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- PDB-5ahr: Crystal structure of human DNA cross-link repair 1A, crystal form B -

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Basic information

Entry
Database: PDB / ID: 5ahr
TitleCrystal structure of human DNA cross-link repair 1A, crystal form B
ComponentsDNA CROSS-LINK REPAIR 1A PROTEIN
KeywordsHYDROLASE / DCLRE1A / INTERSTRAND CROSSLINK REPAIR
Function / homology
Function and homology information


5'-3' DNA exonuclease activity / interstrand cross-link repair / Fanconi Anemia Pathway / fibrillar center / double-strand break repair via nonhomologous end joining / beta-lactamase activity / beta-lactamase / damaged DNA binding / cell cycle / cell division ...5'-3' DNA exonuclease activity / interstrand cross-link repair / Fanconi Anemia Pathway / fibrillar center / double-strand break repair via nonhomologous end joining / beta-lactamase activity / beta-lactamase / damaged DNA binding / cell cycle / cell division / nucleoplasm / metal ion binding
Similarity search - Function
Rossmann fold - #12650 / DNA repair metallo-beta-lactamase / DNA repair metallo-beta-lactamase / Rad18, zinc finger UBZ4-type / Zinc finger UBZ4-type profile. / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Metallo-beta-lactamase; Chain A / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / 4-Layer Sandwich / Rossmann fold ...Rossmann fold - #12650 / DNA repair metallo-beta-lactamase / DNA repair metallo-beta-lactamase / Rad18, zinc finger UBZ4-type / Zinc finger UBZ4-type profile. / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Metallo-beta-lactamase; Chain A / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / 4-Layer Sandwich / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DNA cross-link repair 1A protein
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.19 Å
AuthorsAllerston, C.K. / Newman, J.A. / Vollmar, M. / Goubin, S. / Forese, D.S. / Chaikuad, A. / von Delft, F. / Arrowsmith, C.H. / Edwards, A. / Bountra, C. / Gileadi, O.
CitationJournal: Nucleic Acids Res. / Year: 2015
Title: The Structures of the Snm1A and Snm1B/Apollo Nuclease Domains Reveal a Potential Basis for Their Distinct DNA Processing Activities.
Authors: Allerston, C.K. / Lee, S.Y. / Newman, J.A. / Schofield, C.J. / Mchugh, P.J. / Gileadi, O.
History
DepositionFeb 6, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 18, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2016Group: Database references
Revision 1.2Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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: DNA CROSS-LINK REPAIR 1A PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,0093
Polymers38,8821
Non-polymers1272
Water3,423190
1
A: DNA CROSS-LINK REPAIR 1A PROTEIN
hetero molecules

A: DNA CROSS-LINK REPAIR 1A PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,0196
Polymers77,7642
Non-polymers2554
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Buried area2350 Å2
ΔGint-74.7 kcal/mol
Surface area29710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.199, 113.199, 125.736
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein DNA CROSS-LINK REPAIR 1A PROTEIN


Mass: 38881.984 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PFB LIC BSE / Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: Q6PJP8
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 190 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsFIRST TWO RESIDUES REMAIN AFTER CLEAVAGE OF PURIFICATION TAG

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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

CrystalDescription: NONE
Crystal growDetails: 0.20M NAF; 0.1M BTPROP PH 8.5; 20.0% PEG 3350; 10.0% ETGLY

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Dec 19, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.19→125 Å / Num. obs: 42700 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 13.3 % / Biso Wilson estimate: 38 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 13.3
Reflection shellResolution: 2.19→2.26 Å / Redundancy: 13.5 % / Rmerge(I) obs: 1.5 / Mean I/σ(I) obs: 1.8 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: NONE

Resolution: 2.19→80.044 Å / SU ML: 0.21 / σ(F): 1.35 / Phase error: 20.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2011 2151 5.1 %
Rwork0.1791 --
obs0.1802 42630 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 48 Å2
Refinement stepCycle: LAST / Resolution: 2.19→80.044 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2621 0 5 190 2816
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082725
X-RAY DIFFRACTIONf_angle_d1.0673700
X-RAY DIFFRACTIONf_dihedral_angle_d13.322998
X-RAY DIFFRACTIONf_chiral_restr0.047413
X-RAY DIFFRACTIONf_plane_restr0.005466
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.19-2.2410.31911400.28342642X-RAY DIFFRACTION100
2.241-2.2970.25721460.25712638X-RAY DIFFRACTION100
2.297-2.35910.25031500.23132655X-RAY DIFFRACTION100
2.3591-2.42860.23961220.21592677X-RAY DIFFRACTION100
2.4286-2.5070.27541420.20352656X-RAY DIFFRACTION100
2.507-2.59660.2261430.20082653X-RAY DIFFRACTION100
2.5966-2.70050.24961480.20752671X-RAY DIFFRACTION100
2.7005-2.82340.23921400.20192686X-RAY DIFFRACTION100
2.8234-2.97230.24061490.19742679X-RAY DIFFRACTION100
2.9723-3.15850.1911390.18942686X-RAY DIFFRACTION100
3.1585-3.40240.20131400.18662707X-RAY DIFFRACTION100
3.4024-3.74480.19741610.17132684X-RAY DIFFRACTION100
3.7448-4.28670.1831430.16012733X-RAY DIFFRACTION100
4.2867-5.40060.16421340.13512795X-RAY DIFFRACTION100
5.4006-80.09730.17111540.17522917X-RAY DIFFRACTION100

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