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- PDB-4ddw: Thermotoga maritima reverse gyrase, c-centered orthorhombic form -

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Basic information

Entry
Database: PDB / ID: 4ddw
TitleThermotoga maritima reverse gyrase, c-centered orthorhombic form
ComponentsReverse gyrase
KeywordsHYDROLASE / TOPOISOMERASE / DNA SUPERCOILING / ARCHAEA / HELICASE
Function / homology
Function and homology information


reverse gyrase activity / Isomerases; Isomerases altering macromolecular conformation; Enzymes altering nucleic acid conformation / DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity / DNA unwinding involved in DNA replication / DNA topological change / ATP hydrolysis activity / DNA binding / zinc ion binding / ATP binding / cytoplasm
Similarity search - Function
Phenylalanyl-tRNA Synthetase; Chain B, domain 1 - #80 / EV matrix protein fold - #20 / Reverse gyrase, zinc finger / Reverse gyrase zinc finger / EV matrix protein fold / Reverse gyrase / Reverse gyrase, TOPRIM domain / Zinc finger reverse gyrase N-terminal-type profile. / Zinc finger reverse gyrase C-terminal-type profile. / Topoisomerase I; domain 2 ...Phenylalanyl-tRNA Synthetase; Chain B, domain 1 - #80 / EV matrix protein fold - #20 / Reverse gyrase, zinc finger / Reverse gyrase zinc finger / EV matrix protein fold / Reverse gyrase / Reverse gyrase, TOPRIM domain / Zinc finger reverse gyrase N-terminal-type profile. / Zinc finger reverse gyrase C-terminal-type profile. / Topoisomerase I; domain 2 / Topoisomerase I, domain 2 / Rossmann fold - #140 / Topoisomerase I; domain 4 / Topoisomerase I, domain 4 / Topoisomerase (Topo) IA-type catalytic domain profile. / Phenylalanyl-tRNA Synthetase; Chain B, domain 1 / 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 domain / DEAD/DEAH box helicase / 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 / Sandwich / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PYROPHOSPHATE 2- / Reverse gyrase
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.9 Å
AuthorsRudolph, M.G. / Klostermeier, D.
CitationJournal: Nucleic Acids Res. / Year: 2013
Title: Crystal structures of Thermotoga maritima reverse gyrase: inferences for the mechanism of positive DNA supercoiling.
Authors: Rudolph, M.G. / Del Toro Duany, Y. / Jungblut, S.P. / Ganguly, A. / Klostermeier, D.
History
DepositionJan 19, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 26, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 6, 2013Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Revision 1.3Sep 13, 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_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_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_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

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Assembly

Deposited unit
A: Reverse gyrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,8105
Polymers128,4791
Non-polymers3314
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)174.325, 175.646, 104.135
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Reverse gyrase / Helicase / Topoisomerase


Mass: 128478.594 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: rgy, topR, TM_0173 / Production host: Escherichia coli (E. coli) / References: UniProt: O51934, DNA helicase, EC: 5.99.1.3
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-POP / PYROPHOSPHATE 2-


Mass: 175.959 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H2O7P2
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg

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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: 3.1 Å3/Da / Density % sol: 60.35 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 0.2M Mg(OAc)2, 20% PEG3350, 0.15M sodium citrate, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.27832
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 28, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.27832 Å / Relative weight: 1
ReflectionResolution: 3.9→48.98 Å / Num. obs: 14481 / % possible obs: 96.9 % / Observed criterion σ(I): 1 / Redundancy: 5.45 % / Rmerge(I) obs: 0.1622 / Rsym value: 0.1622 / Net I/σ(I): 7.7
Reflection shellResolution: 3.9→4 Å / Redundancy: 5.54 % / Rmerge(I) obs: 0.8273 / Mean I/σ(I) obs: 1.23 / Rsym value: 0.8273 / % possible all: 94

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Processing

Software
NameVersionClassification
PHASERphasing
PHENIX(phenix.refine: dev_881)refinement
XDS(VERSION December 6data reduction
SADABSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 4DDT

4ddt


Resolution: 3.9→48.749 Å / SU ML: 0.49 / σ(F): 1.35 / Phase error: 31.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2888 716 4.96 %
Rwork0.209 --
obs0.2129 14446 96.82 %
Solvent computationShrinkage radii: 1.11 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 123.498 Å2 / ksol: 0.295 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-23.4925 Å20 Å2-0 Å2
2--11.1654 Å2-0 Å2
3----34.658 Å2
Refinement stepCycle: LAST / Resolution: 3.9→48.749 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9030 0 12 0 9042
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0059210
X-RAY DIFFRACTIONf_angle_d0.612382
X-RAY DIFFRACTIONf_dihedral_angle_d13.573562
X-RAY DIFFRACTIONf_chiral_restr0.0441368
X-RAY DIFFRACTIONf_plane_restr0.0021576
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.9001-4.20110.36761330.3072623X-RAY DIFFRACTION95
4.2011-4.62360.31661390.24032563X-RAY DIFFRACTION92
4.6236-5.29190.31721520.20822736X-RAY DIFFRACTION98
5.2919-6.66460.3381440.2462847X-RAY DIFFRACTION100
6.6646-48.75310.23431480.16432961X-RAY DIFFRACTION100
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)
13.24051.84230.50295.08771.12294.07590.7407-0.8344-0.24220.6616-0.5904-0.45490.4854-0.1665-0.18381.09160.1091-0.08691.2076-0.01330.8833-19.654453.276810.4259
23.47790.3617-3.32172.16490.18855.82340.22630.16150.0950.1225-0.4023-0.0645-0.96670.12790.19371.3634-0.0127-0.11121.15520.07461.3959-23.799578.3992-28.1352
30.95760.4263-0.01831.34620.5793.99950.07490.0669-0.21040.06340.0141-0.2820.71910.518-0.05380.91650.0475-0.04471.2104-0.05431.0996-26.621536.6955-31.7166
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 2:287)
2X-RAY DIFFRACTION2chain 'A' and (resseq 288:491)
3X-RAY DIFFRACTION3chain 'A' and (resseq 492:1103)

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