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- PDB-2wj0: Crystal structures of Holliday junction resolvases from Archaeogl... -

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Basic information

Entry
Database: PDB / ID: 2wj0
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
COBALT HEXAMMINE(III) / DNA / DNA (> 10) / Crossover junction endodeoxyribonuclease Hjc
Similarity search - Component
Biological speciesARCHAEOGLOBUS FULGIDUS (archaea)
SYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 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 1.1Oct 28, 2015Group: Derived calculations / Non-polymer description ...Derived calculations / Non-polymer description / Other / Refinement description / Source and taxonomy / Version format compliance
Revision 1.2Dec 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: ARCHAEAL HJC
B: ARCHAEAL HJC
C: HALF-JUNCTION
D: HALF-JUNCTION
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,2515
Polymers46,0904
Non-polymers1611
Water1267
1
A: ARCHAEAL HJC
B: ARCHAEAL HJC
C: HALF-JUNCTION
D: HALF-JUNCTION
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)92,50210
Polymers92,1808
Non-polymers3222
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation9_555-x,-x+y,-z1
Buried area14050 Å2
ΔGint-91.5 kcal/mol
Surface area37640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.980, 110.980, 150.500
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.08295, -0.2035, -0.9756), (-0.2384, -0.9546, 0.1788), (-0.9676, 0.2177, -0.1277)
Vector: 31.12, -99.87, 57.28)

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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 (archaea) / Strain: 4304 / Description: GERMAN COLLECTION OF MICROORGANISMS (DSM) / Plasmid: PETM12 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS / References: UniProt: O28314
#2: DNA chain HALF-JUNCTION


Mass: 7370.753 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: 7370.753 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: SYNTHESIZED BY METABION GMBH, MARTINSRIED, GERMANY / Source: (synth.) SYNTHETIC CONSTRUCT (others)
#4: Chemical ChemComp-NCO / COBALT HEXAMMINE(III)


Mass: 161.116 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CoH18N6
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: H2O
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: 3.2 Å3/Da / Density % sol: 61.3 % / Description: NONE
Crystal growpH: 7.5
Details: 20% W/V PEG 3350, 0.2 M TRI-LITHIUM CITRATE TETRAHYDRATE, 0.01M HEXAAMINE- COBALT(III) CHLORIDE, 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: Oct 4, 2008 / 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: 3.1→50 Å / Num. obs: 9975 / % possible obs: 95.1 % / Observed criterion σ(I): 0 / Redundancy: 11.86 % / Biso Wilson estimate: 68.13 Å2 / Rmerge(I) obs: 0.14 / Net I/σ(I): 15.18
Reflection shellResolution: 3.1→3.18 Å / Redundancy: 12.41 % / Rmerge(I) obs: 0.89 / Mean I/σ(I) obs: 2.89 / % possible all: 86.3

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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 2WIZ

