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- PDB-7cmp: parE in complex with AMPPNP -

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Basic information

Entry
Database: PDB / ID: 7cmp
TitleparE in complex with AMPPNP
ComponentsDNA topoisomerase 4 subunit BTopoisomerase
KeywordsANTIBIOTIC / parE / topoisomeraseIV
Function / homology
Function and homology information


DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity / DNA topoisomerase (ATP-hydrolysing) / DNA topological change / chromosome segregation / chromosome / DNA binding / ATP binding
Similarity search - Function
DNA topoisomerase IV, subunit B, Gram-negative / 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 ...DNA topoisomerase IV, subunit B, Gram-negative / 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 / Toprim domain profile. / TOPRIM domain / 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
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / DNA topoisomerase 4 subunit B
Similarity search - Component
Biological speciesXanthomonas oryzae pv. oryzae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.886 Å
AuthorsJung, H.Y. / Heo, Y.-S.
CitationJournal: To Be Published
Title: Crystal structure of parE in complex with AMPPNP
Authors: Jung, H.Y. / Heo, Y.-S.
History
DepositionJul 28, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 4, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA topoisomerase 4 subunit B
B: DNA topoisomerase 4 subunit B
C: DNA topoisomerase 4 subunit B
D: DNA topoisomerase 4 subunit B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)183,83912
Polymers181,7174
Non-polymers2,1228
Water1,04558
1
A: DNA topoisomerase 4 subunit B
B: DNA topoisomerase 4 subunit B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,9196
Polymers90,8582
Non-polymers1,0614
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6850 Å2
ΔGint-32 kcal/mol
Surface area29840 Å2
MethodPISA
2
C: DNA topoisomerase 4 subunit B
D: DNA topoisomerase 4 subunit B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,9196
Polymers90,8582
Non-polymers1,0614
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6490 Å2
ΔGint-33 kcal/mol
Surface area30640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.016, 126.747, 96.044
Angle α, β, γ (deg.)90.000, 109.610, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B
31chain C
41chain D

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain AA48 - 3093
211chain BB48 - 3093
311chain CC48 - 3093
411chain DD48 - 3093

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Components

#1: Protein
DNA topoisomerase 4 subunit B / Topoisomerase / Topoisomerase IV subunit B


Mass: 45429.238 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xanthomonas oryzae pv. oryzae (strain KACC10331 / KXO85) (bacteria)
Strain: KACC10331 / KXO85 / Gene: parE, XOO2969 / Production host: Escherichia coli (E. coli)
References: UniProt: Q5GYJ8, DNA topoisomerase (ATP-hydrolysing)
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 58 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.34 Å3/Da / Density % sol: 47.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.2 M Ammonium acetate, 0.1 M HEPES pH 7.5, 45% v/v 2-metyl-2,4-pentanediol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 11C / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 24, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.886→50 Å / Num. obs: 37042 / % possible obs: 98.46 % / Redundancy: 3.9 % / Biso Wilson estimate: 47.33 Å2 / CC1/2: 0.98 / Net I/σ(I): 21.2
Reflection shellResolution: 2.89→2.94 Å / Num. unique obs: 1849 / CC1/2: 0.88

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIX1.13_2998refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3LPS

