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- PDB-2gv9: Crystal structure of the Herpes Simplex virus type 1 DNA polymerase -

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Basic information

Entry
Database: PDB / ID: 2gv9
TitleCrystal structure of the Herpes Simplex virus type 1 DNA polymerase
ComponentsDNA polymerase
KeywordsTRANSFERASE / Polymerase alpha fold
Function / homology
Function and homology information


viral DNA genome replication / ribonuclease H / RNA-DNA hybrid ribonuclease activity / DNA replication / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / nucleotide binding / host cell nucleus / DNA binding
Similarity search - Function
DNA polymerase catalytic subunit Pol, C-terminal / DNA polymerase catalytic subunit Pol / B family DNA polymerase, thumb domain / Topoisomerase I; Chain A, domain 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 family B ...DNA polymerase catalytic subunit Pol, C-terminal / DNA polymerase catalytic subunit Pol / B family DNA polymerase, thumb domain / Topoisomerase I; Chain A, domain 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 family B / DNA polymerase family B, exonuclease domain / DNA-directed DNA polymerase, family B, exonuclease domain / DNA-directed DNA polymerase, family B, multifunctional domain / DNA polymerase, palm domain superfamily / DNA polymerase type-B family / DNA-directed DNA polymerase, family B / Ribonuclease H-like superfamily/Ribonuclease H / 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
GUANIDINE / : / DNA polymerase catalytic subunit
Similarity search - Component
Biological speciesHuman herpesvirus 1 (Herpes simplex virus type 1)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.68 Å
AuthorsLiu, S.
CitationJournal: J.Biol.Chem. / Year: 2006
Title: Crystal structure of the herpes simplex virus 1 DNA polymerase.
Authors: Liu, S. / Knafels, J.D. / Chang, J.S. / Waszak, G.A. / Baldwin, E.T. / Deibel, M.R. / Thomsen, D.R. / Homa, F.L. / Wells, P.A. / Tory, M.C. / Poorman, R.A. / Gao, H. / Qiu, X. / Seddon, A.P.
History
DepositionMay 2, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 16, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Refinement description ...Advisory / Refinement description / Source and taxonomy / Version format compliance
Revision 1.3Feb 14, 2024Group: 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 / struct_conn / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_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 polymerase
B: DNA polymerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)265,9676
Polymers265,5152
Non-polymers4524
Water1,56787
1
A: DNA polymerase


Theoretical massNumber of molelcules
Total (without water)132,7571
Polymers132,7571
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: DNA polymerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,2095
Polymers132,7571
Non-polymers4524
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)103.917, 125.550, 220.577
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B
32A
42B
13A
23B
14A
24B
34A
44B
15A
25B
35A
45B
16A
26B

NCS domain segments:

Refine code: 4

Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111GLYGLYPHEPHEAA60 - 14018 - 98
211GLYGLYPHEPHEBB60 - 14018 - 98
112ASNASNTYRTYRAA141 - 36299 - 320
212ASNASNTYRTYRBB141 - 36299 - 320
322PROPROTHRTHRAA594 - 639552 - 597
422PROPROTHRTHRBB594 - 639552 - 597
113LYSLYSLEULEUAA363 - 593321 - 551
213LYSLYSLEULEUBB363 - 593321 - 551
114PROPROLYSLYSAA704 - 766662 - 724
214PROPROLYSLYSBB704 - 766662 - 724
324GLYGLYLYSLYSAA826 - 953784 - 911
424GLYGLYLYSLYSBB826 - 953784 - 911
115THRTHRLEULEUAA969 - 990927 - 948
215THRTHRLEULEUBB969 - 990927 - 948
325TYRTYRLYSLYSAA1160 - 11891118 - 1147
425TYRTYRLYSLYSBB1160 - 11891118 - 1147
116ALAALAHISHISAA767 - 825725 - 783
216ALAALAHISHISBB767 - 825725 - 783

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein DNA polymerase /


Mass: 132757.438 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human herpesvirus 1 (Herpes simplex virus type 1)
Genus: Simplexvirus / Strain: KOS / Gene: UL30 / Plasmid: MBP-HSV1 POL / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): SF9 / References: UniProt: P04292, DNA-directed DNA polymerase
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-HG / MERCURY (II) ION / Mercury (element)


Mass: 200.590 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Hg
#4: Chemical ChemComp-GAI / GUANIDINE / Guanidine