2wiz


Resolution: 3.1→48.056 Å / SU ML: 0.42 / σ(F): 0.02 / Phase error: 25.94 / 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
Rfree0.2781 484 4.8 %
Rwork0.2015 --
obs0.2051 9975 95.17 %
Solvent computationShrinkage radii: 1.4 Å / VDW probe radii: 1.4 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 74.706 Å2 / ksol: 0.342 e/Å3
Displacement parametersBiso mean: 86.84 Å2
Baniso -1Baniso -2Baniso -3
1--5.3845 Å20 Å20 Å2
2---5.3845 Å20 Å2
3---10.6682 Å2
Refinement stepCycle: LAST / Resolution: 3.1→48.056 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1991 978 7 7 2983
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053251
X-RAY DIFFRACTIONf_angle_d1.0474451
X-RAY DIFFRACTIONf_dihedral_angle_d23.7531227
X-RAY DIFFRACTIONf_chiral_restr0.053486
X-RAY DIFFRACTIONf_plane_restr0.003399
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1001-3.54860.31931460.24912886X-RAY DIFFRACTION90
3.5486-4.47040.25651740.19883157X-RAY DIFFRACTION97
4.4704-48.06150.27741640.18633448X-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)
12.69112.49562.17826.6008-0.81473.4158-0.1319-0.0379-1.1185-0.10380.3731-1.90610.58380.50570.16140.43890.08230.00550.39720.08890.445235.9438-49.373523.2142
23.29982.43170.04261.79210.0369-0.0016-0.61860.1238-1.6434-0.69230.4563-0.8280.1243-1.88970.03391.0277-0.50530.01172.2510.52420.384425.674-46.79737.6064
32.8012-1.48312.062.92860.30263.42830.39211.0592-0.17960.4690.2281-0.0469-0.2005-0.4513-0.00060.2891-0.0343-0.04140.48830.03620.241330.4846-39.539720.7126
46.50481.4522-6.69473.66490.9248.7325-0.37791.38120.7427-0.39951.37240.0729-0.7314-1.62240.6921-0.0426-0.1871-0.05450.6572-0.05760.218419.5213-41.533917.204
55.3416-3.3639-1.40215.27541.04454.9353-0.4694-0.89880.28410.63160.0425-0.7065-0.4864-0.201-0.00130.2954-0.0987-0.07490.32550.06830.16431.2837-33.739726.8249
60.1280.0680.12440.3521-0.08480.1758-1.1857-1.1212.5195-1.09890.0681.1592-0.35012.2247-0.00631.1610.33890.44470.92380.4561.227124.7417-60.53732.6556
76.6915.96427.56497.01868.91682.0141-0.6047-0.1691.9224-1.562-1.57810.099-0.5235-0.3735-0.72150.226-0.01040.13780.36060.37510.459716.069-55.36478.2012
82.59890.77870.78763.12862.68363.2049-0.2344-1.1006-0.13131.0630.4653-0.75860.63310.4493-0.06280.18480.0561-0.10570.44140.10090.424825.3564-57.138417.4736
94.82921.1421.19524.12740.23633.3344-0.56360.0057-0.9486-1.15380.6312-1.37560.07130.51960.03290.4133-0.11710.18830.59710.22470.38422.0967-68.590517.0954
102.8312.87480.41316.61580.10333.8081-0.424-0.0716-0.0961-0.16760.25940.65540.2662-0.70780.00020.214-0.1554-0.06210.28680.09440.409115.9591-68.336118.2757
110.5419-0.2518-0.2040.23350.29990.745-3.10053.16771.76070.03231.57320.64740.03190.4967-0.00760.57570.0123-0.04191.01790.22611.403863.8287-41.724712.1221
121.49940.28790.43280.379-0.58591.2046-0.8176-0.2236-0.4480.04210.6476-0.67880.367-1.05490.00120.4488-0.04740.0311.267-0.20360.958151.556-53.53087.5134
130.22520.1312-0.23220.1027-0.28990.8559-0.9947-1.47841.78570.6861-0.0424-1.06140.17520.0127-0.00930.8031-0.1807-0.14581.00370.12511.400237.5836-68.404913.2173
140.19330.09260.35430.25340.26940.6419-0.1771-0.7405-1.626-0.36560.17580.81410.55360.88040.00681.1615-0.02940.5310.8004-0.0292.298232.9371-85.03788.4008
150.07540.05310.07180.20710.21040.2068-1.3161-0.5813-0.99720.7510.01292.07660.74860.7004-0.00161.36-0.07750.34741.10180.37312.766126.5623-95.705520.3491
160.5188-0.3103-0.13080.2330.11480.063-1.1638-0.88371.40013.26250.8091-1.43340.00150.15650.00811.17470.08470.08091.43120.06051.430471.1407-67.6642-12.1943
170.14730.04150.10630.2079-0.3040.6796-1.4712-1.1595-1.4274-0.3908-0.25380.66590.718-1.08260.00250.8558-0.23440.31651.1190.05972.222657.0762-69.0205-17.1838
180.36610.3734-0.14440.47780.02410.2495-1.62142.3883-1.18390.35160.92961.53581.65290.55170.00290.4897-0.03290.24051.13630.02631.415745.6212-71.7495-6.337
190.21810.14110.18590.3672-0.0780.21850.1728-2.16891.03860.16090.16710.9131-0.94771.3815-0.00290.7364-0.33190.10261.1574-0.30851.613741.9879-58.124210.2492
202.04340.21871.85771.76861.35362.39470.3723-0.50970.52250.6017-1.56420.5049-2.4143-0.6210.00110.8409-0.22530.06041.2307-0.00950.734859.2648-48.56788.1722
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 3:27)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 28:35)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 36:67)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 68:79)
5X-RAY DIFFRACTION5(CHAIN A AND RESID 80:127)
6X-RAY DIFFRACTION6(CHAIN B AND RESID 4:10)
7X-RAY DIFFRACTION7(CHAIN B AND RESID 11:18)
8X-RAY DIFFRACTION8(CHAIN B AND RESID 19:44)
9X-RAY DIFFRACTION9(CHAIN B AND RESID 45:68)
10X-RAY DIFFRACTION10(CHAIN B AND RESID 69:128)
11X-RAY DIFFRACTION11(CHAIN C AND RESID 1:4)
12X-RAY DIFFRACTION12(CHAIN C AND RESID 5:10)
13X-RAY DIFFRACTION13(CHAIN C AND RESID 11:15)
14X-RAY DIFFRACTION14(CHAIN C AND RESID 16:20)
15X-RAY DIFFRACTION15(CHAIN C AND RESID 21:24)
16X-RAY DIFFRACTION16(CHAIN D AND RESID 1:4)
17X-RAY DIFFRACTION17(CHAIN D AND RESID 5:8)
18X-RAY DIFFRACTION18(CHAIN D AND RESID 9:12)
19X-RAY DIFFRACTION19(CHAIN D AND RESID 13:17)
20X-RAY DIFFRACTION20(CHAIN D AND RESID 18:24)

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