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- PDB-5q1v: PanDDA analysis group deposition -- Crystal Structure of DCLRE1A ... -

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Basic information

Entry
Database: PDB / ID: 5q1v
TitlePanDDA analysis group deposition -- Crystal Structure of DCLRE1A in complex with FMOPL000166a
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 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-AXS / 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: 1.57 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)39,2924
Polymers38,9221
Non-polymers3703
Water5,567309
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.220, 57.126, 115.159
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


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


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#4: Chemical ChemComp-AXS / 1-(4-fluorophenyl)-~{N}-[[(2~{R})-oxolan-2-yl]methyl]methanamine


Mass: 209.260 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H16FNO
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 309 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer details yes c1cc(ccc1C[NH2+]C[C@H]2CCCO2)F None 6.23429077114 -6.56984255767 -6.56984255767 ... yes c1cc(ccc1C[NH2+]C[C@H]2CCCO2)F 6.23429077114 -6.56984255767 -6.56984255767 c1cc(ccc1C[NH2+]C[C@H]2CCCO2)F Low None 0.6 29.556666666666672 1.2782643168630845 0.82999999999999996 0.11899999999999999 0.5 0.37577200534366584 -5.60811136668 21.7968021335 21.7968021335 c1cc(ccc1C[NH2+]C[C@H]2CCCO2)F Low None 0.63 30.768666666666668 1.2650596203357058 0.80800000000000005 0.13600000000000001 1.1000000000000001 0.1772860212575528 -6.3517421123 22.1972777842 22.1972777842 c1cc(ccc1C[NH2+]C[C@H]2CCCO2)F 2 - Correct Ligand, Weak Density None 0.63 30.768666666666668 1.2650596203357058 0.80800000000000005 0.13600000000000001 1.1000000000000001 0.1772860212575528 6.6342179989 -6.55756630328 -6.55756630328 c1cc(ccc1C[NH2+]C[C@H]2CCCO2)F Low None 0.6 29.556666666666672 1.2782643168630845 0.82999999999999996 0.11899999999999999 0.5 0.37577200534366584

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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: 2.21 Å3/Da / Density % sol: 44.26 % / Mosaicity: 0.08 °
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: 1.57→28.79 Å / Num. obs: 48938 / % possible obs: 99.9 % / Redundancy: 6.6 % / CC1/2: 1 / Rmerge(I) obs: 0.045 / Rpim(I) all: 0.019 / Rrim(I) all: 0.049 / Net I/σ(I): 22.5 / Num. measured all: 320762 / 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
1.57-1.616.60.752349535370.8180.3130.8142.598.8
7.02-28.796.10.023384663510.010.02575.798.5

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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: 1.57→28.79 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.959 / SU B: 3.512 / SU ML: 0.055 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.096 / ESU R Free: 0.079 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1924 2352 4.8 %RANDOM
Rwork0.1481 ---
obs0.1503 46519 99.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 129.84 Å2 / Biso mean: 29.511 Å2 / Biso min: 12.6 Å2
Baniso -1Baniso -2Baniso -3
1-0.38 Å20 Å2-0 Å2
2--0.74 Å2-0 Å2
3----1.12 Å2
Refinement stepCycle: final / Resolution: 1.57→28.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2692 0 23 309 3024
Biso mean--27.54 42.93 -
Num. residues----341
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0192846
X-RAY DIFFRACTIONr_bond_other_d0.0020.022661
X-RAY DIFFRACTIONr_angle_refined_deg1.4461.953877
X-RAY DIFFRACTIONr_angle_other_deg0.9842.9916139
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4385351
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.55823.983118
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.29415462
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.064158
X-RAY DIFFRACTIONr_chiral_restr0.0920.2430
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213215
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02671
X-RAY DIFFRACTIONr_mcbond_it2.7232.6851392
X-RAY DIFFRACTIONr_mcbond_other2.72.6841391
X-RAY DIFFRACTIONr_mcangle_it3.4254.0321747
X-RAY DIFFRACTIONr_rigid_bond_restr1.73435507
X-RAY DIFFRACTIONr_sphericity_free33.1655218
X-RAY DIFFRACTIONr_sphericity_bonded14.12455517
LS refinement shellResolution: 1.57→1.611 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.248 158 -
Rwork0.208 3373 -
all-3531 -
obs--98.63 %

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