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- PDB-5q1q: PanDDA analysis group deposition -- Crystal Structure of DCLRE1A ... -

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Basic information

Entry
Database: PDB / ID: 5q1q
TitlePanDDA analysis group deposition -- Crystal Structure of DCLRE1A in complex with FMOPL000294a
ComponentsDNA cross-link repair 1A protein
KeywordsCELL CYCLE / SGC - Diamond I04-1 fragment screening / PanDDA / XChemExplorer
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
Chem-AWS / MALONATE ION / NICKEL (II) ION / DNA cross-link repair 1A protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / molecular replacement / Resolution: 1.44 Å
AuthorsNewman, J.A. / Aitkenhead, H. / Lee, S.Y. / Kupinska, K. / Burgess-Brown, N. / Tallon, R. / Krojer, T. / von Delft, F. / Arrowsmith, C.H. / Edwards, A. ...Newman, J.A. / Aitkenhead, H. / Lee, S.Y. / Kupinska, K. / Burgess-Brown, N. / Tallon, R. / Krojer, T. / von Delft, F. / Arrowsmith, C.H. / Edwards, A. / Bountra, C. / Gileadi, O.
CitationJournal: To Be Published
Title: PanDDA analysis group deposition
Authors: Newman, J.A. / Aitkenhead, H. / Lee, S.Y. / Kupinska, K. / Burgess-Brown, N. / Tallon, R. / Krojer, T. / von Delft, F. / Arrowsmith, C.H. / Edwards, A. / Bountra, C. / Gileadi, O.
History
DepositionMay 15, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 8, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA cross-link repair 1A protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,3164
Polymers38,9221
Non-polymers3943
Water5,585310
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.060, 56.990, 114.850
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein DNA cross-link repair 1A protein / DCLRE1A / SNM1 homolog A / hSNM1A


Mass: 38922.070 Da / Num. of mol.: 1 / Fragment: UNP residues 698-1040
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DCLRE1A, KIAA0086, SNM1, SNM1A / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q6PJP8
#2: Chemical ChemComp-MLI / MALONATE ION / Malonic acid


Mass: 102.046 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H2O4
#3: Chemical ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#4: Chemical ChemComp-AWS / 8-[(dimethylamino)methyl]-4-methyl-7-oxidanyl-chromen-2-one


Mass: 233.263 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H15NO3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 310 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer details yes Cc1cc(=O)oc2c1ccc(c2C[NH+](C)C)O None 21.3281867307 13.1992993845 13.1992993845 Cc1cc(=O) ... yes Cc1cc(=O)oc2c1ccc(c2C[NH+](C)C)O 21.3281867307 13.1992993845 13.1992993845 Cc1cc(=O)oc2c1ccc(c2C[NH+](C)C)O Medium None 1.0 48.94117647058824 1.801606721378922 0.79900000000000004 0.161 0.0 0.32288725039955996 19.9436760048 13.863383047 13.863383047 Cc1cc(=O)oc2c1ccc(c2C[NH+](C)C)O 4 - High Confidence None 1.0 48.94117647058824 1.801606721378922 0.79900000000000004 0.161 0.0 0.32288725039955996 20.3827311176 13.8359557855 13.8359557855 Cc1cc(=O)oc2c1ccc(c2C[NH+](C)C)O Medium None 1.0 48.94117647058824 1.801606721378922 0.79900000000000004 0.161 0.0 0.32288725039955996 20.3827311176 13.8359557855 13.8359557855 Cc1cc(=O)oc2c1ccc(c2C[NH+](C)C)O Low None 1.0 48.94117647058824 1.801606721378922 0.79900000000000004 0.161 0.0 0.32288725039955996 20.1710628704 13.2432270377 13.2432270377 Cc1cc(=O)oc2c1ccc(c2C[NH+](C)C)O 0 - no ligand present None 1.0 48.94117647058824 1.801606721378922 0.79900000000000004 0.161 0.0 0.32288725039955996 -1.52240926177 13.1923647735 13.1923647735 Cc1cc(=O)oc2c1ccc(c2C[NH+](C)C)O Low None 0.76 36.79705882352942 1.5287519245338352 0.81299999999999994 0.159 1.1000000000000001 0.1148597610387654

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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: 2.19 Å3/Da / Density % sol: 43.8 % / Mosaicity: 0 °
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 30% PEG1000, 0.1 M MIB buffer

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 29, 2016
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.44→56.99 Å / Num. obs: 62718 / % possible obs: 100 % / Redundancy: 6.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.07 / Rpim(I) all: 0.03 / Rrim(I) all: 0.076 / Net I/σ(I): 14.4 / Num. measured all: 406691 / Scaling rejects: 0
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique allCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.44-1.485.71.3832635245890.5070.6261.5221.3100
6.44-56.9960.03749028120.9970.0160.04144.499.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0155refinement
Aimless0.5.27data scaling
PDB_EXTRACT3.23data extraction
XDSdata reduction
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 5aho

5aho


Resolution: 1.44→56.99 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.964 / SU B: 2.788 / SU ML: 0.047 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.072 / ESU R Free: 0.063 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.19 3024 4.8 %RANDOM
Rwork0.1584 ---
obs0.1599 59618 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 170.9 Å2 / Biso mean: 24.514 Å2 / Biso min: 9.63 Å2
Baniso -1Baniso -2Baniso -3
1--0.51 Å2-0 Å20 Å2
2--0.95 Å2-0 Å2
3----0.44 Å2
Refinement stepCycle: final / Resolution: 1.44→56.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2692 0 25 310 3027
Biso mean--39.66 39.4 -
Num. residues----341
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0192830
X-RAY DIFFRACTIONr_bond_other_d0.0020.022647
X-RAY DIFFRACTIONr_angle_refined_deg1.4221.9473856
X-RAY DIFFRACTIONr_angle_other_deg0.972.9936099
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.495348
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.95923.932117
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.48215460
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.492158
X-RAY DIFFRACTIONr_chiral_restr0.0880.2427
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213199
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02667
X-RAY DIFFRACTIONr_mcbond_it2.092.1821383
X-RAY DIFFRACTIONr_mcbond_other2.0682.181382
X-RAY DIFFRACTIONr_mcangle_it2.5573.2821734
X-RAY DIFFRACTIONr_rigid_bond_restr1.48735477
X-RAY DIFFRACTIONr_sphericity_free29.3775239
X-RAY DIFFRACTIONr_sphericity_bonded11.24755469
LS refinement shellResolution: 1.44→1.477 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.305 225 -
Rwork0.31 4355 -
all-4580 -
obs--99.89 %

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