3lps


Resolution: 2.886→46.104 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 28.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2599 1847 4.99 %
Rwork0.2016 35195 -
obs0.2046 37042 98.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 135.13 Å2 / Biso mean: 52.312 Å2 / Biso min: 18.42 Å2
Refinement stepCycle: final / Resolution: 2.886→46.104 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11692 0 128 58 11878
Biso mean--38.92 36.79 -
Num. residues----1496
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A4572X-RAY DIFFRACTION4.551TORSIONAL
12B4572X-RAY DIFFRACTION4.551TORSIONAL
13C4572X-RAY DIFFRACTION4.551TORSIONAL
14D4572X-RAY DIFFRACTION4.551TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.89-2.96360.37261250.2917246690
2.9636-3.05080.3651330.2942272599
3.0508-3.14920.33751320.2697270999
3.1492-3.26180.33351490.2594271399
3.2618-3.39230.33131370.2435271299
3.3923-3.54670.28521550.2166272699
3.5467-3.73360.25471450.2046270899
3.7336-3.96740.30391200.1884276999
3.9674-4.27350.21250.1794272099
4.2735-4.70320.2451480.1634274899
4.7032-5.38280.21361620.16752726100
5.3828-6.77840.24321630.19682739100
6.7784-46.10.19211530.1646273498
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)
13.895-2.3047-0.2934.506-1.70711.07410.10620.431-0.10730.3001-0.3869-0.2842-0.09950.05850.22390.30240.028-0.07040.2547-0.03510.20435.6511-46.674825.4955
22.86661.2086-0.28851.84320.39652.04950.2948-0.03770.31250.1733-0.1655-0.3897-0.28870.1-0.16180.46790.00180.07180.1815-0.00210.322834.9035-24.349935.6148
33.68340.3606-1.02243.08441.04711.84860.50370.04440.42770.2997-0.21-0.4577-0.29140.4379-0.20440.43590.02110.0420.26080.04610.400839.4668-24.866733.6109
42.3673-0.259-0.50491.04610.21051.9460.65560.39090.565-0.0252-0.25470.1188-0.1319-0.3453-0.2890.48170.09420.04930.26530.09090.300421.2362-24.121733.1105
54.544-0.1194-0.94961.7034-0.21023.3096-0.0081-0.4114-0.23180.3087-0.07470.40280.0699-0.17960.06080.5327-0.04930.0570.2858-0.02280.270911.9078-35.71856.527
63.7557-0.8453-2.58560.24321.59815.908-0.3074-0.6765-0.27760.39010.14250.11550.75620.49420.1550.5807-0.0143-0.05440.48110.08070.272722.0268-39.25956.6506
76.4904-1.2430.01114.9320.35585.07480.4464-0.1727-0.42280.5215-0.71661.55320.0434-1.74760.46950.5642-0.22260.14640.7438-0.12770.4418-0.4904-39.866463.4171
81.0610.5106-0.43444.3866-0.24291.5008-0.0665-0.098-0.16740.6426-0.0999-0.78220.30450.16640.11820.33740.0778-0.13530.2830.03650.408638.4097-61.138537.1992
97.346-0.96580.11922.26530.80283.7589-0.283-0.0717-0.36320.1907-0.2360.920.3486-0.82870.30390.2766-0.07030.09980.3939-0.1550.49636.8148-58.276828.7949
102.98790.54870.61456.4608-0.29191.4466-0.0230.00180.35160.73390.0576-0.8001-0.1969-0.127-0.15480.30550.1139-0.12320.4206-0.07110.343922.4712-15.13779.6216
113.77490.84310.5163.61720.2977.0012-0.154-0.3781-0.5831-0.16750.1170.25910.20310.01070.05320.1983-0.0156-0.01070.29590.09710.2788.6838-36.4268-1.9337
124.4380.39011.28281.60110.10432.71140.0343-0.0524-0.4215-0.07680.1874-0.34360.4020.2705-0.1610.26470.0403-0.06050.2096-0.01030.385819.7385-33.1668-3.0621
132.2741.72550.94163.38711.68523.2133-0.0963-0.0608-0.96650.01810.2522-0.03590.82390.704-0.13870.45010.1808-0.05420.3099-0.02630.533325.7052-43.4351-0.6633
141.04061.09350.12943.00482.06912.61370.4204-1.0712-0.42180.45130.0172-0.7275-0.1093-0.57130.51810.41740.1189-0.10960.46830.32060.25714.0511-33.085912.0173
153.58870.4329-2.02662.27930.52442.9880.2124-0.8744-1.97510.502-1.14750.25130.2955-1.0165-0.41560.4678-0.38240.04040.59840.44720.33210.2375-40.23864.1105
165.04820.00711.79153.6691-1.66761.8808-0.2037-0.7942-0.70020.3549-0.06240.94250.4661-1.21060.20850.2977-0.11560.03890.85290.02930.6231-15.2691-34.8093-3.3194
