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Basic information

Entry
Database: PDB / ID: 2wiz
TitleCrystal structures of Holliday junction resolvases from Archaeoglobus fulgidus bound to DNA substrate
Components
  • (HALF-JUNCTION) x 2
  • ARCHAEAL HJC
KeywordsHYDROLASE/DNA / HYDROLASE DNA COMPLEX / TYPE II RESTRICTION ENDONUCLEASE / HOLLIDAY JUNCTION RESOLVASE / HYDROLASE / DNA BINDING PROTEIN / HYDROLASE-DNA complex
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
DNA / DNA (> 10) / Crossover junction endodeoxyribonuclease Hjc
Similarity search - Component
Biological speciesARCHAEOGLOBUS FULGIDUS DSM 4304 (archaea)
SYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsCarolis, C. / Koehler, C. / Sauter, C. / Basquin, J. / Suck, D. / Toeroe, I.
CitationJournal: To be Published
Title: Crystal Structures of Holliday Junction Resolvases from Archaeoglobus Fulgidus Bound to DNA Substrate
Authors: Carolis, C. / Koehler, C. / Sauter, C. / Basquin, J. / Suck, D. / Toeroe, I.
History
DepositionMay 18, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 26, 2009Provider: repository / Type: Initial release
Revision 1.1Sep 30, 2015Group: Derived calculations / Refinement description ...Derived calculations / Refinement description / Source and taxonomy / Version format compliance
Revision 1.2Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ARCHAEAL HJC
B: ARCHAEAL HJC
C: HALF-JUNCTION
D: HALF-JUNCTION


Theoretical massNumber of molelcules
Total (without water)43,6174
Polymers43,6174
Non-polymers00
Water00
1
A: ARCHAEAL HJC
B: ARCHAEAL HJC
C: HALF-JUNCTION
D: HALF-JUNCTION

A: ARCHAEAL HJC
B: ARCHAEAL HJC
C: HALF-JUNCTION
D: HALF-JUNCTION


Theoretical massNumber of molelcules
Total (without water)87,2358
Polymers87,2358
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_554-y,-x,-z-1/31
Buried area11780 Å2
ΔGint-85.27 kcal/mol
Surface area35890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.650, 122.650, 125.510
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.7397, -0.3324, 0.5851), (-0.2903, -0.6269, -0.723), (0.6071, -0.7047, 0.3672)
Vector: 69.45, -63.22, -63.03)

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Components

#1: Protein ARCHAEAL HJC


Mass: 15674.213 Da / Num. of mol.: 2 / Fragment: RESIDUES 2-136
Source method: isolated from a genetically manipulated source
Details: N-TERMINUS CONTAINS EXTRA RESIDUES AS A RESULT OF CLONING PROCEDURE
Source: (gene. exp.) ARCHAEOGLOBUS FULGIDUS DSM 4304 (archaea)
Description: GERMAN COLLECTION OF MICROORGANISMS (DSM) / Plasmid: PETM12 / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Variant (production host): PLYSS / References: UniProt: O28314
#2: DNA chain HALF-JUNCTION


Mass: 6078.943 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: SYNTHESIZED BY METABION GMBH, MARTINSRIED, GERMANY / Source: (synth.) SYNTHETIC CONSTRUCT (others)
#3: DNA chain HALF-JUNCTION


Mass: 6190.002 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: SYNTHESIZED BY METABION GMBH, MARTINSRIED, GERMANY / Source: (synth.) SYNTHETIC CONSTRUCT (others)
Sequence detailsINSERTED RESIDUES GTMG AT THE N-TERMINUS ARE A RESULT OF CLONING PROCEDURE

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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: 3.48 Å3/Da / Density % sol: 64.43 % / Description: NONE
Crystal growpH: 7.5 / Details: 20% W/V PEG 3350, 0.2 M AMMONIUM ACETATE, pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 20, 2007 / Details: PT COATED MIRRORS
RadiationMonochromator: SI (111) MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 3.3→50 Å / Num. obs: 8420 / % possible obs: 95 % / Observed criterion σ(I): 0 / Redundancy: 9.34 % / Biso Wilson estimate: 99.85 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 16.18
Reflection shellResolution: 3.3→3.39 Å / Redundancy: 9.67 % / Rmerge(I) obs: 1.03 / Mean I/σ(I) obs: 2.69 / % possible all: 86.5

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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 ENTRY 2WCZ

