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- PDB-2w9m: Structure of family X DNA polymerase from Deinococcus radiodurans -

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Basic information

Entry
Database: PDB / ID: 2w9m
TitleStructure of family X DNA polymerase from Deinococcus radiodurans
ComponentsPOLYMERASE X
KeywordsDNA REPLICATION / SAXS / DNA REPAIR / DNA POLYMERASE
Function / homology
Function and homology information


phosphoric ester hydrolase activity / bacterial-type flagellum-dependent swarming motility / DNA-directed DNA polymerase activity / DNA repair / DNA binding / zinc ion binding / cytosol
Similarity search - Function
DNA polymerase/3'-5' exonuclease PolX-like / Polymerase/histidinol phosphatase, N-terminal / DNA polymerase alpha chain like domain / Polymerase/histidinol phosphatase-like / Helix-hairpin-helix domain / Beta Polymerase; domain 3 / DNA polymerase, thumb domain / DNA polymerase beta, N-terminal domain-like / Metal-dependent hydrolases / DNA-directed DNA polymerase X ...DNA polymerase/3'-5' exonuclease PolX-like / Polymerase/histidinol phosphatase, N-terminal / DNA polymerase alpha chain like domain / Polymerase/histidinol phosphatase-like / Helix-hairpin-helix domain / Beta Polymerase; domain 3 / DNA polymerase, thumb domain / DNA polymerase beta, N-terminal domain-like / Metal-dependent hydrolases / DNA-directed DNA polymerase X / DNA polymerase beta-like, N-terminal domain / Helix-hairpin-helix domain / DNA polymerase X family / DNA polymerase lambda lyase domain superfamily / DNA polymerase, thumb domain superfamily / Beta Polymerase, domain 2 / Helix-hairpin-helix DNA-binding motif, class 1 / Helix-hairpin-helix DNA-binding motif class 1 / Beta Polymerase; domain 2 / Nucleotidyltransferase superfamily / 5' to 3' exonuclease, C-terminal subdomain / DNA polymerase; domain 1 / TIM Barrel / Alpha-Beta Barrel / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
: / Uncharacterized protein
Similarity search - Component
Biological speciesDEINOCOCCUS RADIODURANS (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.46 Å
AuthorsLeulliot, N. / Cladiere, L. / Lecointe, F. / Durand, D. / Hubscher, U. / van Tilbeurgh, H.
CitationJournal: J.Biol.Chem. / Year: 2009
Title: The Family X DNA Polymerase from Deinococcus Radioduran Adopts a Non-Standard Extended Conformation.
Authors: Leulliot, N. / Cladiere, L. / Lecointe, F. / Durand, D. / Hubscher, U. / Van Tilbeurgh, H.
History
DepositionJan 27, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 10, 2009Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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_database_status.status_code_sf / _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.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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: POLYMERASE X
B: POLYMERASE X
hetero molecules


Theoretical massNumber of molelcules
Total (without water)125,26111
Polymers124,4022
Non-polymers8599
Water1,38777
1
A: POLYMERASE X
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,6636
Polymers62,2011
Non-polymers4625
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: POLYMERASE X
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,5985
Polymers62,2011
Non-polymers3974
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.930, 138.250, 67.750
Angle α, β, γ (deg.)90.00, 92.25, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN A AND (RESSEQ 85:219 OR RESSEQ 223:311 )
211CHAIN B AND (RESSEQ 85:311 )
112CHAIN A AND (RESSEQ 313:564 )
212CHAIN B AND (RESSEQ 313:564 )

NCS ensembles :
ID
1
2

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Components

#1: Protein POLYMERASE X


Mass: 62200.949 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DEINOCOCCUS RADIODURANS (radioresistant)
Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q9RX48
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-HG / MERCURY (II) ION / Mercury (element)


Mass: 200.590 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Hg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 77 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.34 Å3/Da / Density % sol: 46.97 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.282
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.282 Å / Relative weight: 1
ReflectionResolution: 2.46→10 Å / Num. obs: 155376 / % possible obs: 95.4 % / Observed criterion σ(I): 2 / Redundancy: 4.2 % / Biso Wilson estimate: 35.59 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 13
Reflection shellResolution: 2.46→2.5 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 3 / % possible all: 77.7

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
PHENIXHYSSphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.46→45.32 Å / SU ML: 0.37 / σ(F): 1.56 / Phase error: 26.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.249 3635 5 %
Rwork0.203 --
obs0.206 72673 94.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 33.83 Å2 / ksol: 0.34 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--6.4619 Å20 Å23.8268 Å2
2--8.0698 Å20 Å2
3----1.6078 Å2
Refinement stepCycle: LAST / Resolution: 2.46→45.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8340 0 9 77 8426
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0048484
X-RAY DIFFRACTIONf_angle_d0.81311516
X-RAY DIFFRACTIONf_dihedral_angle_d18.2993097
X-RAY DIFFRACTIONf_chiral_restr0.0661317
X-RAY DIFFRACTIONf_plane_restr0.0031535
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A1654X-RAY DIFFRACTIONPOSITIONAL
12B1654X-RAY DIFFRACTIONPOSITIONAL0.03
21A1941X-RAY DIFFRACTIONPOSITIONAL
22B1941X-RAY DIFFRACTIONPOSITIONAL0.016
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4649-2.49730.3871710.30741194X-RAY DIFFRACTION43
2.4973-2.53150.36781480.30191986X-RAY DIFFRACTION72
2.5315-2.56770.36631230.29022305X-RAY DIFFRACTION81
2.5677-2.6060.31921420.27762650X-RAY DIFFRACTION92
2.606-2.64670.36231440.2732659X-RAY DIFFRACTION97
2.6467-2.69010.3151370.25432794X-RAY DIFFRACTION97
2.6901-2.73650.32151240.2542710X-RAY DIFFRACTION98
2.7365-2.78620.2781350.24482803X-RAY DIFFRACTION97
2.7862-2.83980.31671170.24782789X-RAY DIFFRACTION98
2.8398-2.89780.32361140.23852691X-RAY DIFFRACTION98
2.8978-2.96080.3121020.24592899X-RAY DIFFRACTION98
2.9608-3.02960.31331310.24312712X-RAY DIFFRACTION98
3.0296-3.10540.3351310.24822816X-RAY DIFFRACTION98
3.1054-3.18930.31241610.21472741X-RAY DIFFRACTION98
3.1893-3.28310.30211580.21312773X-RAY DIFFRACTION98
3.2831-3.38910.2041290.20432784X-RAY DIFFRACTION98
3.3891-3.51010.28561490.21012760X-RAY DIFFRACTION99
3.5101-3.65060.22561580.18462761X-RAY DIFFRACTION98
3.6506-3.81670.25421570.17892769X-RAY DIFFRACTION99
3.8167-4.01780.22611580.16972753X-RAY DIFFRACTION99
4.0178-4.26930.19981560.15882779X-RAY DIFFRACTION99
4.2693-4.59870.18011470.14122782X-RAY DIFFRACTION99
4.5987-5.06090.17521800.15172736X-RAY DIFFRACTION99
5.0609-5.7920.21721730.16932812X-RAY DIFFRACTION99
5.792-7.29240.19371440.17312791X-RAY DIFFRACTION99
7.2924-45.32610.15351460.15782789X-RAY DIFFRACTION99

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