176.24560.09851.18692.8910.6331.935-0.1375-0.57770.8687-0.2082-0.15310.4562-0.3335-0.78480.25120.32560.037-0.10370.5392-0.1870.42-11.2989-21.7804-9.0983
181.5023-0.23670.10570.9365-0.67630.51680.1175-0.0440.83780.3567-0.16250.7462-0.0333-1.1082-0.06570.33250.1870.07080.9543-0.25140.7809-17.9384-15.9925-6.7895
198.45051.72782.36852.14650.97623.168-0.46540.53220.8776-0.5248-0.07040.7256-0.4218-0.17920.34050.31380.0638-0.08150.370.00980.3725-4.989-19.6098-11.8567
204.8544-1.5975-1.22891.8116-1.50613.11130.5565-0.20230.33990.65170.47640.5603-0.5302-0.41140.6973-0.03350.1535-0.02721.2971-0.62791.2432-27.8663-18.716-6.634
212.4012-1.45240.00656.1712-0.17480.4970.05450.335-0.2337-0.4987-0.2801-0.01350.0036-0.08170.1390.2435-0.04170.02760.2707-0.01110.232317.812-18.4737-9.1225
223.1406-0.6053-0.93021.78731.13492.38490.016-0.39880.28250.19720.1784-0.9472-0.19870.2052-0.08740.2566-0.0041-0.01080.3308-0.1240.719322.77822.8792.8783
232.1604-1.0302-0.28093.57521.06372.40.0745-0.03030.32730.09850.1687-1.0764-0.19820.2534-0.12610.2317-0.0084-0.02520.1904-0.04150.513521.46621.9088-0.2632
243.6967-0.26950.00894.2026-0.94878.15180.39340.61150.6991-0.02390.0069-0.3943-0.6191-0.1436-0.14480.37620.1121-0.0260.3881-0.04040.59519.575314.51773.4555
250.35180.945-0.90692.8799-1.37614.3582-0.4545-0.86561.04470.6120.61470.4065-0.4817-0.1582-0.32050.61270.27070.00670.5881-0.14570.5352-5.07389.05417.516
262.6575-0.9280.26063.0271-0.61552.9192-0.4266-0.9381-0.13190.66490.43210.09690.225-0.156-0.01690.53410.2006-0.00690.5562-0.07780.264-1.6349-4.309421.1573
272.80220.3025-0.36742.8282-0.70832.3337-0.328-1.0013-0.16460.76920.34010.32060.2926-0.22980.01270.53070.16990.05960.64380.02730.2593-5.5377-6.979923.1803
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 48 through 76 )A48 - 76
2X-RAY DIFFRACTION2chain 'A' and (resid 77 through 136 )A77 - 136
3X-RAY DIFFRACTION3chain 'A' and (resid 137 through 205 )A137 - 205
4X-RAY DIFFRACTION4chain 'A' and (resid 206 through 257 )A206 - 257
5X-RAY DIFFRACTION5chain 'A' and (resid 258 through 367 )A258 - 367
6X-RAY DIFFRACTION6chain 'A' and (resid 368 through 403 )A368 - 403
7X-RAY DIFFRACTION7chain 'A' and (resid 404 through 421 )A404 - 421
8X-RAY DIFFRACTION8chain 'B' and (resid 48 through 262 )B48 - 262
9X-RAY DIFFRACTION9chain 'B' and (resid 263 through 421 )B263 - 421
10X-RAY DIFFRACTION10chain 'C' and (resid 48 through 76 )C48 - 76
11X-RAY DIFFRACTION11chain 'C' and (resid 77 through 103 )C77 - 103
12X-RAY DIFFRACTION12chain 'C' and (resid 104 through 176 )C104 - 176
13X-RAY DIFFRACTION13chain 'C' and (resid 177 through 205 )C177 - 205
14X-RAY DIFFRACTION14chain 'C' and (resid 206 through 224 )C206 - 224
15X-RAY DIFFRACTION15chain 'C' and (resid 225 through 257 )C225 - 257
16X-RAY DIFFRACTION16chain 'C' and (resid 258 through 281 )C258 - 281
17X-RAY DIFFRACTION17chain 'C' and (resid 282 through 341 )C282 - 341
18X-RAY DIFFRACTION18chain 'C' and (resid 342 through 367 )C342 - 367
19X-RAY DIFFRACTION19chain 'C' and (resid 368 through 403 )C368 - 403
20X-RAY DIFFRACTION20chain 'C' and (resid 404 through 421 )C404 - 421
21X-RAY DIFFRACTION21chain 'D' and (resid 48 through 76 )D48 - 76
22X-RAY DIFFRACTION22chain 'D' and (resid 77 through 136 )D77 - 136
23X-RAY DIFFRACTION23chain 'D' and (resid 137 through 238 )D137 - 238
24X-RAY DIFFRACTION24chain 'D' and (resid 239 through 258 )D239 - 258
25X-RAY DIFFRACTION25chain 'D' and (resid 259 through 281 )D259 - 281
26X-RAY DIFFRACTION26chain 'D' and (resid 282 through 340 )D282 - 340
27X-RAY DIFFRACTION27chain 'D' and (resid 341 through 421 )D341 - 421

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