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- PDB-3m6z: Crystal structure of an N-terminal 44 kDa fragment of topoisomera... -

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Basic information

Entry
Database: PDB / ID: 3m6z
TitleCrystal structure of an N-terminal 44 kDa fragment of topoisomerase V in the presence of guanidium hydrochloride
ComponentsTopoisomerase V
KeywordsISOMERASE / helix-hairpin-helix / topoisomerase / conformational changes in protein
Function / homology
Function and homology information


isomerase activity / DNA repair / DNA binding / metal ion binding
Similarity search - Function
DNA polymerase; domain 1 - #740 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #950 / : / Topoisomerase V, second (HhH)2 tandem domain / DNA topoisomerase V, catalytic domain superfamily / Winged helix-turn-helix DNA-binding / RuvA domain 2-like / Helix-hairpin-helix domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix-hairpin-helix DNA-binding motif, class 1 ...DNA polymerase; domain 1 - #740 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #950 / : / Topoisomerase V, second (HhH)2 tandem domain / DNA topoisomerase V, catalytic domain superfamily / Winged helix-turn-helix DNA-binding / RuvA domain 2-like / Helix-hairpin-helix domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix-hairpin-helix DNA-binding motif, class 1 / Helix-hairpin-helix DNA-binding motif class 1 / Helix non-globular / Special / DNA polymerase; domain 1 / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
GUANIDINE / PHOSPHATE ION / Topoisomerase V
Similarity search - Component
Biological speciesMethanopyrus kandleri (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.4 Å
AuthorsRajan, R. / Taneja, B. / Mondragon, A.
CitationJournal: Structure / Year: 2010
Title: Structures of minimal catalytic fragments of topoisomerase v reveals conformational changes relevant for DNA binding.
Authors: Rajan, R. / Taneja, B. / Mondragon, A.
History
DepositionMar 16, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 4, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Topoisomerase V
B: Topoisomerase V
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,45017
Polymers88,4642
Non-polymers98615
Water10,323573
1
A: Topoisomerase V
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,75510
Polymers44,2321
Non-polymers5239
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Topoisomerase V
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,6957
Polymers44,2321
Non-polymers4636
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)63.640, 80.110, 137.220
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21A
12B
22A

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1114B4 - 280
2114A4 - 280
1124B281 - 374
2124A281 - 374

NCS ensembles :
ID
1
2

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Topoisomerase V /


Mass: 44232.012 Da / Num. of mol.: 2 / Fragment: N-terminal 44 kDa fragment (Topo-44)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanopyrus kandleri (archaea) / Strain: AV19 / Gene: MK1436, top5, Topoisomerase V / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Rosetta (DE3) / References: UniProt: Q977W1

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Non-polymers , 5 types, 588 molecules

#2: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-GAI / GUANIDINE / Guanidine


Mass: 59.070 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: CH5N3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 573 / 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: 1.98 Å3/Da / Density % sol: 37.83 %
Crystal growTemperature: 303 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.1 M phosphate citrate pH 5.5, 0.15M sodium sulfate, 0.01M MgCl2, 1 M guanidium hydrochloride, 28% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 303K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
1781
2781
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 21-ID-G10.97872
SYNCHROTRONAPS 21-ID-D20.97915
Detector
TypeIDDetectorDateDetails
RAYONIX MX-2251CCDJul 24, 2008beryllium lenses
RAYONIX MX-2252CCDJul 24, 2008
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1siliconSINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.978721
20.979151
ReflectionResolution: 1.4→28.9 Å / Num. all: 138158 / Num. obs: 136662 / % possible obs: 98.8 % / Redundancy: 8.5 % / Rmerge(I) obs: 0.048 / Rsym value: 0.045 / Net I/σ(I): 27.5
Reflection shellResolution: 1.4→1.46 Å / Redundancy: 7.9 % / Rmerge(I) obs: 0.405 / Mean I/σ(I) obs: 5.3 / Rsym value: 0.379 / % possible all: 95.5

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Processing

Software
NameVersionClassification
MD2-microdiffractometerdata collection
SHARPphasing
REFMAC5.2.0019refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: SAD / Resolution: 1.4→28.9 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.958 / SU B: 1.897 / SU ML: 0.038 / Cross valid method: THROUGHOUT / ESU R: 0.068 / ESU R Free: 0.066 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18424 6859 5 %RANDOM
Rwork0.16491 ---
obs0.16587 129802 98.68 %-
all-136662 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.181 Å2
Baniso -1Baniso -2Baniso -3
1-0.52 Å20 Å20 Å2
2---0.32 Å20 Å2
3----0.2 Å2
Refinement stepCycle: LAST / Resolution: 1.4→28.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6056 0 52 573 6681
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0217757
X-RAY DIFFRACTIONr_bond_other_d0.0020.025612
X-RAY DIFFRACTIONr_angle_refined_deg1.1951.97810603
X-RAY DIFFRACTIONr_angle_other_deg0.9013.00113490
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7095990
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.87822.409440
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.794151456
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.47615127
X-RAY DIFFRACTIONr_chiral_restr0.0720.21095
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.029168
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021806
X-RAY DIFFRACTIONr_nbd_refined0.2250.21814
X-RAY DIFFRACTIONr_nbd_other0.2020.26329
X-RAY DIFFRACTIONr_nbtor_refined0.1770.23777
X-RAY DIFFRACTIONr_nbtor_other0.0820.24075
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1380.2485
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2660.251
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2420.2163
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1460.267
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7781.56134
X-RAY DIFFRACTIONr_mcbond_other0.1751.51794
X-RAY DIFFRACTIONr_mcangle_it0.89227544
X-RAY DIFFRACTIONr_scbond_it1.65133593
X-RAY DIFFRACTIONr_scangle_it2.1814.53059
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: B / Refine-ID: X-RAY DIFFRACTION

Ens-IDNumberTypeRms dev position (Å)Weight position
13299medium positional0.580.5
21004medium positional0.720.5
13299medium thermal0.932
21004medium thermal0.912
LS refinement shellResolution: 1.4→1.436 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.221 487 -
Rwork0.193 8967 -
obs--93.51 %
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)
10.3087-0.04840.14070.54970.1250.2242-0.0093-0.00190.015-0.07660.0058-0.0037-0.0181-0.01470.0035-0.0158-0.00750.0025-0.03650.0061-0.024233.42354.46330.655
20.47940.01260.28970.69890.5391.59160.02790.1403-0.0148-0.06090.0764-0.0735-0.02890.2435-0.1042-0.0595-0.00520.00390.0073-0.0215-0.040351.72443.31625.416
30.434-0.0332-0.080.5157-0.14970.7313-0.0083-0.0296-0.016-0.00820.0162-0.00230.02180.0143-0.0079-0.0282-0.00180.0054-0.01370.0083-0.019456.65486.92111.267
41.2485-0.4166-0.23670.41150.2331.30320.0655-0.0216-0.083-0.0072-0.01080.01290.0820.0075-0.05480.013-0.0206-0.0252-0.006-0.0017-0.024776.90676.50613.481
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 280
2X-RAY DIFFRACTION2A281 - 378
3X-RAY DIFFRACTION3B4 - 280
4X-RAY DIFFRACTION4B281 - 378

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