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- PDB-2wcz: 1.6A resolution structure of Archaeoglobus fulgidus Hjc, a Hollid... -

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Basic information

Entry
Database: PDB / ID: 2wcz
Title1.6A resolution structure of Archaeoglobus fulgidus Hjc, a Holliday junction resolvase from an archaeal hyperthermophile
ComponentsHOLLIDAY JUNCTION RESOLVASE
KeywordsHYDROLASE / TYPE II RESTRICTION ENDONUCLEASE / DNA BINDING PROTEIN / HOLLIDAY JUNCTION RESOLVASE
Function / homology
Function and homology information


crossover junction endodeoxyribonuclease / crossover junction DNA endonuclease activity / DNA recombination / DNA repair / magnesium ion binding / DNA binding
Similarity search - Function
Holliday junction resolvase Hjc / Holliday junction resolvase Hjc, archaeal / Archaeal holliday junction resolvase (hjc) / Trna Endonuclease; Chain: A, domain 1 - #10 / Trna Endonuclease; Chain: A, domain 1 / tRNA endonuclease-like domain superfamily / Restriction endonuclease type II-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Crossover junction endodeoxyribonuclease Hjc
Similarity search - Component
Biological speciesARCHAEOGLOBUS FULGIDUS (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsCarolis, C. / Koehler, C. / Sauter, C. / Basquin, J. / Suck, D. / Toeroe, I.
CitationJournal: To be Published
Title: 1.6 A Resolution Structure of Archaeoglobus Fulgidus Hjc, a Holliday Junction Resolvase from an Archaeal Hyperthermophile
Authors: Carolis, C. / Koehler, C. / Sauter, C. / Basquin, J. / Suck, D. / Toeroe, I.
History
DepositionMar 18, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 24, 2009Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 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 / 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 / _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: HOLLIDAY JUNCTION RESOLVASE
B: HOLLIDAY JUNCTION RESOLVASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,4194
Polymers31,3482
Non-polymers712
Water2,972165
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2100 Å2
ΔGint-32.8 kcal/mol
Surface area11890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.560, 37.560, 272.510
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.7801, 0.6249, 0.03114), (0.6256, 0.7795, 0.03171), (-0.004457, 0.04422, -0.999)
Vector: 25.15, -9.747, 46.65)

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Components

#1: Protein HOLLIDAY JUNCTION RESOLVASE / HJC


Mass: 15674.213 Da / Num. of mol.: 2 / Fragment: RESIDUES 2-136
Source method: isolated from a genetically manipulated source
Details: THE WILD-TYPE PROTEIN / Source: (gene. exp.) ARCHAEOGLOBUS FULGIDUS (archaea) / Strain: 4304 / Description: GERMAN COLLECTION OF MICROORGANISMS (DSM) / Plasmid: PETM12 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)PLYSS / References: UniProt: O28314
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 165 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsCHLORIDE (CL): CHLORIDE ANION
Sequence detailsG1, T2 (TEV PROTEASE SITE) AND G4 (NCOI RESTRICTION SITE) ARE CLONING ARTIFACTS

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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: 1.78 Å3/Da / Density % sol: 31 % / Description: NONE
Crystal growpH: 7.5 / Details: 20% PEG3350, 200MM MGCL2, pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.931
DetectorType: ADSC CCD / Detector: CCD / Date: Feb 27, 2007 / Details: SINGLE SILICON (111) MONOCHROMATOR
RadiationMonochromator: SINGLE SILICON (111) MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.931 Å / Relative weight: 1
ReflectionResolution: 1.65→50 Å / Num. obs: 27133 / % possible obs: 95.6 % / Observed criterion σ(I): 0 / Redundancy: 10.85 % / Biso Wilson estimate: 26.1 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 25.67
Reflection shellResolution: 1.65→1.69 Å / Redundancy: 4.46 % / Rmerge(I) obs: 0.69 / Mean I/σ(I) obs: 2.14 / % possible all: 77.6

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 1IPI, 1GEF

1ipi

1gef


Resolution: 1.65→32.299 Å / SU ML: 1.27 / σ(F): 0.03 / Phase error: 19.78 / Stereochemistry target values: ML
Details: N-TERMINAL RESIDUES UPTO A5 AND B8, C-TERMINAL RESIDUES FROM A129 AND B126 ARE DISORDERED. LOOP FROM B28 TO B31 MISSING DUE TO LACK OF DENSITY RESIDUES A30-A33 HAVE WEEK ELECTRON DENSITY, ...Details: N-TERMINAL RESIDUES UPTO A5 AND B8, C-TERMINAL RESIDUES FROM A129 AND B126 ARE DISORDERED. LOOP FROM B28 TO B31 MISSING DUE TO LACK OF DENSITY RESIDUES A30-A33 HAVE WEEK ELECTRON DENSITY, THEY HAVE BEEN MODELLED FROM A MUTANT STRUCTURE 2WCW
RfactorNum. reflection% reflection
Rfree0.224 1386 5.1 %
Rwork0.1806 --
obs0.1828 27122 95.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 64.462 Å2 / ksol: 0.447 e/Å3
Displacement parametersBiso mean: 42.2 Å2
Baniso -1Baniso -2Baniso -3
1-2.915 Å20 Å2-0 Å2
2--2.915 Å2-0 Å2
3----5.83 Å2
Refinement stepCycle: LAST / Resolution: 1.65→32.299 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1889 0 2 165 2056
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071967
X-RAY DIFFRACTIONf_angle_d1.0282660
X-RAY DIFFRACTIONf_dihedral_angle_d14.897739
X-RAY DIFFRACTIONf_chiral_restr0.068288
X-RAY DIFFRACTIONf_plane_restr0.004341
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6499-1.70890.31971080.27162096X-RAY DIFFRACTION78
1.7089-1.77730.2611220.22212300X-RAY DIFFRACTION88
1.7773-1.85820.22931170.19112480X-RAY DIFFRACTION94
1.8582-1.95610.19461330.17412555X-RAY DIFFRACTION97
1.9561-2.07870.19341400.16652643X-RAY DIFFRACTION99
2.0787-2.23910.20841620.16032609X-RAY DIFFRACTION100
2.2391-2.46440.21711570.16052647X-RAY DIFFRACTION100
2.4644-2.82080.21451580.16892702X-RAY DIFFRACTION100
2.8208-3.55320.19521330.16552756X-RAY DIFFRACTION100
3.5532-32.30480.24531560.19332948X-RAY DIFFRACTION99
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)
11.97311.635-1.35182.15280.45514.02860.05160.2029-0.5308-0.012-0.3115-0.28830.6036-0.64720.16390.2659-0.0244-0.03810.2029-0.02020.261510.46696.467227.0012
21.1361-0.3376-0.65090.4920.90992.0083-0.0198-0.0002-0.16740.01710.00270.089-0.0214-0.05390.02430.1433-0.0065-0.00030.08860.0030.196711.841212.365638.7321
37.3328-0.5158-1.02420.056-0.12992.1291-0.4497-0.6797-0.5859-0.13630.2452-0.11010.56480.20440.19480.3631-0.01310.00340.24470.03290.312224.7923.451921.0743
41.11370.319-0.06471.11830.27832.5973-0.06380.0599-0.2189-0.1776-0.0186-0.0117-0.2390.04090.06990.2821-0.03580.03390.1879-0.03540.249823.49068.20548.1639
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 6:36)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 37:128)
3X-RAY DIFFRACTION3(CHAIN B AND RESID 9:33)
4X-RAY DIFFRACTION4(CHAIN B AND RESID 34:125)

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