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- PDB-4ddv: Thermotoga maritima reverse gyrase, triclinic form -

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Basic information

Entry
Database: PDB / ID: 4ddv
TitleThermotoga maritima reverse gyrase, triclinic 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
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.46 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

Downloads & links

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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
Water00
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)95.710, 101.251, 104.427
Angle α, β, γ (deg.)113.61, 97.50, 110.42
Int Tables number1
Space group name H-MP1

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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: 3.21 Å3/Da / Density % sol: 61.68 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 0.2M sodium citrate, 20% 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: 1.00148
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 15, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00148 Å / Relative weight: 1
ReflectionResolution: 3.46→49.11 Å / Num. obs: 41027 / % possible obs: 98.3 % / Observed criterion σ(I): 1 / Redundancy: 1.95 % / Biso Wilson estimate: 93.33 Å2 / Rmerge(I) obs: 0.1529 / Rsym value: 0.1529 / Net I/σ(I): 3.91
Reflection shellResolution: 3.46→3.56 Å / Redundancy: 1.99 % / Rmerge(I) obs: 0.5475 / Mean I/σ(I) obs: 1 / Rsym value: 0.5475 / % possible all: 97.5

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Processing

Software
NameVersionClassification
PHASERphasing
BUSTER2.11.2refinement
XDS(VERSION December 6data reduction
SADABSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4DDT

4ddt


Resolution: 3.46→49.11 Å / Cor.coef. Fo:Fc: 0.8671 / Cor.coef. Fo:Fc free: 0.8283 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2779 2069 5.04 %RANDOM
Rwork0.2353 ---
obs0.2374 41016 98.35 %-
Displacement parametersBiso mean: 103.57 Å2
Baniso -1Baniso -2Baniso -3
1-9.8801 Å2-22.7108 Å21.3296 Å2
2---13.4291 Å24.884 Å2
3---3.549 Å2
Refine analyzeLuzzati coordinate error obs: 0.918 Å
Refinement stepCycle: LAST / Resolution: 3.46→49.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18060 0 4 0 18064
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0118382HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1224712HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d6864SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes472HARMONIC2
X-RAY DIFFRACTIONt_gen_planes2620HARMONIC5
X-RAY DIFFRACTIONt_it18382HARMONIC20
X-RAY DIFFRACTIONt_nbd6SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.83
X-RAY DIFFRACTIONt_other_torsion20.27
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion2344SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact21240SEMIHARMONIC4
LS refinement shellResolution: 3.46→3.55 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2434 155 5.15 %
Rwork0.2228 2855 -
all0.2239 3010 -
obs--98.35 %
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)
12.50210.8705-1.39530.5759-0.41742.4777-0.20550.7536-0.3236-0.32670.0635-0.06810.0469-0.16350.1420.1186-0.114-0.07790.26080.0917-0.3869-53.617932.3631-1.9146
21.06261.1231-0.75020.41870.241.3841-0.01110.0170.0773-0.3307-0.2377-0.01370.2708-0.27690.24880.0487-0.1782-0.12350.22270.0612-0.4104-73.895113.979421.9467
30.88790.3165-0.48250.7628-0.83753.76230.0284-0.099-0.1866-0.0915-0.1331-0.120.28840.3010.10470.1245-0.12940.00950.24850.118-0.3258-38.983521.468742.4007
40.94050.1685-0.02362.0441-1.74282.1388-0.2745-0.19190.61420.02490.0683-0.2455-0.67410.30470.2062-0.0139-0.34780.06020.06370.1108-0.2241-7.03267.0065-25.8051
53.8415-1.3172-1.81380.87241.03515.5552-0.18390.17570.3257-0.05290.054-0.076-0.0847-0.40130.1299-0.0537-0.2898-0.0440.15370.0648-0.341310.8127-5.65413.2881
60.68830.0726-0.05860.9979-0.92792.34460.114-0.0820.02930.00950.16950.17050.0605-0.1904-0.28340.0171-0.28440.07940.14790.1033-0.2629-26.2742-22.71454.1124
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|2 - A|308 }A2 - 308
2X-RAY DIFFRACTION2{ A|309 - A|571 }A309 - 571
3X-RAY DIFFRACTION3{ A|572 - A|1103 }A572 - 1103
4X-RAY DIFFRACTION4{ B|2 - B|283 }B2 - 283
5X-RAY DIFFRACTION5{ B|284 - B|491 }B284 - 491
6X-RAY DIFFRACTION6{ B|492 - B|1103 }B492 - 1103

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