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- PDB-4b87: Crystal structure of human DNA cross-link repair 1A -

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Basic information

Entry
Database: PDB / ID: 4b87
TitleCrystal structure of human DNA cross-link repair 1A
ComponentsDNA CROSS-LINK REPAIR 1A PROTEIN
KeywordsHYDROLASE / DCLRE1A / DCLRE / INTERSTRAND CROSSLINK REPAIR / NITROGEN MUSTARD / CANCER / CHEMOTHERAPY / PSO2 HOMOLOG
Function / homology
Function and homology information


5'-3' DNA exonuclease activity / interstrand cross-link repair / Fanconi Anemia Pathway / beta-lactamase / beta-lactamase activity / double-strand break repair via nonhomologous end joining / fibrillar center / damaged DNA binding / cell division / zinc ion binding / nucleoplasm
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 / SAD / Resolution: 2.16 Å
AuthorsAllerston, C.K. / Berridge, G. / Carpenter, E.P. / Kochan, G. / Krojer, T. / Mahajan, P. / Vollmar, M. / Yue, W.W. / Arrowsmith, C.H. / Edwards, A. ...Allerston, C.K. / Berridge, G. / Carpenter, E.P. / Kochan, G. / Krojer, T. / Mahajan, P. / Vollmar, M. / Yue, W.W. / Arrowsmith, C.H. / Edwards, A. / Bountra, C. / von Delft, F. / Gileadi, O.
CitationJournal: To be Published
Title: Crystal Structure of Human DNA Cross-Link Repair 1A
Authors: Allerston, C.K. / Berridge, G. / Carpenter, E.P. / Kochan, G. / Krojer, T. / Mahajan, P. / Vollmar, M. / Yue, W.W. / Arrowsmith, C.H. / Edwards, A. / Bountra, C. / von Delft, F. / Gileadi, O.
History
DepositionAug 24, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 28, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 5, 2012Group: Database references / Structure summary
Revision 1.2Jan 24, 2018Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Revision 1.3Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / 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_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.ptnr3_symmetry / _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.ptnr1_symmetry / _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_conn.ptnr2_symmetry / _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)41,6906
Polymers41,3771
Non-polymers3145
Water3,171176
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)83.400, 83.400, 257.841
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein DNA CROSS-LINK REPAIR 1A PROTEIN / SNM1 HOMOLOG A / HSNM1 / HSNM1A


Mass: 41376.801 Da / Num. of mol.: 1 / Fragment: RESIDUES 676-1040 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) / 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.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 176 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.1 Å3/Da / Density % sol: 60 % / Description: NONE
Crystal growpH: 7.5
Details: 17.5% PEG 3350, 0.2M KCSN PH 8.2, 5% ETHYLENE GLYCOL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795
DetectorType: ADSC CCD / Detector: CCD / Date: Jul 25, 2012 / Details: MIRRORS
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.15→72.23 Å / Num. obs: 29805 / % possible obs: 100 % / Redundancy: 11.9 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 15.2
Reflection shellResolution: 2.15→2.27 Å / Redundancy: 12.2 % / Rmerge(I) obs: 1.19 / Mean I/σ(I) obs: 2 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
MOSFLMdata reduction
SCALAdata scaling
SHARPphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.16→72.23 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.951 / SU B: 9.042 / SU ML: 0.118 / Cross valid method: THROUGHOUT / ESU R: 0.158 / ESU R Free: 0.151 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT. U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.21834 1506 5.1 %RANDOM
Rwork0.17634 ---
obs0.17844 28205 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: 54.778 Å2
Baniso -1Baniso -2Baniso -3
1-0.81 Å20.81 Å20 Å2
2--0.81 Å20 Å2
3----2.63 Å2
Refinement stepCycle: LAST / Resolution: 2.16→72.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2626 0 17 176 2819
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0192710
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.951.9543676
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.375333
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.69223.964111
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.16615441
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.277158
X-RAY DIFFRACTIONr_chiral_restr0.1230.2413
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212023
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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
LS refinement shellResolution: 2.155→2.211 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.308 101 -
Rwork0.29 2038 -
obs--100 %
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)
10.7821-0.33710.08471.4504-0.55830.2565-0.235-0.3007-0.07260.08560.3151-0.0121-0.0035-0.1602-0.08010.14310.0418-0.02930.23260.10.12951.6277-38.085330.6043
20.5725-0.32970.41280.4260.09940.9958-0.1994-0.16080.0908-0.03760.2055-0.0001-0.389-0.0414-0.00610.21150.0159-0.05170.16490.04830.1266-0.1197-22.620222.6211
31.9891-0.77590.18880.39930.60044.72290.2062-0.0289-0.0118-0.0781-0.0137-0.02460.0251-0.1615-0.19240.1806-0.0662-0.10880.15320.08590.0913-9.5474-38.1711.024
40.7476-0.69610.05370.6685-0.07761.941-0.0577-0.05640.1554-0.00520.0878-0.116-0.22850.2877-0.03010.2411-0.1557-0.09130.1575-0.00460.107212.7215-19.245818.5242
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A696 - 767
2X-RAY DIFFRACTION2A768 - 863
3X-RAY DIFFRACTION3A864 - 987
4X-RAY DIFFRACTION4A988 - 1040

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