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

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Basic information

Entry
Database: PDB / ID: 3zkb
TitleCRYSTAL STRUCTURE OF THE ATPASE REGION OF Mycobacterium tuberculosis GyrB WITH AMPPNP
ComponentsDNA GYRASE SUBUNIT B
KeywordsISOMERASE / TYPE IIA TOPOISOMERASE / 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: 2.9 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 1.2May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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

Downloads & links

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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
I: DNA GYRASE SUBUNIT B
J: DNA GYRASE SUBUNIT B
K: DNA GYRASE SUBUNIT B
L: DNA GYRASE SUBUNIT B
M: DNA GYRASE SUBUNIT B
N: DNA GYRASE SUBUNIT B
O: DNA GYRASE SUBUNIT B
P: DNA GYRASE SUBUNIT B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)757,48552
Polymers748,90016
Non-polymers8,58536
Water7,909439
1
C: DNA GYRASE SUBUNIT B
D: DNA GYRASE SUBUNIT B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,7228
Polymers93,6122
Non-polymers1,1106
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7360 Å2
ΔGint-57.7 kcal/mol
Surface area31170 Å2
MethodPISA
2
O: DNA GYRASE SUBUNIT B
P: 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 area6850 Å2
ΔGint-46.3 kcal/mol
Surface area30080 Å2
MethodPISA
3
K: DNA GYRASE SUBUNIT B
L: 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 area6770 Å2
ΔGint-44.7 kcal/mol
Surface area30560 Å2
MethodPISA
4
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 area7140 Å2
ΔGint-41.3 kcal/mol
Surface area30580 Å2
MethodPISA
5
A: DNA GYRASE SUBUNIT B
B: DNA GYRASE SUBUNIT B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,6987
Polymers93,6122
Non-polymers1,0855
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7010 Å2
ΔGint-48.2 kcal/mol
Surface area29840 Å2
MethodPISA
6
G: DNA GYRASE SUBUNIT B
H: DNA GYRASE SUBUNIT B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,6987
Polymers93,6122
Non-polymers1,0855
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6910 Å2
ΔGint-47.5 kcal/mol
Surface area29410 Å2
MethodPISA
7
I: DNA GYRASE SUBUNIT B
J: 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 area6700 Å2
ΔGint-40.3 kcal/mol
Surface area30180 Å2
MethodPISA
8
M: DNA GYRASE SUBUNIT B
N: 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 area6960 Å2
ΔGint-37.4 kcal/mol
Surface area30270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.360, 138.200, 147.690
Angle α, β, γ (deg.)105.28, 92.31, 107.23
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.: 16 / 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.: 16 / 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.: 20 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 439 / 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: 2.52 Å3/Da / Density % sol: 51.27 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.97855
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97855 Å / Relative weight: 1
ReflectionResolution: 2.9→25 Å / Num. obs: 159199 / % possible obs: 98.3 % / Observed criterion σ(I): 0 / Redundancy: 1.91 % / Biso Wilson estimate: 76.57 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 14.1
Reflection shellResolution: 2.9→2.95 Å / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 1.9 / % possible all: 97.7

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Processing

Software
NameVersionClassification
BUSTER2.11.4refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→24.94 Å / Cor.coef. Fo:Fc: 0.9171 / Cor.coef. Fo:Fc free: 0.8866 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.361
Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=MG. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=46932. NUMBER WITH APPROX DEFAULT CCP4 ATOM TYPE=0. ...Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=MG. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=46932. NUMBER WITH APPROX DEFAULT CCP4 ATOM TYPE=0. NUMBER TREATED BY BAD NON-BONDED CONTACTS=20.
RfactorNum. reflection% reflectionSelection details
Rfree0.2397 7966 5.01 %RANDOM
Rwork0.1816 ---
obs0.1845 159159 98.2 %-
Displacement parametersBiso mean: 99.07 Å2
Baniso -1Baniso -2Baniso -3
1--5.3126 Å2-17.1504 Å25.0372 Å2
2--25.6843 Å2-4.7362 Å2
3----20.3718 Å2
Refine analyzeLuzzati coordinate error obs: 0.518 Å
Refinement stepCycle: LAST / Resolution: 2.9→24.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms45997 0 516 439 46952
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00947395HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.164483HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d16027SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes1172HARMONIC2
X-RAY DIFFRACTIONt_gen_planes6985HARMONIC5
X-RAY DIFFRACTIONt_it47395HARMONIC20
X-RAY DIFFRACTIONt_nbd4SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.33
X-RAY DIFFRACTIONt_other_torsion20.61
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion6344SEMIHARMONIC5
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_contact54835SEMIHARMONIC4
LS refinement shellResolution: 2.9→2.98 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3097 564 4.89 %
Rwork0.2392 10968 -
all0.2426 11532 -
obs--98.2 %
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)
11.1828-0.66960.14135.3968-1.03561.73520.0301-0.02870.1365-0.3649-0.1588-0.35710.11790.13360.1287-0.13570.1304-0.0264-0.17680.0146-0.358-19.50058.552-39.3635
21.39970.2847-0.12193.11820.03970.9045-0.0845-0.2144-0.1051-0.0722-0.0308-0.35580.0447-0.04870.1153-0.23860.1083-0.0569-0.1604-0.011-0.1171-18.6087-13.31631.1052
31.2298-0.64320.07012.9767-0.74191.43740.0279-0.10660.24290.4910.15050.0023-0.31040.0117-0.1784-0.15490.04250.0135-0.3269-0.05760.0439-36.401159.600324.818
42.20340.10140.06732.0537-0.2941.8737-0.1395-0.01730.2716-0.1790.01520.04610.23290.12230.1243-0.40280.11660.0394-0.1813-0.0998-0.0159-64.222-16.2894-6.7262
50.9678-0.2749-0.14583.07031.12712.72850.032-0.1445-0.19770.44580.02810.0970.5145-0.2596-0.0602-0.0743-0.2093-0.3272-0.11010.168-0.3253-60.58934.5995-77.1973
60.8002-1.5889-0.14254.57791.23290.9208-0.01470.00590.13360.0553-0.0593-0.3964-0.0653-0.17040.074-0.09780.15680.1656-0.32310.0744-0.0405-45.758678.7737-45.1336
70.4027-0.2934-0.18481.5964-0.41642.2350.13220.0137-0.0329-0.1469-0.3191-0.117-0.28090.12780.1869-0.37770.02560.1812-0.1119-0.31720.2078-88.032955.2832-47.9142
82.1225-0.6627-0.78751.5454-0.240.9691-0.0168-0.0752-0.95110.1658-0.50830.2237-0.29490.21290.5251-0.4659-0.1489-0.2301-0.4540.07770.2576-80.493336.194323.2904
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND RESID 12-602 AND CHAIN B AND RESID 12-602
2X-RAY DIFFRACTION2CHAIN C AND RESID 12-602 AND CHAIN D AND RESID 12-602
3X-RAY DIFFRACTION3CHAIN E AND RESID 12-602 AND CHAIN F AND RESID 12-602
4X-RAY DIFFRACTION4CHAIN G AND RESID 12-602 AND CHAIN H AND RESID 12-602
5X-RAY DIFFRACTION5CHAIN I AND RESID 12-602 AND CHAIN J AND RESID 12-602
6X-RAY DIFFRACTION6CHAIN K AND RESID 12-602 AND CHAIN L AND RESID 12-602
7X-RAY DIFFRACTION7CHAIN M AND RESID 12-602 AND CHAIN N AND RESID 12-602
8X-RAY DIFFRACTION8CHAIN O AND RESID 12-602 AND CHAIN P AND RESID 12-602

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