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- PDB-3zkd: CRYSTAL STRUCTURE OF THE ATPASE REGION OF Mycobacterium tuberculo... -

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Basic information

Entry
Database: PDB / ID: 3zkd
TitleCRYSTAL STRUCTURE OF THE ATPASE REGION OF Mycobacterium tuberculosis GyrB WITH AMPPNP
ComponentsDNA GYRASE SUBUNIT B
KeywordsISOMERASE / GHKL DOMAIN
Function / homology
Function and homology information


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 binding ...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 binding / ATP binding / plasma membrane / cytoplasm
Similarity search - Function
DNA gyrase subunit B, TOPRIM domain / DNA gyrase, subunit B / DNA topoisomerase, type IIA, subunit B / DNA gyrase B subunit, C-terminal / DNA gyrase B subunit, carboxyl terminus / DNA topoisomerase, type IIA, subunit B, domain 2 / DNA gyrase B / DNA topoisomerase, type IIA / DNA topoisomerase, type IIA, conserved site / DNA topoisomerase II signature. ...DNA gyrase subunit B, TOPRIM domain / DNA gyrase, subunit B / DNA topoisomerase, type IIA, subunit B / DNA gyrase B subunit, C-terminal / DNA gyrase B subunit, carboxyl terminus / DNA topoisomerase, type IIA, subunit B, domain 2 / DNA gyrase B / DNA topoisomerase, type IIA / DNA topoisomerase, type IIA, conserved site / DNA topoisomerase II signature. / TopoisomeraseII / DNA topoisomerase, type IIA, subunit B, C-terminal / Toprim domain / DNA topoisomerase, type IIA-like domain superfamily / Ribosomal Protein S5; domain 2 - #10 / Toprim domain profile. / TOPRIM domain / Ribosomal Protein S5; domain 2 / Histidine kinase-like ATPase, C-terminal domain / Heat Shock Protein 90 / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S5 domain 2-type fold / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / : / DNA gyrase subunit B
Similarity search - Component
Biological speciesMYCOBACTERIUM TUBERCULOSIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 Å
AuthorsAgrawal, A. / Roue, M. / Spitzfaden, C. / Petrella, S. / Aubry, A. / Volker, C. / Mossakowska, D. / Hann, M. / Bax, B. / Mayer, C.
CitationJournal: Biochem.J. / Year: 2013
Title: Mycobacterium Tuberculosis DNA Gyrase ATPase Domain Structures Suggest a Dissociative Mechanism that Explains How ATP Hydrolysis is Coupled to Domain Motion.
Authors: Agrawal, A. / Roue, M. / Spitzfaden, C. / Petrella, S. / Aubry, A. / Hann, M.M. / Bax, B. / Mayer, C.
History
DepositionJan 22, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 18, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2013Group: Database references
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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_database_status.status_code_sf / _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_conn.ptnr2_label_seq_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: DNA GYRASE SUBUNIT B
B: DNA GYRASE SUBUNIT B
C: DNA GYRASE SUBUNIT B
D: DNA GYRASE SUBUNIT B
E: DNA GYRASE SUBUNIT B
F: DNA GYRASE SUBUNIT B
G: DNA GYRASE SUBUNIT B
H: DNA GYRASE SUBUNIT B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)378,69424
Polymers374,4508
Non-polymers4,24416
Water2,072115
1
C: DNA GYRASE SUBUNIT B
D: DNA GYRASE SUBUNIT B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,6736
Polymers93,6122
Non-polymers1,0614
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6330 Å2
ΔGint-41.5 kcal/mol
Surface area30360 Å2
MethodPISA
2
G: DNA GYRASE SUBUNIT B
H: DNA GYRASE SUBUNIT B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,6736
Polymers93,6122
Non-polymers1,0614
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6810 Å2
ΔGint-42.8 kcal/mol
Surface area29300 Å2
MethodPISA
3
E: DNA GYRASE SUBUNIT B
F: DNA GYRASE SUBUNIT B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,6736
Polymers93,6122
Non-polymers1,0614
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6880 Å2
ΔGint-37.5 kcal/mol
Surface area29740 Å2
MethodPISA
4
A: DNA GYRASE SUBUNIT B
B: DNA GYRASE SUBUNIT B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,6736
Polymers93,6122
Non-polymers1,0614
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6560 Å2
ΔGint-39.4 kcal/mol
Surface area29890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.953, 97.851, 138.075
Angle α, β, γ (deg.)108.21, 105.18, 91.04
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
DNA GYRASE SUBUNIT B /


