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- PDB-3uc1: Mycobacterium tuberculosis gyrase type IIA topoisomerase C-termin... -

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Basic information

Entry
Database: PDB / ID: 3uc1
TitleMycobacterium tuberculosis gyrase type IIA topoisomerase C-terminal domain
ComponentsDNA gyrase subunit A
KeywordsISOMERASE / DNA binding protein / Topoisomerase / Gyrase
Function / homology
Function and homology information


DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) complex / DNA negative supercoiling activity / DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity / DNA topoisomerase (ATP-hydrolysing) / DNA topological change / peptidoglycan-based cell wall / DNA-templated DNA replication / chromosome / response to antibiotic / magnesium ion binding ...DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) complex / DNA negative supercoiling activity / DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity / DNA topoisomerase (ATP-hydrolysing) / DNA topological change / peptidoglycan-based cell wall / DNA-templated DNA replication / chromosome / response to antibiotic / magnesium ion binding / ATP hydrolysis activity / DNA binding / ATP binding / plasma membrane / cytoplasm
Similarity search - Function
DNA gyrase/topoisomerase IV, subunit A, C-terminal / DNA gyrase, subunit A / : / DNA gyrase/topoisomerase IV, subunit A, C-terminal repeat / DNA gyrase/topoisomerase IV, subunit A, C-terminal / DNA gyrase C-terminal domain, beta-propeller / Topoisomerase (Topo) IIA-type catalytic domain profile. / DNA topoisomerase, type IIA, alpha-helical domain superfamily / DNA topoisomerase, type IIA, domain A / DNA topoisomerase, type IIA, domain A, alpha-beta ...DNA gyrase/topoisomerase IV, subunit A, C-terminal / DNA gyrase, subunit A / : / DNA gyrase/topoisomerase IV, subunit A, C-terminal repeat / DNA gyrase/topoisomerase IV, subunit A, C-terminal / DNA gyrase C-terminal domain, beta-propeller / Topoisomerase (Topo) IIA-type catalytic domain profile. / DNA topoisomerase, type IIA, alpha-helical domain superfamily / DNA topoisomerase, type IIA, domain A / DNA topoisomerase, type IIA, domain A, alpha-beta / DNA gyrase/topoisomerase IV, subunit A / DNA Topoisomerase IV / DNA topoisomerase, type IIA-like domain superfamily / 6 Propeller / Neuraminidase / EF-hand calcium-binding domain. / Mainly Beta
Similarity search - Domain/homology
ACETATE ION / DNA gyrase subunit A / DNA gyrase subunit A
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsTretter, E.M. / Berger, J.M.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Mechanisms for Defining Supercoiling Set Point of DNA Gyrase Orthologs: II. THE SHAPE OF THE GyrA SUBUNIT C-TERMINAL DOMAIN (CTD) IS NOT A SOLE DETERMINANT FOR CONTROLLING SUPERCOILING EFFICIENCY.
Authors: Tretter, E.M. / Berger, J.M.
History
DepositionOct 25, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 28, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 25, 2012Group: Database references
Revision 1.2Jun 13, 2012Group: Database references
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / 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.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.value / _struct_conn.pdbx_dist_value / _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_ref_seq_dif.details / _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 gyrase subunit A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,5425
Polymers35,2921
Non-polymers2504
Water5,350297
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)38.871, 82.842, 83.433
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 DNA gyrase subunit A


