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- PDB-3p4x: Helicase domain of reverse gyrase from Thermotoga maritima -

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Basic information

Entry
Database: PDB / ID: 3p4x
TitleHelicase domain of reverse gyrase from Thermotoga maritima
Componentsreverse gyrase helicase-like domain
KeywordsISOMERASE / TOPOISOMERASE / DNA SUPERCOILING / ARCHAEA / HELICASE
Function / homology
Function and homology information


Isomerases; Isomerases altering macromolecular conformation; Enzymes altering nucleic acid conformation / reverse gyrase activity / DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity / DNA unwinding involved in DNA replication / DNA topological change / helicase activity / ATP hydrolysis activity / DNA binding / zinc ion binding / ATP binding / cytoplasm
Similarity search - Function
Reverse gyrase, zinc finger / Reverse gyrase zinc finger / Reverse gyrase / Reverse gyrase, TOPRIM domain / Zinc finger reverse gyrase N-terminal-type profile. / Zinc finger reverse gyrase C-terminal-type profile. / Topoisomerase (Topo) IA-type catalytic domain profile. / DNA topoisomerase, type IA, domain 2 / DNA topoisomerase, type IA, DNA-binding domain / DNA topoisomerase, type IA, central ...Reverse gyrase, zinc finger / Reverse gyrase zinc finger / Reverse gyrase / Reverse gyrase, TOPRIM domain / Zinc finger reverse gyrase N-terminal-type profile. / Zinc finger reverse gyrase C-terminal-type profile. / Topoisomerase (Topo) IA-type catalytic domain profile. / DNA topoisomerase, type IA, domain 2 / DNA topoisomerase, type IA, DNA-binding domain / DNA topoisomerase, type IA, central / DNA topoisomerase, type IA, central region, subdomain 1 / DNA topoisomerase, type IA, central region, subdomain 3 / DNA topoisomerase, type IA, core domain / DNA topoisomerase / Bacterial DNA topoisomeraes I ATP-binding domain / Bacterial DNA topoisomerase I DNA-binding domain / TOPRIM / Toprim domain / Toprim domain profile. / TOPRIM domain / DEAD/DEAH box helicase / DEAD/DEAH box helicase domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase superfamily 1/2, ATP-binding domain / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Reverse gyrase
Similarity search - Component
Biological speciesthermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.41 Å
AuthorsRudolph, M.G. / Klostermeier, D.
CitationJournal: Biochemistry / Year: 2011
Title: The Conformational Flexibility of the Helicase-like Domain from Thermotoga maritima Reverse Gyrase Is Restricted by the Topoisomerase Domain.
Authors: Del Toro Duany, Y. / Klostermeier, D. / Rudolph, M.G.
History
DepositionOct 7, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 15, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Sep 6, 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_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.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.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_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: reverse gyrase helicase-like domain
B: reverse gyrase helicase-like domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,6685
Polymers96,1812
Non-polymers4873
Water93752
1
A: reverse gyrase helicase-like domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,5423
Polymers48,0901
Non-polymers4522
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: reverse gyrase helicase-like domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,1262
Polymers48,0901
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.259, 111.231, 129.726
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein reverse gyrase helicase-like domain


Mass: 48090.434 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) thermotoga maritima (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: O51934*PLUS
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 52 / 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: 2.22 Å3/Da / Density % sol: 44.66 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 20% PEG3350, 0.2M Mg-formiate, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 27, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→129.73 Å / Num. obs: 34066 / % possible obs: 99.1 % / Observed criterion σ(I): 1 / Redundancy: 3.6 % / Rmerge(I) obs: 0.064 / Rsym value: 0.064 / Net I/σ(I): 12
Reflection shellResolution: 2.4→2.5 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.635 / Rsym value: 0.635 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHASERphasing
PHENIX(phenix.refine: 1.6_289)refinement
XDS(VERSION May 10data reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3OIY

3oiy


Resolution: 2.41→56.032 Å / SU ML: 0.36 / σ(F): 0.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2563 1522 5.11 %random
Rwork0.1863 ---
obs0.1899 29793 87.9 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.728 Å2 / ksol: 0.281 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-3.8846 Å20 Å2-0 Å2
2--0.4248 Å2-0 Å2
3----4.3094 Å2
Refinement stepCycle: LAST / Resolution: 2.41→56.032 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6648 0 29 52 6729
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0096807
X-RAY DIFFRACTIONf_angle_d1.1449143
X-RAY DIFFRACTIONf_dihedral_angle_d18.4362576
X-RAY DIFFRACTIONf_chiral_restr0.0761002
X-RAY DIFFRACTIONf_plane_restr0.0041146
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.41-2.48780.41451090.32732042X-RAY DIFFRACTION71
2.4878-2.57670.35771230.31112208X-RAY DIFFRACTION76
2.5767-2.67990.37731200.27292289X-RAY DIFFRACTION80
2.6799-2.80180.33911380.2592317X-RAY DIFFRACTION80
2.8018-2.94960.3041360.23182500X-RAY DIFFRACTION87
2.9496-3.13430.31131360.22842642X-RAY DIFFRACTION91
3.1343-3.37630.27471350.21052753X-RAY DIFFRACTION95
3.3763-3.7160.26651460.17452838X-RAY DIFFRACTION96
3.716-4.25360.23211520.15242839X-RAY DIFFRACTION97
4.2536-5.35840.17421760.12922872X-RAY DIFFRACTION97
5.3584-56.04720.23841510.16242971X-RAY DIFFRACTION95
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)
12.04620.22080.23941.2478-0.93635.27760.20820.0960.0963-0.18980.0169-0.01580.5459-0.1482-0.16530.18210.0105-0.01230.1564-0.03920.173411.7353-41.222414.3295
21.2703-0.0459-1.54230.63511.79065.6821-0.16520.26710.0847-0.32540.07240.0420.242-0.29460.05460.2279-0.0865-0.0230.34970.02520.0482-20.997-50.982943.0815
32.98910.05811.94481.68770.87961.3901-0.3597-0.2410.1414-0.13610.3048-0.1568-0.2535-0.16050.05020.26210.02310.00040.2341-0.06060.13764.994-74.884336.4405
40.80470.06040.96490.65030.37151.85070.0434-0.03280.00920.13370.0513-0.02730.2805-0.1227-0.06120.22780.0201-0.01110.221-0.02140.0531-16.004-62.55437.4907
51.1858-0.4306-0.88530.15630.31910.66040.2460.3890.15390.16480.33010.01590.31840.2752-0.37871.73580.3351-0.1511.4791-0.06780.439311.3875-50.3313-0.5041
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 59:285)
2X-RAY DIFFRACTION2CHAIN A AND (RESID 286:532)
3X-RAY DIFFRACTION3CHAIN B AND (RESID 58:285)
4X-RAY DIFFRACTION4CHAIN B AND (RESID 286:538)
5X-RAY DIFFRACTION5CHAIN A AND (RESID 800)

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