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- PDB-1mx0: Structure of topoisomerase subunit -

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Basic information

Entry
Database: PDB / ID: 1mx0
TitleStructure of topoisomerase subunit
ComponentsType II DNA topoisomerase VI subunit BType II topoisomerase
KeywordsISOMERASE / GHKL ATPase / topoisomerase
Function / homology
Function and homology information


DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) complex / DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity / DNA topoisomerase (ATP-hydrolysing) / DNA unwinding involved in DNA replication / DNA topological change / DNA binding / ATP binding / identical protein binding
Similarity search - Function
DNA topoisomerase VI, subunit B / DNA topoisomerase VI, subunit B, transducer / Topoisomerase VI B subunit, transducer / NFACT N-terminal and middle domains / Helicase, Ruva Protein; domain 3 - #50 / Ribosomal Protein S5; domain 2 - #10 / Ribosomal Protein S5; domain 2 / Histidine kinase-like ATPase, C-terminal domain / Heat Shock Protein 90 / Helicase, Ruva Protein; domain 3 ...DNA topoisomerase VI, subunit B / DNA topoisomerase VI, subunit B, transducer / Topoisomerase VI B subunit, transducer / NFACT N-terminal and middle domains / Helicase, Ruva Protein; domain 3 - #50 / Ribosomal Protein S5; domain 2 - #10 / Ribosomal Protein S5; domain 2 / Histidine kinase-like ATPase, C-terminal domain / Heat Shock Protein 90 / Helicase, Ruva Protein; domain 3 / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Type 2 DNA topoisomerase 6 subunit B
Similarity search - Component
Biological speciesSulfolobus shibatae (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å
AuthorsCorbett, K.D. / Berger, J.M.
CitationJournal: Embo J. / Year: 2003
Title: Structure of the topoisomerase VI-B subunit: implications for type II topoisomerase mechanism and evolution
Authors: Corbett, K.D. / Berger, J.M.
History
DepositionOct 1, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 7, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Remark 999SEQUENCE Authors state the database/coordinate conflicts for residues 303 and 435 of chains ...SEQUENCE Authors state the database/coordinate conflicts for residues 303 and 435 of chains A,B,C,D,E and F are due to strain-specific sequence differences between the protein in the entry and the database sequence.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Type II DNA topoisomerase VI subunit B
B: Type II DNA topoisomerase VI subunit B
C: Type II DNA topoisomerase VI subunit B
D: Type II DNA topoisomerase VI subunit B
E: Type II DNA topoisomerase VI subunit B
F: Type II DNA topoisomerase VI subunit B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)327,23119
Polymers324,0256
Non-polymers3,20613
Water14,610811
1
A: Type II DNA topoisomerase VI subunit B
B: Type II DNA topoisomerase VI subunit B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,0696
Polymers108,0082
Non-polymers1,0614
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8360 Å2
ΔGint-35 kcal/mol
Surface area36420 Å2
MethodPISA
2
C: Type II DNA topoisomerase VI subunit B
D: Type II DNA topoisomerase VI subunit B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,0927
Polymers108,0082
Non-polymers1,0845
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8550 Å2
ΔGint-48 kcal/mol
Surface area37520 Å2
MethodPISA
3
E: Type II DNA topoisomerase VI subunit B
F: Type II DNA topoisomerase VI subunit B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,0696
Polymers108,0082
Non-polymers1,0614
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8160 Å2
ΔGint-35 kcal/mol
Surface area36440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)146.655, 219.192, 106.921
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein
Type II DNA topoisomerase VI subunit B / Type II topoisomerase


Mass: 54004.164 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus shibatae (archaea) / Gene: top6b / Production host: Escherichia coli (E. coli) / References: UniProt: O05207, EC: 5.99.1.3
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 811 / 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: 2.66 Å3/Da / Density % sol: 53.33 %
Crystal growTemperature: 298 K / Method: microbatch / pH: 5.5
Details: PEG 3000, Sodium Citrate, Magnesium Chloride, AMP-PNP, pH 5.5, Microbatch, temperature 298K
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 7 / Method: batch method
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
120 mMTris-HCl11pH7.0
2100 mM11NaCl
312 mg/mlprotein11
420 %PEG300011
5100 mMTris-HCl12pH7.0
6200 mM12Ca(OAc)2

