNA polymerase; domain 5 / DNA-directed DNA polymerase, family B, mitochondria/virus / DNA-directed DNA polymerase, family B, phi29-like virus / DNA polymerase type B, organellar and viral / DNA polymerase; domain 6 / Rhinovirus 14, subunit 4 / B family DNA polymerase, finger domain / Palm domain of DNA polymerase ...TPR 1 domain of DNA polymerase / TPR 1 domain of DNA polymerase / DNA polymerase; domain 5 / DNA-directed DNA polymerase, family B, mitochondria/virus / DNA-directed DNA polymerase, family B, phi29-like virus / DNA polymerase type B, organellar and viral / DNA polymerase; domain 6 / Rhinovirus 14, subunit 4 / B family DNA polymerase, finger domain / Palm domain of DNA polymerase / B family DNA polymerase, palm domain / DNA polymerase family B signature. / DNA-directed DNA polymerase, family B, conserved site / DNA polymerase, palm domain superfamily / DNA polymerase type-B family / DNA-directed DNA polymerase, family B / Ribonuclease H-like superfamily/Ribonuclease H / Few Secondary Structures / Irregular / Helix Hairpins / Nucleotidyltransferase; domain 5 / Ribonuclease H superfamily / Ribonuclease H-like superfamily / DNA/RNA polymerase superfamily / Alpha-Beta Complex / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesBacillus phage phi29 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsKamtekar, S. / Berman, A.J. / Wang, J. / Lazaro, J.M. / de Vega, M. / Blanco, L. / Salas, M. / Steitz, T.A.
Citation
Journal: Mol.Cell / Year: 2004
Title: Insights into Strand Displacement and Processivity from the Crystal Structure of the Protein-Primed DNA Polymerase of Bacteriophage phi29
Authors: Kamtekar, S. / Berman, A.J. / Wang, J. / Lazaro, J.M. / de Vega, M. / Blanco, L. / Salas, M. / Steitz, T.A.
#1: Journal: To be Published
Title: Correction of X-ray intensities from single crystals containing lattice translocation defects
Authors: Wang, J. / Kamtekar, S. / Berman, A.J. / Steitz, T.A.
History
DepositionSep 21, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 7, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_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_conn.ptnr2_symmetry / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA polymerase
B: DNA polymerase
C: DNA polymerase
D: DNA polymerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)267,1248
Polymers266,8844
Non-polymers2414
Water27,1851509
1
A: DNA polymerase


Theoretical massNumber of molelcules
Total (without water)66,7211
Polymers66,7211
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: DNA polymerase


Theoretical massNumber of molelcules
Total (without water)66,7211
Polymers66,7211
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: DNA polymerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,7703
Polymers66,7211
Non-polymers492
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: DNA polymerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,9133
Polymers66,7211
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)96.256, 149.911, 199.024
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Detailsmonomer is active

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Components

#1: Protein
DNA polymerase / Early protein GP2


Mass: 66720.914 Da / Num. of mol.: 4 / Mutation: D12A D66A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus phage phi29 (virus) / Genus: Phi29-like viruses / Gene: 2 / Production host: Escherichia coli (E. coli) / References: UniProt: P03680, DNA-directed DNA polymerase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1509 / 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: 2.7 Å3/Da / Density % sol: 54 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Magnesium Acetate, Tris-HCl, PEG 8000, Ammonium sulfate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.976 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 3, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.35→20 Å / Num. all: 119733 / Num. obs: 119733 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 36 Å2 / Rmerge(I) obs: 0.098 / Net I/σ(I): 17
Reflection shellResolution: 2.35→2.5 Å / % possible all: 98.3

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Processing

Software
NameVersionClassification
CNS1refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.35→19.96 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 2204663.87 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.257 11990 10 %RANDOM
Rwork0.206 ---
all0.206 119733 --
obs0.206 119733 99.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 48.1825 Å2 / ksol: 0.320362 e/Å3
Displacement parametersBiso mean: 54.1 Å2
Baniso -1Baniso -2Baniso -3
1--5.71 Å20 Å20 Å2
2--5.43 Å20 Å2
3---0.27 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.38 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.41 Å0.34 Å
Refinement stepCycle: LAST / Resolution: 2.35→19.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18672 0 12 1509 20193
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d22.8
X-RAY DIFFRACTIONc_improper_angle_d0.73
X-RAY DIFFRACTIONc_mcbond_it3.41.5
X-RAY DIFFRACTIONc_mcangle_it5.072
X-RAY DIFFRACTIONc_scbond_it5.142
X-RAY DIFFRACTIONc_scangle_it7.242.5
LS refinement shellResolution: 2.35→2.5 Å / Rfactor Rfree error: 0.008 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.345 1985 10.2 %
Rwork0.299 17461 -
obs--98.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMDNA-RNA_REP.TOP
X-RAY DIFFRACTION3DNA-RNA_REP.PARAMSO4.TOP
X-RAY DIFFRACTION4ION.PARAM
X-RAY DIFFRACTION5SO4.PARAM

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