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- PDB-2bhn: XPF from Aeropyrum pernix -

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Basic information

Entry
Database: PDB / ID: 2bhn
TitleXPF from Aeropyrum pernix
ComponentsXPF ENDONUCLEASE
KeywordsHYDROLASE / STRUCTURE SPECIFIC ENDONUCLEASE / NUCLEOTIDE EXCISION REPAIR
Function / homology
Function and homology information


nucleotide-excision repair involved in interstrand cross-link repair / single-stranded DNA endodeoxyribonuclease activity / double-strand break repair via homologous recombination / single-stranded DNA binding / damaged DNA binding / metal ion binding
Similarity search - Function
Rossmann fold - #10130 / ERCC4 domain / ERCC4 domain / ERCC4 domain / Helix-hairpin-helix motif / RuvA domain 2-like / Restriction endonuclease type II-like / Helix-hairpin-helix domain / Helix-hairpin-helix DNA-binding motif, class 1 / Helix-hairpin-helix DNA-binding motif class 1 ...Rossmann fold - #10130 / ERCC4 domain / ERCC4 domain / ERCC4 domain / Helix-hairpin-helix motif / RuvA domain 2-like / Restriction endonuclease type II-like / Helix-hairpin-helix domain / Helix-hairpin-helix DNA-binding motif, class 1 / Helix-hairpin-helix DNA-binding motif class 1 / 5' to 3' exonuclease, C-terminal subdomain / DNA polymerase; domain 1 / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Repair endonuclease XPF
Similarity search - Component
Biological speciesAeropyrum pernix (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsNewman, M. / Murray-Rust, J. / Lally, J. / Rudolf, J. / Fadden, A. / Knowles, P.P. / White, M.F. / McDonald, N.Q.
CitationJournal: EMBO J. / Year: 2005
Title: Structure of an XPF endonuclease with and without DNA suggests a model for substrate recognition.
Authors: Newman, M. / Murray-Rust, J. / Lally, J. / Rudolf, J. / Fadden, A. / Knowles, P.P. / White, M.F. / McDonald, N.Q.
History
DepositionJan 14, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 23, 2005Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 14, 2018Group: Database references / Source and taxonomy / Structure summary
Category: audit_author / citation ...audit_author / citation / citation_author / entity_src_gen
Item: _audit_author.name / _citation.journal_abbrev ..._audit_author.name / _citation.journal_abbrev / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_variant
Revision 1.4May 8, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.method
Revision 1.5Dec 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: XPF ENDONUCLEASE
B: XPF ENDONUCLEASE
C: XPF ENDONUCLEASE
D: XPF ENDONUCLEASE


Theoretical massNumber of molelcules
Total (without water)98,2064
Polymers98,2064
Non-polymers00
Water00
1
A: XPF ENDONUCLEASE
B: XPF ENDONUCLEASE

A: XPF ENDONUCLEASE
B: XPF ENDONUCLEASE


Theoretical massNumber of molelcules
Total (without water)98,2064
Polymers98,2064
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
MethodPQS
2
C: XPF ENDONUCLEASE
D: XPF ENDONUCLEASE

C: XPF ENDONUCLEASE
D: XPF ENDONUCLEASE


Theoretical massNumber of molelcules
Total (without water)98,2064
Polymers98,2064
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
MethodPQS
Unit cell
Length a, b, c (Å)210.325, 42.752, 118.736
Angle α, β, γ (deg.)90.00, 121.42, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:

Ens-ID: 1 / Refine code: 6

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ARGARGSERSERAA20 - 1473 - 130
21ARGARGSERSERBB20 - 1473 - 130
31ARGARGSERSERCC20 - 1473 - 130
41ARGARGSERSERDD20 - 1473 - 130
12SERSERLYSLYSAA164 - 229147 - 212
22SERSERLYSLYSBB164 - 229147 - 212
32SERSERLYSLYSCC164 - 229147 - 212
42SERSERLYSLYSDD164 - 229147 - 212

NCS oper:
IDCodeMatrixVector
1given(-0.81452, -0.46264, 0.35003), (-0.45476, 0.13456, -0.88039), (0.3602, -0.87627, -0.32)97.84138, 43.09292, 4.54055
2given(-0.60968, 0.43026, 0.66571), (0.56926, -0.34675, 0.74546), (0.55158, 0.83345, -0.03352)38.03769, -47.70517, -1.09623
3given(0.5318, -0.20301, -0.82218), (-0.05069, -0.97673, 0.20838), (-0.84535, -0.06915, -0.52971)1.93644, -1.5396, 89.51183
4given(0.43528, -0.02452, -0.89996), (-0.03253, -0.9994, 0.01149), (-0.89971, 0.02427, -0.43582)94.18008, -20.55905, 150.65569
5given(0.97792, -0.02507, -0.20746), (0.02292, 0.99966, -0.01279), (0.20771, 0.00776, 0.97816)-66.5201, 25.00196, -77.18398
6given(0.5974, -0.00727, -0.80191), (-0.00228, -0.99997, 0.00737), (-0.80194, -0.00258, -0.5974)-3.33572, 3.34292, 89.99927