Mass: 59.070 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH5N3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 87 / 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: 2.63 Å3/Da / Density % sol: 53.23 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 7
Details: 100mM HEPES, 50mM ammonium sulphate, 5mM DTT, 100mM guanidine-HCl, 4% PEG 3350, pH 7.0, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1.0, 0.9794, 0.9504
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 1, 2002
RadiationMonochromator: Graphite / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.97941
30.95041
ReflectionResolution: 2.675→48.3 Å / Num. all: 81295 / Num. obs: 81295 / % possible obs: 100 % / Observed criterion σ(F): 4 / Observed criterion σ(I): 2.4 / Redundancy: 9.1 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 30.2
Reflection shellResolution: 2.675→2.8 Å / Redundancy: 8.2 % / Rmerge(I) obs: 0.849 / Mean I/σ(I) obs: 2.4 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0003refinement
ADSCdata collection
HKL-2000data scaling
SHELXSphasing
RefinementMethod to determine structure: MAD / Resolution: 2.68→48.3 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.897 / SU B: 27.05 / SU ML: 0.261 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.669 / ESU R Free: 0.349 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28057 4070 5 %RANDOM
Rwork0.22182 ---
obs0.2248 77153 98.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 52.287 Å2
Baniso -1Baniso -2Baniso -3
1--0.64 Å20 Å20 Å2
2--0.3 Å20 Å2
3---0.34 Å2
Refinement stepCycle: LAST / Resolution: 2.68→48.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15905 0 15 87 16007
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.02216290
X-RAY DIFFRACTIONr_bond_other_d0.0020.0211160
X-RAY DIFFRACTIONr_angle_refined_deg1.8151.96422094
X-RAY DIFFRACTIONr_angle_other_deg1.016326997
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.82452007
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.24722.703740
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.681152687
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.38415137
X-RAY DIFFRACTIONr_chiral_restr0.0990.22457
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0218135
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023537
X-RAY DIFFRACTIONr_nbd_refined0.2490.23985
X-RAY DIFFRACTIONr_nbd_other0.2080.211632
X-RAY DIFFRACTIONr_nbtor_refined0.1980.27911
X-RAY DIFFRACTIONr_nbtor_other0.0970.28971
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.180.2419
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0290.24
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1540.220
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3170.287
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1670.27
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9181.512676
X-RAY DIFFRACTIONr_mcbond_other0.1371.54071
X-RAY DIFFRACTIONr_mcangle_it1.137216138
X-RAY DIFFRACTIONr_scbond_it1.70737293
X-RAY DIFFRACTIONr_scangle_it2.514.55956
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Refine-ID: X-RAY DIFFRACTION

Ens-IDNumberTypeRms dev position (Å)Weight position
11134medium positional0.60.5
23558medium positional0.830.5
32951medium positional0.680.5
42517medium positional0.990.5
5646medium positional0.490.5
6803medium positional0.620.5
11134medium thermal1.714
23558medium thermal1.384
32951medium thermal1.84
42517medium thermal0.934
5646medium thermal1.044
6803medium thermal1.154
LS refinement shellResolution: 2.675→2.745 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.415 223 -
Rwork0.359 4876 -
obs--85.25 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.1790.0276-0.66441.81161.16772.1018-0.2296-0.3088-0.23930.15130.0984-0.19190.23040.0490.1312-0.13350.10690.06520.08780.15690.022356.798162.760517.6741
21.8321.0513-0.27832.794-0.59741.3842-0.06070.0619-0.3162-0.639-0.06570.02630.4250.0020.1264-0.17040.107-0.0403-0.1305-0.1015-0.063238.3133-36.58722.8223
34.10822.89552.87286.60920.15552.7738-0.33230.2318-0.08110.10960.063-0.6587-0.1818-0.65130.26930.0207-0.1630.18350.0139-0.0619-0.061346.11846.05661.8027
40.93880.4039-0.35442.40681.14891.63210.0911-0.17550.2415-0.13840.0719-0.50530.0030.5081-0.1631-0.31540.01510.00390.0707-0.12090.075762.5821-4.94211.4367
51.47690.3443-0.53432.4978-0.29450.73510.0911-0.37010.1070.1137-0.16570.22540.05250.02010.0746-0.30320.037-0.0323-0.0046-0.1481-0.080332.4328-24.479516.1708
62.05010.3791-0.7850.84120.98721.96340.02120.44760.0127-0.11890.38440.0349-0.2423-0.0602-0.40560.1748-0.17170.3637-0.0291-0.12650.162321.717131.777615.174
74.05090.3448-1.83730.5680.22581.73190.2321-0.63760.36190.43370.03530.1628-0.28860.3044-0.2674-0.0133-0.22140.08060.0282-0.2271-0.060139.5916.72844.6527
82.40570.7038-0.48336.02212.25971.4748-0.02560.09610.1882-0.16620.1565-0.2195-0.0688-0.0314-0.13090.09340.05950.3513-0.15640.0546-0.05414.663657.390239.8927
91.2471-0.719-0.68465.09692.13841.9514-0.0535-0.086-0.02720.43870.11960.13620.20530.2038-0.06620.0011-0.07110.1533-0.013-0.0282-0.192818.3724-18.916753.9984
102.56030.87062.32661.1602-1.68269.1961-0.12210.2801-0.30450.2792-0.0367-0.38860.12260.33070.15880.1375-0.08830.2883-0.0096-0.0330.288944.927935.489713.5312
111.5450.75530.34412.4730.47151.58440.2302-0.07680.0273-0.0669-0.16960.1318-0.15140.1821-0.0606-0.31-0.07380.0117-0.0582-0.2592-0.054944.389110.130222.1637
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A61 - 613
2X-RAY DIFFRACTION2B61 - 140
3X-RAY DIFFRACTION3A614 - 639
4X-RAY DIFFRACTION4B141 - 362
5X-RAY DIFFRACTION4B594 - 639
6X-RAY DIFFRACTION5B363 - 593
7X-RAY DIFFRACTION6A701 - 766
8X-RAY DIFFRACTION6A826 - 956
9X-RAY DIFFRACTION7B701 - 766
10X-RAY DIFFRACTION7B826 - 956
11X-RAY DIFFRACTION8A957 - 1197
12X-RAY DIFFRACTION9B957 - 1197
13X-RAY DIFFRACTION10A767 - 825
14X-RAY DIFFRACTION11B767 - 825

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