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

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Basic information

Entry
Database: PDB / ID: 2wcw
Title1.6A resolution structure of Archaeoglobus fulgidus Hjc, a Holliday junction resolvase from an archaeal hyperthermophile
ComponentsHJC
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
ACETATE ION / AMMONIUM ION / Crossover junction endodeoxyribonuclease Hjc
Similarity search - Component
Biological speciesARCHAEOGLOBUS FULGIDUS (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.58 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 17, 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 1.3May 1, 2024Group: 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: HJC
B: HJC
C: HJC
D: HJC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,61215
Polymers62,1684
Non-polymers44411
Water9,476526
1
A: HJC
B: HJC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,2977
Polymers31,0842
Non-polymers2135
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2430 Å2
ΔGint-22.06 kcal/mol
Surface area12940 Å2
MethodPISA
2
C: HJC
D: HJC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,3158
Polymers31,0842
Non-polymers2316
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2440 Å2
ΔGint-18.03 kcal/mol
Surface area12670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.510, 75.480, 60.920
Angle α, β, γ (deg.)90.00, 115.34, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.9961, -0.08793, -0.003701), (-0.08564, 0.9782, -0.1893), (0.02027, -0.1883, -0.9819)2.489, 0.1006, -1.51
2given(0.9645, 0.0752, 0.2532), (-0.08426, 0.9961, 0.02514), (-0.2503, -0.04559, 0.9671)34.92, -22.09, -34.55
3given(-0.952, -0.1897, -0.2402), (-0.115, 0.949, -0.2934), (0.2836, -0.2517, -0.9253)-30.64, -14.94, 37.03

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Components

#1: Protein
HJC


Mass: 15542.008 Da / Num. of mol.: 4 / Fragment: RESIDUES 2-136 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ARCHAEOGLOBUS FULGIDUS (archaea) / Strain: 4304 / Description: GERMAN COLLECTION OF MICROORGANISMS (DSM) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)PLYSS / References: UniProt: O28314
#2: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical
ChemComp-NH4 / AMMONIUM ION


Mass: 18.038 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: H4N
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 526 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, SER 29 TO ALA ENGINEERED RESIDUE IN CHAIN A, LYS 90 TO ALA ...ENGINEERED RESIDUE IN CHAIN A, SER 29 TO ALA ENGINEERED RESIDUE IN CHAIN A, LYS 90 TO ALA ENGINEERED RESIDUE IN CHAIN A, LYS 91 TO ALA ENGINEERED RESIDUE IN CHAIN B, SER 29 TO ALA ENGINEERED RESIDUE IN CHAIN B, LYS 90 TO ALA ENGINEERED RESIDUE IN CHAIN B, LYS 91 TO ALA ENGINEERED RESIDUE IN CHAIN C, SER 29 TO ALA ENGINEERED RESIDUE IN CHAIN C, LYS 90 TO ALA ENGINEERED RESIDUE IN CHAIN C, LYS 91 TO ALA ENGINEERED RESIDUE IN CHAIN D, SER 29 TO ALA ENGINEERED RESIDUE IN CHAIN D, LYS 90 TO ALA ENGINEERED RESIDUE IN CHAIN D, LYS 91 TO ALA
Sequence detailsN-TERMINAL GT AND G4 FOLLOWING THE FIRST METHIONINE 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: 1.93 Å3/Da / Density % sol: 36 % / Description: NONE
Crystal growpH: 8.5 / Details: 4.5 M AMMONIUM ACETATE 0.1 M TRIS-HCL PH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.93
DetectorType: ADSC CCD / Detector: CCD / Date: Jun 30, 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: 0.93 Å / Relative weight: 1
ReflectionResolution: 1.58→50 Å / Num. obs: 60375 / % possible obs: 93.5 % / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Biso Wilson estimate: 18.2 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 15.48
Reflection shellResolution: 1.58→1.62 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 2.06 / % possible all: 79.6