Mass: 35291.652 Da / Num. of mol.: 1 / Fragment: UNP residues 514-838
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: gyrA, MRA_0006 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: A5TY74, UniProt: P9WG47*PLUS, EC: 5.99.1.3
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 297 / 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: 1.9 Å3/Da / Density % sol: 35.37 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.2 M (CH3COO)2Ca xH2O. 20% PEG3350, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 9, 2008
RadiationMonochromator: Double flat crystal, Si(111) / Protocol: Native / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.65→50 Å / Num. obs: 33301 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.1 % / Rmerge(I) obs: 0.074 / Rsym value: 0.074 / Net I/σ(I): 27.131
Reflection shellResolution: 1.65→1.71 Å / Redundancy: 7 % / Mean I/σ(I) obs: 3.59 / Num. unique all: 3280 / Rsym value: 0.56 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.6.2_432)refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.65→41.716 Å / SU ML: 0.21 / σ(F): 1.34 / Phase error: 21.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2221 1683 5.07 %RANDOM
Rwork0.1876 ---
obs0.1894 33225 99.8 %-
all-33301 --
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.28 Å2 / ksol: 0.354 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.5495 Å2-0 Å20 Å2
2---0.7168 Å2-0 Å2
3---2.2664 Å2
Refinement stepCycle: LAST / Resolution: 1.65→41.716 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2295 0 15 297 2607
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092461
X-RAY DIFFRACTIONf_angle_d1.1823348
X-RAY DIFFRACTIONf_dihedral_angle_d13.475955
X-RAY DIFFRACTIONf_chiral_restr0.081390
X-RAY DIFFRACTIONf_plane_restr0.005443
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.69720.28181250.25132568X-RAY DIFFRACTION98
1.6972-1.7520.26261110.22542585X-RAY DIFFRACTION100
1.752-1.81460.2451420.21292585X-RAY DIFFRACTION100
1.8146-1.88730.21941200.18792615X-RAY DIFFRACTION100
1.8873-1.97320.21881380.18312608X-RAY DIFFRACTION100
1.9732-2.07720.25691320.18642618X-RAY DIFFRACTION100
2.0772-2.20730.22481720.18352584X-RAY DIFFRACTION100
2.2073-2.37780.1961540.17642600X-RAY DIFFRACTION100
2.3778-2.6170.21241370.1852646X-RAY DIFFRACTION100
2.617-2.99560.20461410.19792659X-RAY DIFFRACTION100
2.9956-3.77370.21331430.18022675X-RAY DIFFRACTION100
3.7737-41.72980.22721680.17842799X-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)
10.099-0.0838-0.07560.17470.0070.0691-0.05240.1182-0.45090.33710.01070.25220.09640.0463-0.00680.04190.0040.01920.0861-0.00750.132916.723641.844618.6707
20.22770.14040.01870.05-0.10160.4321-0.0076-0.0514-0.07250.1466-0.03570.01030.0882-0.0067-0.00080.1220.00650.00280.09320.00310.116321.775636.90525.0361
30.15340.09840.12930.1455-0.03910.1678-0.10690.1494-0.17670.00890.0699-0.01580.028-0.0103-0.00180.05260.0106-0.00390.0935-0.01460.111624.426148.900314.0447
40.0231-0.0253-0.00460.03210.03360.09810.0071-0.04060.0333-0.2413-0.05480.0865-0.027-0.0907-0.00170.0963-0.02080.01670.1282-0.03080.078429.212549.89877.9591
50.16920.0313-0.08410.17510.22750.29520.0542-0.0272-0.3369-0.0027-0.04370.24260.01460.0642-00.08940.01240.01550.11650.03670.139122.269636.99114.5715
60.36960.27080.45150.24350.18081.0891-0.0294-0.01540.0350.02410.10740.00260.08270.11270.01660.0254-0.00260.01040.0792-0.01660.08628.430251.100713.6562
70.1687-0.0213-0.31580.3297-0.15960.4050.05210.08720.0511-0.0651-0.0276-0.00350.04140.05070.05010.0550.0015-0.00570.0686-0.0260.072933.875958.453910.9905
80.33720.4649-0.01680.5775-0.12070.17530.05040.0666-0.08270.0716-0.0640.0187-0.01320.10360.00020.0532-0.00130.01120.0701-0.00360.063539.225857.930821.9332
90.19660.5218-0.10390.7041-0.1120.83190.00810.07590.01580.0937-0.1091-0.01-0.07950.2808-0.01040.0879-0.00030.01740.1044-0.00190.071441.732862.885520.8006
100.59210.7017-0.42040.6858-0.50580.52330.1135-0.0542-0.06990.5889-0.0120.4049-0.44080.04460.14950.2296-0.01590.09820.0794-0.02010.083335.424455.574737.528
110.14620.0819-0.1050.15580.11020.19270.2245-0.0672-0.02930.3742-0.2845-0.1064-0.16620.34460.0080.2084-0.0692-0.04230.12540.020.1144.969262.290933.1519
120.10120.1936-0.04460.4864-0.14460.26280.1175-0.159-0.15580.23-0.0836-0.0134-0.22640.11010.00080.1633-0.01610.02730.14860.02830.113439.31248.955537.064
130.1313-0.14640.00760.3593-0.35880.63560.08530.0538-0.16640.0534-0.14680.0882-0.25810.0884-0.01990.1901-0.03650.02710.08350.01790.064135.734445.255440.3758
14-0.00030.010.01420.0851-0.01950.11640.1782-0.1828-0.27510.337-0.511-0.25130.00550.1962-00.19650.00630.01160.19240.05630.181341.392337.84743.3627
150.05220.0724-0.00930.0780.01650.0716-0.0424-0.15180.2521-0.1350.2214-0.1173-0.0018-0.3868-00.20060.0250.01980.21960.00260.145637.491942.054532.4714
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 512:521)
2X-RAY DIFFRACTION2(chain A and resid 522:559)
3X-RAY DIFFRACTION3(chain A and resid 560:574)
4X-RAY DIFFRACTION4(chain A and resid 575:579)
5X-RAY DIFFRACTION5(chain A and resid 580:598)
6X-RAY DIFFRACTION6(chain A and resid 599:622)
7X-RAY DIFFRACTION7(chain A and resid 623:653)
8X-RAY DIFFRACTION8(chain A and resid 654:679)
9X-RAY DIFFRACTION9(chain A and resid 680:714)
10X-RAY DIFFRACTION10(chain A and resid 715:739)
11X-RAY DIFFRACTION11(chain A and resid 740:755)
12X-RAY DIFFRACTION12(chain A and resid 756:773)
13X-RAY DIFFRACTION13(chain A and resid 774:800)
14X-RAY DIFFRACTION14(chain A and resid 801:810)
15X-RAY DIFFRACTION15(chain A and resid 811:817)

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