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- PDB-5q20: PanDDA analysis group deposition -- Crystal Structure of DCLRE1A ... -

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Basic information

Entry
Database: PDB / ID: 5q20
TitlePanDDA analysis group deposition -- Crystal Structure of DCLRE1A in complex with FMOPL000524a
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 / beta-lactamase activity / double-strand break repair via nonhomologous end joining / beta-lactamase / damaged DNA binding / cell cycle / cell division ...5'-3' DNA exonuclease activity / interstrand cross-link repair / Fanconi Anemia Pathway / fibrillar center / beta-lactamase activity / double-strand break repair via nonhomologous end joining / 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-AYV / 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: 1.76 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)39,3074
Polymers38,9221
Non-polymers3853
Water5,513306
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.899, 56.799, 115.031
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-AYV / 1-[2-methyl-1,3-bis(oxidanyl)propan-2-yl]-3-phenyl-urea


Mass: 224.256 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H16N2O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 306 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer details yes CC(CO)(CO)NC(=O)Nc1ccccc1 None -12.9579483987 14.3555341045 14.3555341045 CC(CO)(CO)NC(=O) ... yes CC(CO)(CO)NC(=O)Nc1ccccc1 -12.9579483987 14.3555341045 14.3555341045 CC(CO)(CO)NC(=O)Nc1ccccc1 4 - High Confidence None 1.0 66.5125 3.0300288519943304 0.63900000000000001 0.224 0.29999999999999999 1.8617451322616636

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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: 2.18 Å3/Da / Density % sol: 43.53 % / 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: Apr 11, 2017
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.76→56.82 Å / Num. obs: 34543 / % possible obs: 100 % / Redundancy: 6.3 % / CC1/2: 0.998 / Rmerge(I) obs: 0.111 / Rpim(I) all: 0.048 / Rrim(I) all: 0.121 / Net I/σ(I): 8.5 / Num. measured all: 218723 / Scaling rejects: 24
Reflection shell

Diffraction-ID: 1 / Redundancy: 6 %

Resolution (Å)Rmerge(I) obsNum. measured allNum. unique allCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.76-1.811.4551514025140.4890.641.5921.1100
7.87-56.820.0328094670.9990.0130.03330.799.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0155refinement
Aimless0.5.31data scaling
PDB_EXTRACT3.23data extraction
XDSdata reduction
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 5aho

5aho


Resolution: 1.76→56.82 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.934 / SU B: 4.264 / SU ML: 0.123 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.143 / ESU R Free: 0.136 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2472 1706 5 %RANDOM
Rwork0.2058 ---
obs0.2078 32646 99.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 132.17 Å2 / Biso mean: 26.101 Å2 / Biso min: 8.59 Å2
Baniso -1Baniso -2Baniso -3
1--0.32 Å20 Å20 Å2
2--0.95 Å2-0 Å2
3----0.63 Å2
Refinement stepCycle: final / Resolution: 1.76→56.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2692 0 24 306 3022
Biso mean--52.13 36.53 -
Num. residues----341
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0192828
X-RAY DIFFRACTIONr_bond_other_d0.0020.022646
X-RAY DIFFRACTIONr_angle_refined_deg1.4291.9493851
X-RAY DIFFRACTIONr_angle_other_deg0.9532.9936097
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3145348
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.65223.814118
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.65715460
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.28158
X-RAY DIFFRACTIONr_chiral_restr0.0820.2427
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213195
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02671
X-RAY DIFFRACTIONr_mcbond_it1.5882.4421383
X-RAY DIFFRACTIONr_mcbond_other1.5862.441382
X-RAY DIFFRACTIONr_mcangle_it2.5623.6531734
LS refinement shellResolution: 1.76→1.805 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.346 134 -
Rwork0.366 2317 -
all-2451 -
obs--98.28 %

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