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: WILD-TYPE CRYSTAL FORM

Resolution: 1.58→29.18 Å / SU ML: 1.25 / σ(F): 0.02 / Phase error: 18.34 / Stereochemistry target values: ML
Details: HYDROGENS WERE ADDED IN THE RIDING POSITIONS, BUT REMOVED PRIOR TO DEPOSITION. IN CHAIN B RESIDUES 29-33 ARE DISORDERED.
RfactorNum. reflection% reflection
Rfree0.19 3061 5.1 %
Rwork0.154 --
obs0.156 60364 93.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.18 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 28.57 Å2
Baniso -1Baniso -2Baniso -3
1--2.6068 Å20 Å22.3012 Å2
2--1.5531 Å20 Å2
3---1.0537 Å2
Refinement stepCycle: LAST / Resolution: 1.58→29.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3906 0 29 526 4461
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084102
X-RAY DIFFRACTIONf_angle_d1.1285551
X-RAY DIFFRACTIONf_dihedral_angle_d15.7041521
X-RAY DIFFRACTIONf_chiral_restr0.068599
X-RAY DIFFRACTIONf_plane_restr0.005721
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5801-1.60470.27651080.27212201X-RAY DIFFRACTION79
1.6047-1.63110.26621190.24922271X-RAY DIFFRACTION82
1.6311-1.65920.26861250.23432291X-RAY DIFFRACTION84
1.6592-1.68930.25051340.21552412X-RAY DIFFRACTION86
1.6893-1.72180.2111130.20482414X-RAY DIFFRACTION87
1.7218-1.7570.23871260.19462504X-RAY DIFFRACTION89
1.757-1.79520.23121220.18822539X-RAY DIFFRACTION91
1.7952-1.83690.22041650.17632467X-RAY DIFFRACTION91
1.8369-1.88290.19761610.16082580X-RAY DIFFRACTION95
1.8829-1.93380.20751240.15512675X-RAY DIFFRACTION95
1.9338-1.99060.18181450.15162652X-RAY DIFFRACTION96
1.9906-2.05490.18531410.14232712X-RAY DIFFRACTION97
2.0549-2.12830.19081590.13412663X-RAY DIFFRACTION98
2.1283-2.21350.14571550.1342717X-RAY DIFFRACTION98
2.2135-2.31420.16041430.13122745X-RAY DIFFRACTION98
2.3142-2.43610.17041450.13932761X-RAY DIFFRACTION99
2.4361-2.58870.18671240.13832727X-RAY DIFFRACTION98
2.5887-2.78840.17211520.14432780X-RAY DIFFRACTION99
2.7884-3.06880.18741450.14752782X-RAY DIFFRACTION100
3.0688-3.51220.1761570.14272782X-RAY DIFFRACTION100
3.5122-4.42250.1521550.12812799X-RAY DIFFRACTION100
4.4225-29.18140.21521430.15942829X-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)
14.5438-0.0506-1.89770.76962.03626.33350.52740.02491.7345-0.19230.31350.2298-1.572-0.1294-0.77860.4146-0.00390.20050.1592-0.00490.54552.1117-3.933413.018
21.5561-0.7358-1.02741.24020.50641.63330.0062-0.0756-0.0676-0.0066-0.01630.07470.06050.04450.0050.12940.0064-0.01910.10660.0040.1019-6.3353-16.885912.2795
34.903-0.9619-1.90890.2813-0.22635.03360.2776-0.0461.16160.13630.0423-0.282-1.2019-0.0473-0.3580.37690.0480.04660.1556-0.01330.32752.7566-6.3065-12.9767
41.45650.1463-0.6560.9187-0.32451.3812-0.0418-0.0188-0.0434-0.01570.0211-0.0584-0.07140.0680.01690.13190.0082-0.0040.0893-0.01340.0910.3333-18.5785-10.9176
52.3347-0.89050.78363.3392-4.69656.72860.33390.03631.03820.5536-0.0557-0.395-1.0030.2303-0.30140.4894-0.07670.26690.2562-0.0140.6888-45.599512.753636.7725
63.19720.0786-0.17370.96680.47721.31630.0298-0.22380.16480.1231-0.1540.14980.0453-0.11810.11390.1124-0.02480.00480.1151-0.04210.149-52.24890.622934.7862
74.15962.147-2.96331.4117-2.50625.36550.26040.16451.88950.4490.15470.0211-0.8044-0.0765-0.33350.28390.0586-00.15250.05040.6127-37.615511.625412.8223
81.87770.0939-0.77070.9039-0.02810.50080.01590.0587-0.0511-0.0729-0.05510.0336-0.0255-0.00650.03290.12640.0062-0.0350.11040.02020.119-30.03170.382217.3455
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 4:11)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 12:129)
3X-RAY DIFFRACTION3(CHAIN B AND RESID 3:10)
4X-RAY DIFFRACTION4(CHAIN B AND RESID 11:129)
5X-RAY DIFFRACTION5(CHAIN C AND RESID 5:10)
6X-RAY DIFFRACTION6(CHAIN C AND RESID 11:125)
7X-RAY DIFFRACTION7(CHAIN D AND RESID 3:10)
8X-RAY DIFFRACTION8(CHAIN D AND RESID 11:127)

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