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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 4 / Detector: CCD / Date: Jan 31, 2001
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.3→20 Å / Num. all: 153022 / Num. obs: 150115 / % possible obs: 98.1 % / Observed criterion σ(F): 4.1 / Observed criterion σ(I): 4.1 / Rsym value: 0.111 / Net I/σ(I): 10
Reflection shellResolution: 2.3→2.38 Å / Mean I/σ(I) obs: 2.24 / Num. unique all: 13432 / Rsym value: 0.413 / % possible all: 88.7
Reflection
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 20 Å / Num. obs: 149698 / % possible obs: 96.1 % / Num. measured all: 2006747 / Rmerge(I) obs: 0.111
Reflection shell
*PLUS
% possible obs: 88.9 % / Rmerge(I) obs: 0.473 / Mean I/σ(I) obs: 1.8

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
REFMAC5refinement
RefinementMethod to determine structure: MAD / Resolution: 2.3→20 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.883 / SU B: 8.174 / SU ML: 0.199 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.365 / ESU R Free: 0.257 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: Bound nucleotide and MG2+ ions are assigned residue numbers 500 and 501. Residue G1 (NA ION) assigned as NA+ on the basis of coordination. Geometry, short hydrogen bond distances, and low ...Details: Bound nucleotide and MG2+ ions are assigned residue numbers 500 and 501. Residue G1 (NA ION) assigned as NA+ on the basis of coordination. Geometry, short hydrogen bond distances, and low refined b-factor of water when placed in this location.
RfactorNum. reflection% reflectionSelection details
Rfree0.26327 12535 8.4 %RANDOM
Rwork0.21447 ---
all0.21854 150115 --
obs0.21854 137434 98.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 25.95 Å2
Baniso -1Baniso -2Baniso -3
1-0.31 Å20 Å20 Å2
2--0.55 Å20 Å2
3----0.86 Å2
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22053 0 193 811 23057
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.02222729
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4241.98230805
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.24932741
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.603154417
X-RAY DIFFRACTIONr_chiral_restr0.1050.23429
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0216914
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2720.311373
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1691962
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2910.3113
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2720.517
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.7351.513787
X-RAY DIFFRACTIONr_mcangle_it1.397222497
X-RAY DIFFRACTIONr_scbond_it2.31738942
X-RAY DIFFRACTIONr_scangle_it3.8494.58308
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.359 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.307 791
Rwork0.257 8944
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)
10.1283-0.05930.02340.72110.10890.3938-0.0303-0.0138-0.0194-0.01660.07070.0005-0.0958-0.013-0.04040.35550.00460.02580.30740.00740.326948.939438.313923.4422
22.8612-0.24280.44552.25881.47043.7980.14460.1101-0.06330.24350.1955-0.21570.27040.347-0.340.27570.068-0.08320.2997-0.07810.31273.034116.963444.227
31.4857-0.4459-0.37061.4840.45041.74670.0025-0.1996-0.16940.19270.07150.1613-0.0218-0.2014-0.0740.32440.0320.05180.36080.06890.302940.35729.079449.8905
