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- PDB-3zm7: CRYSTAL STRUCTURE OF THE ATPASE REGION OF Mycobacterium tuberculo... -

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Basic information

Entry
Database: PDB / ID: 3zm7
TitleCRYSTAL STRUCTURE OF THE ATPASE REGION OF Mycobacterium tuberculosis GyrB WITH AMPPCP
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 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
PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / : / DNA gyrase subunit B
Similarity search - Component
Biological speciesMYCOBACTERIUM TUBERCULOSIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 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
DepositionFeb 5, 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

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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)292,80818
Polymers289,6316
Non-polymers3,17712
Water1,63991
1
A: DNA GYRASE SUBUNIT B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,8013
Polymers48,2721
Non-polymers5302
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: DNA GYRASE SUBUNIT B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,8013
Polymers48,2721
Non-polymers5302
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: DNA GYRASE SUBUNIT B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,8013
Polymers48,2721
Non-polymers5302
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: DNA GYRASE SUBUNIT B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,8013
Polymers48,2721
Non-polymers5302
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: DNA GYRASE SUBUNIT B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,8013
Polymers48,2721
Non-polymers5302
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: DNA GYRASE SUBUNIT B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,8013
Polymers48,2721
Non-polymers5302
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)78.615, 171.916, 109.230
Angle α, β, γ (deg.)90.00, 110.22, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
DNA GYRASE SUBUNIT B


Mass: 48271.797 Da / Num. of mol.: 6 / Fragment: N-TERMINAL ATPASE REGION, RESIDUES 40-467
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS
References: UniProt: I6WX66, UniProt: P9WG45*PLUS, EC: 5.99.1.3
#2: Chemical
ChemComp-ACP / PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / ADENOSINE-5'-[BETA, GAMMA-METHYLENE]TRIPHOSPHATE


Mass: 505.208 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C11H18N5O12P3 / Comment: AMP-PCP, energy-carrying molecule analogue*YM
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 91 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsWE USE A DIFFERENT START SITE AND NUMBERING THAN IN THIS ENTRY. OUR START SITE IS VAA AND WE CALL V RESIDUE 1.

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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: 2.39 Å3/Da / Density % sol: 48.57 % / Description: NONE
Crystal growpH: 6.5
Details: 24% PEG-1500, 0.1 M MES PH 6.5, 5 MM MGCL2, AND 1.2% MYO-INOSITOL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.91942
DetectorType: ADSC QUANTUM 315r / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91942 Å / Relative weight: 1
ReflectionResolution: 3.3→50 Å / Num. obs: 41737 / % possible obs: 98.8 % / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 108.81 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 16.5
Reflection shellResolution: 3.3→3.5 Å / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 2.4 / % possible all: 95.5

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Processing

Software
NameVersionClassification
BUSTER2.11.4refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3ZKB

