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- PDB-3m6k: Crystal Structure of N-terminal 44 kDa fragment of topoisomerase ... -

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Basic information

Entry
Database: PDB / ID: 3m6k
TitleCrystal Structure of N-terminal 44 kDa fragment of topoisomerase V in the presence of guanidium hydrochloride
ComponentsTopoisomerase V
KeywordsISOMERASE / helix-hairpin-helix / topoisomerase / conformational change in protein / guanidium hydrochloride
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 / DNA topoisomerase V, catalytic domain superfamily / : / : / Topoisomerase V, second (HhH)2 tandem domain / SAM domain-like / Topoisomerase V, HHH domain / Winged helix-turn-helix DNA-binding / RuvA domain 2-like ...DNA polymerase; domain 1 - #740 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #950 / DNA topoisomerase V, catalytic domain superfamily / : / : / Topoisomerase V, second (HhH)2 tandem domain / SAM domain-like / Topoisomerase V, HHH domain / 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
PHOSPHATE ION / Topoisomerase V
Similarity search - Component
Biological speciesMethanopyrus kandleri (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.6 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 15, 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)88,7495
Polymers88,4642
Non-polymers2853
Water54030
1
A: Topoisomerase V


Theoretical massNumber of molelcules
Total (without water)44,2321
Polymers44,2321
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Topoisomerase V
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,5174
Polymers44,2321
Non-polymers2853
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)70.090, 70.090, 349.630
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-386-

HOH

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

#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 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Rosetta (DE3) / References: UniProt: Q977W1
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 30 / 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: 2.43 Å3/Da / Density % sol: 49.36 %
Crystal growTemperature: 303 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 0.1 M phosphate-citrate pH 5, 0.2 M NaCl, 16% PEG 8000, 1M Guanidium hydrochloride, 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-2251CCDApr 23, 2008beryllium lenses
RAYONIX MX-2252CCDApr 23, 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: 2.6→29.5 Å / Num. all: 28160 / Num. obs: 28151 / % possible obs: 99.9 % / Redundancy: 8.1 % / Biso Wilson estimate: 42.1 Å2 / Rmerge(I) obs: 0.079 / Rsym value: 0.074 / Net I/σ(I): 19
Reflection shellResolution: 2.6→2.72 Å / Redundancy: 6 % / Rmerge(I) obs: 0.572 / Mean I/σ(I) obs: 3.2 / Num. unique all: 3331 / Rsym value: 0.522 / % possible all: 100

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Processing

Software
NameVersionClassification
MD2-microdiffractometerdata collection
SHARPphasing
REFMAC5.2.0019refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.6→29.14 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.898 / SU B: 28.292 / SU ML: 0.279 / Cross valid method: THROUGHOUT / ESU R: 0.963 / ESU R Free: 0.363 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28883 1438 5.1 %RANDOM
Rwork0.24132 ---
all0.24371 28151 --
obs0.24371 26710 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 55.918 Å2
Baniso -1Baniso -2Baniso -3
1-2.02 Å20 Å20 Å2
2--2.02 Å20 Å2
3----4.04 Å2
Refinement stepCycle: LAST / Resolution: 2.6→29.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5967 0 15 30 6012
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0226092
X-RAY DIFFRACTIONr_bond_other_d0.0020.024314
X-RAY DIFFRACTIONr_angle_refined_deg1.2031.988241
X-RAY DIFFRACTIONr_angle_other_deg0.893.00110376
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5385722
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.32622.822326
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.444151102
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8281581
X-RAY DIFFRACTIONr_chiral_restr0.0670.2906
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.026728
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021297
X-RAY DIFFRACTIONr_nbd_refined0.2260.21527
X-RAY DIFFRACTIONr_nbd_other0.1850.24572
X-RAY DIFFRACTIONr_nbtor_refined0.1790.23020
X-RAY DIFFRACTIONr_nbtor_other0.0850.23361
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.150.2148
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2020.239
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2630.286
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.160.27
X-RAY DIFFRACTIONr_mcbond_it0.5221.54780
X-RAY DIFFRACTIONr_mcbond_other0.0861.51453
X-RAY DIFFRACTIONr_mcangle_it0.5825886
X-RAY DIFFRACTIONr_scbond_it0.96832805
X-RAY DIFFRACTIONr_scangle_it1.4644.52355
Refine LS restraints NCS

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

Ens-IDNumberTypeRms dev position (Å)Weight position
13747medium positional0.560.5
21283medium positional0.680.5
13747medium thermal0.442
21283medium thermal0.442
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.451 93 -
Rwork0.366 1897 -
obs-1897 100 %
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)
12.9583-0.25171.63311.167-0.30770.92640.31080.1228-0.44770.4169-0.0102-0.24310.0472-0.0382-0.30060.0868-0.0745-0.12940.0277-0.0727-0.036233.42354.46330.655
21.9926-1.2413-0.50371.07520.09440.2866-0.535-1.13160.38410.24990.4697-0.4251-0.07560.20880.0653-0.0276-0.00410.00170.0273-0.019-0.011951.72443.31625.416
33.0438-0.6794-0.57081.5150.68015.00310.23460.41220.0134-0.2364-0.079-0.20410.20310.7726-0.15560.1147-0.00040.1592-0.0019-0.0633-0.064256.65486.92111.267
41.5646-0.10920.23533.7517-0.62362.51760.1448-0.143-0.1504-0.0835-0.0435-0.71680.03160.9569-0.1013-0.03440.0250.0292-0.0241-0.0348-0.045876.90676.50613.481
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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