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- PDB-4ddx: Thermotoga maritima reverse gyrase, primitive monoclinic form -

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Basic information

Entry
Database: PDB / ID: 4ddx
TitleThermotoga maritima reverse gyrase, primitive monoclinic form
ComponentsReverse gyrase
KeywordsHYDROLASE / 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 / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.17 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _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_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_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
B: Reverse gyrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)257,2196
Polymers256,9572
Non-polymers2624
Water0
1
A: Reverse gyrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,6093
Polymers128,4791
Non-polymers1312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Reverse gyrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,6093
Polymers128,4791
Non-polymers1312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)125.815, 104.896, 126.181
Angle α, β, γ (deg.)90.00, 91.72, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain 'A' and (resseq 2:1103 )
211chain 'B' and (resseq 2:1103 )

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Components

#1: Protein Reverse gyrase / / Helicase / Topoisomerase


Mass: 128478.594 Da / Num. of mol.: 2
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.: 4 / Source method: obtained synthetically / Formula: Zn

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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: 3.24 Å3/Da / Density % sol: 62.02 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.8
Details: 20mM citric acid, 80mM Bis-Tris propane pH 8.8, 16% PEG3350, 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
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 15, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 4.17→49.2 Å / Num. obs: 24000 / % possible obs: 96.8 % / Observed criterion σ(I): 1 / Redundancy: 2.94 % / Rmerge(I) obs: 0.2842 / Rsym value: 0.2842 / Net I/σ(I): 3.12
Reflection shellResolution: 4.17→4.27 Å / Redundancy: 2.86 % / Rmerge(I) obs: 0.6313 / Mean I/σ(I) obs: 1.21 / Rsym value: 0.6313 / % possible all: 97.7

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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: 4.17→48.428 Å / SU ML: 0.61 / σ(F): 1.34 / Phase error: 33.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3049 1220 5.09 %
Rwork0.2445 --
obs0.2476 23955 96.8 %
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 132.755 Å2 / ksol: 0.332 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.3375 Å2-0 Å23.1636 Å2
2---38.9971 Å20 Å2
3---38.6596 Å2
Refinement stepCycle: LAST / Resolution: 4.17→48.428 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18060 0 4 0 18064
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00318398
X-RAY DIFFRACTIONf_angle_d2.35124736
X-RAY DIFFRACTIONf_dihedral_angle_d12.4627120
X-RAY DIFFRACTIONf_chiral_restr0.042736
X-RAY DIFFRACTIONf_plane_restr0.0023152
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A9030X-RAY DIFFRACTIONPOSITIONAL0.003
12B9030X-RAY DIFFRACTIONPOSITIONAL0.003
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.17-4.33690.37071340.33632546X-RAY DIFFRACTION97
4.3369-4.53410.35621240.30072524X-RAY DIFFRACTION97
4.5341-4.7730.33171360.27252501X-RAY DIFFRACTION97
4.773-5.07170.33321220.25322531X-RAY DIFFRACTION98
5.0717-5.46280.32891650.25852543X-RAY DIFFRACTION98
5.4628-6.01160.36511330.26962522X-RAY DIFFRACTION97
6.0116-6.87940.32241350.26972501X-RAY DIFFRACTION97
6.8794-8.65920.27041340.19422537X-RAY DIFFRACTION96
8.6592-48.43090.2181370.17652530X-RAY DIFFRACTION94

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