40.43910.08420.04591.0768-0.04740.26190.02010.0094-0.05570.05820.0962-0.07030.0326-0.0056-0.11630.30560.0116-0.02880.28120.00310.362352.61171.536625.1796
52.73592.0486-0.42484.3386-1.11692.4712-0.16130.0657-0.0424-0.39770.1544-0.03230.0172-0.00040.0070.313-0.01710.01390.27590.01240.269338.49223.4858-2.6595
61.63210.1178-0.26631.2672-0.45980.9132-0.0004-0.0909-0.1030.09450.0940.1508-0.0693-0.0926-0.09370.27510.00820.00240.30790.06660.36525.39679.12125.6661
70.25310.0985-0.38740.3492-0.0810.7633-0.0555-0.0549-0.00590.06840.05580.02630.04290.1354-0.00020.31450.0512-0.00660.40610.01170.293148.691546.14743.0581
82.27050.0954-1.07221.4593-1.09512.8878-0.04620.0015-0.0684-0.0607-0.0853-0.01390.17770.11440.13150.29050.0645-0.00070.3109-0.00210.2898157.489127.081711.375
92.03510.6939-0.43790.69630.14040.17780.0181-0.0269-0.01160.0744-0.06690.11120.02220.02060.04880.31590.01070.02140.32780.01610.3378126.537632.739727.8624
100.4071-0.14620.04580.4277-0.07860.63540.0062-0.0064-0.0183-0.067-0.01770.0077-0.02740.07950.01150.32720.0242-0.02430.3375-0.00140.3061149.008757.45237.6374
112.3417-0.36461.16091.51670.13132.0852-0.0266-0.15170.05290.00280.0351-0.0067-0.19260.1415-0.00850.3263-0.0236-0.01020.3314-0.06110.2601151.559177.615540.0348
121.7609-0.43870.42550.85-0.07031.60940.0119-0.0542-0.06380.01890.04950.0809-0.0407-0.1724-0.06140.31010.0256-0.01330.34460.00860.2886124.853366.187221.1324
130.8641-0.02560.27770.43510.18660.50580.0620.1355-0.06530.01890.0196-0.0050.0110.0702-0.08160.33220.0262-0.01540.3279-0.01370.3211119.694735.7404-32.0975
144.4131-2.96680.48785.74350.33392.60450.2985-0.1628-0.37020.07050.0808-0.22190.1360.0875-0.37930.24090.0386-0.22830.15520.01460.4373139.286713.8784-7.5551
152.0442-0.8380.12361.89160.76740.91160.0052-0.345-0.17170.16240.07780.07350.0579-0.0772-0.0830.3073-0.0086-0.01550.36440.07870.2863110.77533.1981-4.9806
161.83140.92460.77050.76010.09511.14140.73140.0733-0.79810.2120.0082-0.46150.58610.119-0.73960.57950.02-0.53860.00560.01050.7162115.01820.5892-22.9146
176.5232.5525-0.03491.51780.24382.00340.08111.118-0.69690.05470.2312-0.2114-0.0960.1077-0.31240.250.0923-0.05750.4763-0.23730.2851104.474519.4135-54.5413
184.46820.6011-0.72421.1986-0.45752.97820.4724-0.3212-0.4550.2709-0.0096-0.01840.2273-0.3636-0.46280.3838-0.1396-0.17240.23820.16280.346989.641712.9344-24.1531
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA4 - 2296 - 231
2X-RAY DIFFRACTION2AA230 - 310232 - 312
3X-RAY DIFFRACTION3AA311 - 467313 - 469
4X-RAY DIFFRACTION4BB4 - 2296 - 231
5X-RAY DIFFRACTION5BB230 - 310232 - 312
6X-RAY DIFFRACTION6BB311 - 458313 - 460
7X-RAY DIFFRACTION7CC4 - 2296 - 231
8X-RAY DIFFRACTION8CC230 - 310232 - 312
9X-RAY DIFFRACTION9CC311 - 469313 - 471
10X-RAY DIFFRACTION10DD4 - 2296 - 231
11X-RAY DIFFRACTION11DD230 - 310232 - 312
12X-RAY DIFFRACTION12DD311 - 464313 - 466
13X-RAY DIFFRACTION13EE4 - 2296 - 231
14X-RAY DIFFRACTION14EE230 - 310232 - 312
15X-RAY DIFFRACTION15EE311 - 461313 - 463
16X-RAY DIFFRACTION16FF4 - 2296 - 231
17X-RAY DIFFRACTION17FF230 - 310232 - 312
18X-RAY DIFFRACTION18FF311 - 463313 - 465
Refinement
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 20 Å / Rfactor Rfree: 0.263 / Rfactor Rwork: 0.214
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.013
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.423

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