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Components

#1: Protein
XPF ENDONUCLEASE


Mass: 24551.436 Da / Num. of mol.: 4 / Fragment: 19-231
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aeropyrum pernix (archaea)
Description: A PERNIX GENOME SEQUENCING PROJECT GNE APE 1436, ACCESSION CODE C72622
Plasmid: PET-14B-3C / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): ROSETTA/PLYSS
References: UniProt: Q9YC15, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases
Sequence detailsRESIDUES 19-231 ONLY

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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: 2.32 Å3/Da / Density % sol: 47 %
Description: SOLUTION CHECKED BY CROSS-PHASING OF AN OSMATE DERIVATIVE
Crystal growMethod: vapor diffusion, sitting drop / Details: 65% V/V MPD, 0.1M TRIS-HCL PH8.0. SITTING DROPS.

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.2 / Wavelength: 1
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.2→38.93 Å / Num. obs: 52273 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 50 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 10.6
Reflection shellResolution: 3.2→3.37 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 2.4 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: SEPARATE DOMAINS FROM PART-REFINED PDB ENTRY 2BGW

2bgw


Resolution: 3.2→25 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.836 / SU B: 62.516 / SU ML: 0.535 / Cross valid method: THROUGHOUT / ESU R Free: 0.663 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.32 768 5 %RANDOM
Rwork0.216 ---
obs0.221 14575 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 60.83 Å2
Baniso -1Baniso -2Baniso -3
1-1.02 Å20 Å20.05 Å2
2---1.34 Å20 Å2
3---0.38 Å2
Refinement stepCycle: LAST / Resolution: 3.2→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5905 0 0 0 5905
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0226018
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7031.9818205
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.15808
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.36723.317205
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.25915882
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.7581533
X-RAY DIFFRACTIONr_chiral_restr0.1070.2981
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024502
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2710.23173
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3260.24124
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1970.2280
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2980.257
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2910.210
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4361.54130
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.76226431
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.16432114
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.9854.51774
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 1310 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Aloose positional8.025
2Bloose positional7.925
3Cloose positional8.015
4Dloose positional7.895
1Aloose thermal2.310
2Bloose thermal2.3110
3Cloose thermal2.6910
4Dloose thermal1.8510
LS refinement shellResolution: 3.2→3.28 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.455 59
Rwork0.275 1059
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)
13.7404-0.00311.42212.41220.21782.41750.01180.25610.1476-0.01740.0994-0.2135-0.41720.1268-0.1112-0.3622-0.00460.0336-0.26270.0539-0.348267.89352.978419.7337
25.00572.52980.09853.39112.86225.52710.0642-0.07420.31610.1006-0.06310.2488-0.1904-0.3769-0.001-0.43590.1197-0.0384-0.26250.0627-0.385648.1695-4.695520.1231
35.8693-0.0212-2.17142.26892.58754.9675-0.0123-1.2015-0.35580.4222-0.0077-0.00380.13160.76290.01990.24250.11090.11760.4065-0.03490.291310.54974.041138.0647
46.737-0.4431-1.49143.22932.06012.85720.15220.1424-0.04280.25160.0163-0.385-0.28930.448-0.16850.15780.1115-0.03190.1498-0.08540.071620.9757-3.890821.2822
52.8684-0.00511.21436.00841.67759.05440.17190.1372-0.7415-0.321-0.097-1.04990.70240.075-0.0749-0.19280.0984-0.0084-0.3105-0.03620.144190.1001-18.222745.8415
612.1468-3.71931.571712.73910.82943.0848-0.19840.37410.0968-0.00370.1984-1.25450.04190.16830.0001-0.2881-0.00110.0445-0.4822-0.0356-0.211691.856-4.950148.5745
76.7339-0.3118-1.581610.0918-0.27867.6563-0.11870.3386-0.5031-0.5852-0.2633-0.46840.57660.47390.382-0.4228-0.0250.0121-0.4043-0.0095-0.262212.52948.1534-13.0352
85.94311.26351.06098.9245-0.01188.0222-0.1314-0.25220.5230.0275-0.0961-0.2067-0.44290.21690.2275-0.3793-0.00970.0239-0.3529-0.0346-0.189913.87222.2627-9.7803
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A19 - 151
2X-RAY DIFFRACTION2B19 - 149
3X-RAY DIFFRACTION3C20 - 147
4X-RAY DIFFRACTION4D19 - 151
5X-RAY DIFFRACTION5A166 - 229
6X-RAY DIFFRACTION6B162 - 229
7X-RAY DIFFRACTION7C164 - 229
8X-RAY DIFFRACTION8D166 - 229

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