3zkb


Resolution: 3.3→25 Å / Cor.coef. Fo:Fc: 0.9331 / Cor.coef. Fo:Fc free: 0.9143 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.445
RfactorNum. reflection% reflectionSelection details
Rfree0.2231 2055 5.04 %RANDOM
Rwork0.1957 ---
obs0.197 40735 99.74 %-
Displacement parametersBiso mean: 113.9 Å2
Baniso -1Baniso -2Baniso -3
1-8.9817 Å20 Å2-9.9014 Å2
2---13.891 Å20 Å2
3---4.9094 Å2
Refine analyzeLuzzati coordinate error obs: 0.684 Å
Refinement stepCycle: LAST / Resolution: 3.3→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16012 0 192 91 16295
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0116486HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1922423HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d5586SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes408HARMONIC2
X-RAY DIFFRACTIONt_gen_planes2491HARMONIC5
X-RAY DIFFRACTIONt_it16486HARMONIC20
X-RAY DIFFRACTIONt_nbd6SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion4.14
X-RAY DIFFRACTIONt_other_torsion20.45
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion2234SEMIHARMONIC5
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_contact19390SEMIHARMONIC4
LS refinement shellResolution: 3.3→3.39 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3114 137 4.56 %
Rwork0.2391 2870 -
all0.2424 3007 -
obs--99.74 %
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)
13.28620.73520.92563.37480.12987.6255-0.11260.23350.1234-0.2786-0.1435-0.2848-0.16070.31560.2561-0.1966-0.05280.0539-0.22270.0031-0.172-2.6507-8.076334.3965
24.85541.86571.41014.90772.40454.6972-0.05620.0036-0.03570.35680.1219-0.2537-0.16960.2321-0.0656-0.2738-0.1371-0.0395-0.287-0.0676-0.033714.58482.837660.7401
35.85640.998-1.24334.3176-0.51784.46610.1035-0.0855-0.4017-0.1904-0.24470.416-0.10940.03390.1412-0.3104-0.0098-0.0294-0.1962-0.0522-0.0612-36.3885-20.707847.3083
43.0384-0.00050.80382.11940.87339.5330.04020.1058-0.1593-0.2640.0076-0.27080.0594-0.0574-0.04780.0358-0.0121-0.0739-0.29010.0162-0.2593-23.7089-16.843616.3927
55.02540.80570.03052.94510.41013.3464-0.00740.1566-0.04350.54520.0931-0.0554-0.2665-0.1493-0.0857-0.1025-0.08570.0028-0.1007-0.0762-0.3212-9.6283-8.012272.1197
63.8620.5366-2.72431.3489-0.9884.76650.0099-0.1868-0.11890.13370.08220.24940.2420.0245-0.092-0.1330.12370.2115-0.11830.0965-0.1607-41.8819-17.571775.5846
72.0949-0.2727-0.6393.6563-0.66625.5128-0.1056-0.2257-0.10240.0367-0.3443-0.34680.0086-0.14350.4499-0.3231-0.03980.00730.01030.0383-0.1315-1.8488-56.6139115.4647
83.49360.2418-0.2462.99871.76713.7548-0.07150.0174-0.1984-0.1975-0.0898-0.13260.20250.16390.1614-0.13030.15740.16-0.2656-0.0074-0.03915.0743-68.01389.7517
98.3108-2.3045-0.31560.51250.78860.1142-0.1986-0.1342-0.0247-0.35480.23990.11450.2344-0.0611-0.0413-0.22230.0177-0.0823-0.1234-0.1534-0.3725-8.4711-56.618577.931
104.6711-0.41421.1493.4939-0.84615.97750.03730.1770.0558-0.20670.0890.1569-0.2323-0.0668-0.1263-0.1887-0.1951-0.1563-0.08260.0901-0.282-40.966-47.423974.5324
116.07480.01541.55873.2504-0.13856.2563-0.04930.16030.17120.14480.09590.1287-0.00790.1616-0.0467-0.23960.0069-0.0354-0.17820.0057-0.2252-35.315-44.0104102.7118
125.97871.830.06923.81450.19076.95390.1608-0.2305-0.09380.2685-0.1025-0.1852-0.36930.2071-0.05820.09750.14820.0481-0.29210.0325-0.2931-22.5277-47.3809133.5932
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND RESID 23-253 AND 525-526
2X-RAY DIFFRACTION2CHAIN A AND RESID 257-413
3X-RAY DIFFRACTION3CHAIN B AND RESID 23-253 AND 525-526
4X-RAY DIFFRACTION4CHAIN B AND RESID 257-413
5X-RAY DIFFRACTION5CHAIN C AND RESID 23-253 AND 525-526
6X-RAY DIFFRACTION6CHAIN C AND RESID 257-413
7X-RAY DIFFRACTION7CHAIN D AND RESID 23-253 AND 525-526
8X-RAY DIFFRACTION8CHAIN D AND RESID 257-413
9X-RAY DIFFRACTION9CHAIN E AND RESID 23-253 AND 525-526
10X-RAY DIFFRACTION10CHAIN E AND RESID 257-413
11X-RAY DIFFRACTION11CHAIN F AND RESID 23-253 AND 525-526
12X-RAY DIFFRACTION12CHAIN F AND RESID 257-413

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