2wcz


Resolution: 3.3→34.56 Å / SU ML: 0.4 / σ(F): 0.06 / Phase error: 25.33 / Stereochemistry target values: ML
Details: WATSON-CRICK BASE PAIRING WAS RESTRAINED BY GEOMETRY_RESTRAINTS. EDITS WITH BOND PARAMETERS DERIVED FROM DNA-RNA_RESTRAINTS.DEF FILE OF CNS. AS THE HOLLIDAY JUNCTION SITS ON A TWO-FOLD ...Details: WATSON-CRICK BASE PAIRING WAS RESTRAINED BY GEOMETRY_RESTRAINTS. EDITS WITH BOND PARAMETERS DERIVED FROM DNA-RNA_RESTRAINTS.DEF FILE OF CNS. AS THE HOLLIDAY JUNCTION SITS ON A TWO-FOLD SYMMETRY AXIS THE HALF JUNCTION HAS BEEN MODELED USING ONE OF THE CONTINUOUS STRAND (STRAND 2) AND ITS COMPLEMENTARY STRAND AS THE CROSSOVER STRAND. THUS THE CROSSOVER STRAND IN THE HALF-JUNCTION IS A CHIMERA OF THE REAL SEQUENCES (STRANDS 1 AND 3).
RfactorNum. reflection% reflection
Rfree0.2832 403 4.8 %
Rwork0.2043 --
obs0.2079 8408 95.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 92.12 Å2 / ksol: 0.337 e/Å3
Displacement parametersBiso mean: 119.35 Å2
Baniso -1Baniso -2Baniso -3
1--2.4645 Å20 Å20 Å2
2---2.4645 Å20 Å2
3---4.929 Å2
Refinement stepCycle: LAST / Resolution: 3.3→34.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1977 814 0 0 2791
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063033
X-RAY DIFFRACTIONf_angle_d1.054138
X-RAY DIFFRACTIONf_dihedral_angle_d22.0991142
X-RAY DIFFRACTIONf_chiral_restr0.053453
X-RAY DIFFRACTIONf_plane_restr0.004391
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3001-3.77710.35131290.2752450X-RAY DIFFRACTION90
3.7771-4.75680.26911280.19352686X-RAY DIFFRACTION97
4.7568-34.56210.26651460.18932869X-RAY DIFFRACTION98
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)
11.9133-0.531-0.66013.55022.25311.60770.71460.27660.0367-2.176-0.7871-1.2151-1.22050.1710.00150.6146-0.1771-0.03840.81480.05640.739450.9972-33.9319-7.3414
20.10030.12940.06510.5168-0.27820.2552.5699-1.326-0.4571-1.2909-0.1163-0.4708-0.1187-0.12240.02511.946-0.0706-0.351.76940.1972.329734.6458-42.6841-8.6325
35.491-0.1293-2.21926.62573.00767.38010.027-0.3276-0.00170.2806-0.05410.6422-0.1214-0.3431-0.00030.4024-0.0143-0.02940.57550.10340.456743.0319-31.86384.57
41.0987-0.6446-0.70111.53121.63721.6241-0.2674-0.0427-0.4426-0.3979-0.83150.1195-1.1749-1.2543-0.00080.6651-0.0801-0.09941.17210.16370.994540.34-50.1069-11.6594
54.42570.7969-0.73466.24932.19787.2009-0.56890.2437-0.1263-0.33060.239-0.09680.77310.39560.00060.709-0.0971-0.11990.75690.13620.697451.6745-57.8344-14.0842
60.47640.0103-0.39760.2212-0.17770.47120.78411.1542-0.66173.61281.2142-0.36422.7671-0.8396-0.00751.6442-0.0379-0.02931.0520.29761.12145.0578-63.4702-1.9351
70.2583-0.28120.24570.2283-0.17250.19660.16811.0341-1.54343.2357-1.1224-0.78092.3312-0.26560.01532.76030.1016-0.09732.1909-0.12531.823640.1539-46.5477-35.1708
82.51961.53661.99231.55620.60651.322-0.10350.11230.38090.3725-0.64060.95260.457-1.494-0.00041.68410.04090.14761.40570.05361.411831.8669-27.75-16.6139
90.08450.0547-0.01210.0637-0.09350.2891-0.0916-1.4341.26722.2043-0.18241.7422-1.14090.1855-0.00932.47640.75460.26482.9551-0.04491.413321.3275-13.89643.295
100.1837-0.1558-0.00650.1119-0.01170.0089-0.7459-2.7122-1.2818-0.3544-2.37715.03271.6003-2.63870.00551.721-0.1831-0.11192.3304-0.48732.669526.023-18.8966-48.8758
110.76051.3460.33191.47630.17851.0155-1.6339-0.9510.8345-0.03830.40220.4352-0.5861-2.20450.00041.24710.1499-0.23461.2953-0.02831.426333.599-16.8479-29.9619
120.4425-0.0985-0.10850.8531-0.10750.47280.88360.8482-0.0688-0.1814-0.5498-0.2051-1.2038-3.81390.00042.1874-0.13080.1331.6474-0.19861.495533.0164-41.2886-30.7617
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 6:27)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 28:35)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 36:128)
4X-RAY DIFFRACTION4(CHAIN B AND RESID 6:32)
5X-RAY DIFFRACTION5(CHAIN B AND RESID 33:118)
6X-RAY DIFFRACTION6(CHAIN B AND RESID 119:127)
7X-RAY DIFFRACTION7(CHAIN C AND RESID 1:4)
8X-RAY DIFFRACTION8(CHAIN C AND RESID 5:16)
9X-RAY DIFFRACTION9(CHAIN C AND RESID 17:20)
10X-RAY DIFFRACTION10(CHAIN D AND RESID 1:4)
11X-RAY DIFFRACTION11(CHAIN D AND RESID 5:12)
12X-RAY DIFFRACTION12(CHAIN D AND RESID 13:20)

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