Mass: 46806.246 Da / Num. of mol.: 8 / Fragment: N-TERMINAL ATPASE REGION, RESIDUES 40-466
Source method: isolated from a genetically manipulated source
Details: AMPPNP IN IMINO FORM / Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA
References: UniProt: I6WX66, UniProt: P9WG45*PLUS, EC: 5.99.1.3
#2: Chemical
ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 115 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsAMPPNP IN IMINO FORM. THIS IS THE IMINO FORM OF AMPPNP.
Sequence detailsNOTE - WE USED NEW CONSENSUS START SITE (A VALINE) WHICH IS RESIDUE 40 IN THIS ENTRY.

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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: 2.37 Å3/Da / Density % sol: 48.01 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97955
DetectorType: ADSC QUANTUM 315r / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97955 Å / Relative weight: 1
ReflectionResolution: 2.95→40 Å / Num. obs: 64548 / % possible obs: 84.5 % / Observed criterion σ(I): 0 / Redundancy: 1.68 % / Biso Wilson estimate: 66.66 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 10.8
Reflection shellResolution: 2.95→3 Å / Rmerge(I) obs: 0.27 / Mean I/σ(I) obs: 1.9 / % possible all: 86.2

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Processing

Software
NameVersionClassification
BUSTER2.11.4refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1EI1

1ei1


Resolution: 2.95→24.81 Å / Cor.coef. Fo:Fc: 0.9079 / Cor.coef. Fo:Fc free: 0.8564 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.469
RfactorNum. reflection% reflectionSelection details
Rfree0.257 2459 4.03 %RANDOM
Rwork0.1817 ---
obs0.1847 61070 84.6 %-
Displacement parametersBiso mean: 80.27 Å2
Baniso -1Baniso -2Baniso -3
1--6.4261 Å29.168 Å29.6716 Å2
2---13.2597 Å2-10.8555 Å2
3---19.6859 Å2
Refine analyzeLuzzati coordinate error obs: 0.417 Å
Refinement stepCycle: LAST / Resolution: 2.95→24.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22821 0 256 115 23192
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00923506HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1631959HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d7958SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes566HARMONIC2
X-RAY DIFFRACTIONt_gen_planes3457HARMONIC5
X-RAY DIFFRACTIONt_it23506HARMONIC20
X-RAY DIFFRACTIONt_nbd3SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.67
X-RAY DIFFRACTIONt_other_torsion21.04
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion3159SEMIHARMONIC5
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_contact28750SEMIHARMONIC4
LS refinement shellResolution: 2.95→3.03 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3266 173 3.75 %
Rwork0.2095 4442 -
all0.2137 4615 -
obs--84.6 %
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)
11.3775-0.59840.56761.4023-1.28952.3730.13770.1587-0.0031-0.0276-0.1609-0.0290.17540.10940.0231-0.07450.0468-0.0514-0.1716-0.1263-0.3046-25.124227.8239-24.6683
20.88590.4561-0.31020.8589-0.69093.69560.2246-0.15980.05030.2727-0.09690.0296-0.18230.0823-0.12780.01-0.17570.1046-0.1768-0.0869-0.3031-25.7061-27.7648-4.1705
31.4332-0.19680.30310.4984-0.26763.64230.0241-0.11320.1095-0.1034-0.05940.04770.17320.23530.0353-0.1416-0.0593-0.0307-0.2254-0.0279-0.1991-9.39595.858544.4141
41.43960.9038-1.39961.0425-1.43344.862-0.02430.2183-0.01340.01330.0415-0.00520.0868-0.1076-0.0172-0.1059-0.07680.0753-0.2785-0.0267-0.3007-9.0669-6.018-72.8355
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{A|12-A|412 B|12-B|412 A|601-A|602 B|601-B|602}
2X-RAY DIFFRACTION2{C|12-C|412 D|12-D|412 C|601-C|602 D|601-D|602}
3X-RAY DIFFRACTION3{E|12-E|412 F|12-F|412 E|601-E|602 F|601-F|602}
4X-RAY DIFFRACTION4{G|12-G|412 H|12-H|412 G|601-G|602 H|601-H|602}

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