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- PDB-5q23: PanDDA analysis group deposition -- Crystal Structure of DCLRE1A ... -

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Basic information

Entry
Database: PDB / ID: 5q23
TitlePanDDA analysis group deposition -- Crystal Structure of DCLRE1A in complex with FMOPL000543a
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 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
(phenylmethyl) 4-oxidanylpiperidine-1-carboxylate / 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: 1.32 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)39,3184
Polymers38,9221
Non-polymers3963
Water5,657314
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.060, 57.054, 115.268
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-B0G / (phenylmethyl) 4-oxidanylpiperidine-1-carboxylate


Mass: 235.279 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H17NO3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 314 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer details yes c1ccc(cc1)COC(=O)N2CCC(CC2)O None -0.713448603866 17.3391238639 17.3391238639 c1ccc(cc1) ... yes c1ccc(cc1)COC(=O)N2CCC(CC2)O -0.713448603866 17.3391238639 17.3391238639 c1ccc(cc1)COC(=O)N2CCC(CC2)O 4 - High Confidence None 1.0 42.27882352941177 1.5127083620333384 0.91500000000000004 0.092999999999999999 1.6000000000000001 6.783913190517003 -0.405065505969 17.3490836841 17.3490836841 c1ccc(cc1)COC(=O)N2CCC(CC2)O 0 - no ligand present None 1.0 42.27882352941177 1.5127083620333384 0.91500000000000004 0.092999999999999999 1.6000000000000001 6.783913190517003

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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: 2.2 Å3/Da / Density % sol: 44.07 % / 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 12, 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: 1.32→57.05 Å / Num. obs: 81458 / % possible obs: 100 % / Redundancy: 6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.057 / Rpim(I) all: 0.025 / Rrim(I) all: 0.062 / Net I/σ(I): 11.5 / Num. measured all: 487509 / Scaling rejects: 14
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
1.32-1.354.31.1352569159230.5330.6111.2941.299.8
5.9-57.055.90.028625110520.9990.0120.0314399.9

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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: 1.32→57.05 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.963 / SU B: 3.217 / SU ML: 0.054 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.06 / ESU R Free: 0.058 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2159 3943 4.9 %RANDOM
Rwork0.1773 ---
obs0.1792 76788 99.07 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 159.92 Å2 / Biso mean: 23.357 Å2 / Biso min: 8.67 Å2
Baniso -1Baniso -2Baniso -3
1-0.29 Å20 Å20 Å2
2--0.15 Å2-0 Å2
3----0.44 Å2
Refinement stepCycle: final / Resolution: 1.32→57.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2696 0 25 314 3035
Biso mean--35.47 38.97 -
Num. residues----341
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0192834
X-RAY DIFFRACTIONr_bond_other_d0.0020.022651
X-RAY DIFFRACTIONr_angle_refined_deg1.4671.9483858
X-RAY DIFFRACTIONr_angle_other_deg0.9672.9916114
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.285348
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.27723.866119
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.79515462
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.768158
X-RAY DIFFRACTIONr_chiral_restr0.0930.2427
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213197
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02669
X-RAY DIFFRACTIONr_mcbond_it2.3812.0681383
X-RAY DIFFRACTIONr_mcbond_other2.3732.0671382
X-RAY DIFFRACTIONr_mcangle_it3.1033.111734
X-RAY DIFFRACTIONr_rigid_bond_restr1.67135485
X-RAY DIFFRACTIONr_sphericity_free34.8715235
X-RAY DIFFRACTIONr_sphericity_bonded14.10155485
LS refinement shellResolution: 1.32→1.354 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.417 294 -
Rwork0.407 5470 -
all-5764 -
obs--96.86 %

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