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- PDB-5q1j: PanDDA analysis group deposition -- Crystal Structure of DCLRE1A ... -

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Basic information

Entry
Database: PDB / ID: 5q1j
TitlePanDDA analysis group deposition -- Crystal Structure of DCLRE1A in complex with FMSOA000341b
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
N-(2-hydroxyphenyl)acetamide / 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: 1.42 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)39,2344
Polymers38,9221
Non-polymers3123
Water5,531307
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.257, 57.216, 115.279
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-9KS / N-(2-hydroxyphenyl)acetamide


Mass: 151.163 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H9NO2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 307 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer details yes CC(=O)Nc1ccccc1O None -21.3689372335 0.612652350905 0.612652350905 CC(=O)Nc1ccccc1O Low None ... yes CC(=O)Nc1ccccc1O -21.3689372335 0.612652350905 0.612652350905 CC(=O)Nc1ccccc1O Low None 0.42 18.22 0.9385695353055393 0.91700000000000004 0.091999999999999998 0.20000000000000001 0.2535694274660382 1.88615077343 18.5574000225 18.5574000225 CC(=O)Nc1ccccc1O Low None 0.75 43.04363636363635 0.9069837827897586 0.66200000000000003 0.224 2.2000000000000002 0.23817029812529333 1.88615077343 18.5574000225 18.5574000225 CC(=O)Nc1ccccc1O Low None 0.75 43.04363636363635 0.9069837827897586 0.66200000000000003 0.224 2.2000000000000002 0.23817029812529333 -13.6142107168 9.12792387518 9.12792387518 CC(=O)Nc1ccccc1O 4 - High confidence None 0.57 21.17727272727273 1.0063609857268634 0.90000000000000002 0.095000000000000001 2.2000000000000002 0.2017230324434515 14.1320266851 9.12676153745 9.12676153745 CC(=O)Nc1ccccc1O Low None 0.42 18.22 0.9385695353055393 0.91700000000000004 0.091999999999999998 0.20000000000000001 0.2535694274660382 -14.1478454084 9.04894406432 9.04894406432 CC(=O)Nc1ccccc1O Low None 0.57 21.17727272727273 1.0063609857268634 0.90000000000000002 0.095000000000000001 2.2000000000000002 0.2017230324434515 -14.0840034826 8.99116893418 8.99116893418 CC(=O)Nc1ccccc1O Low None 0.57 21.17727272727273 1.0063609857268634 0.90000000000000002 0.095000000000000001 2.2000000000000002 0.2017230324434515 -21.3689372335 0.612652350905 0.612652350905 CC(=O)Nc1ccccc1O Low None 0.57 21.17727272727273 1.0063609857268634 0.90000000000000002 0.095000000000000001 2.2000000000000002 0.2017230324434515

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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: 44.44 % / Mosaicity: 0.07 °
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: 1.42→28.82 Å / Num. obs: 66189 / % possible obs: 99.9 % / Redundancy: 6.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.043 / Rpim(I) all: 0.018 / Rrim(I) all: 0.047 / Net I/σ(I): 20.7 / Num. measured all: 427127 / 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
1.42-1.465.50.6572629048010.8470.3060.7272.399.4
6.35-28.8260.02950938470.9990.0130.03261.598.8

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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: PDB entry 5AHO

5aho


Resolution: 1.42→28.82 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.964 / SU B: 2.296 / SU ML: 0.04 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.067 / ESU R Free: 0.06 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1885 3197 4.8 %RANDOM
Rwork0.1567 ---
obs0.1582 62917 99.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 128.29 Å2 / Biso mean: 25.694 Å2 / Biso min: 10.44 Å2
Baniso -1Baniso -2Baniso -3
1-0.2 Å20 Å20 Å2
2--0.9 Å2-0 Å2
3----1.1 Å2
Refinement stepCycle: final / Resolution: 1.42→28.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2692 0 19 307 3018
Biso mean--20.06 40.26 -
Num. residues----341
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0192884
X-RAY DIFFRACTIONr_bond_other_d0.0020.022699
X-RAY DIFFRACTIONr_angle_refined_deg1.3881.953927
X-RAY DIFFRACTIONr_angle_other_deg0.9612.9966219
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2415356
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.33123.833120
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.60415472
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.078159
X-RAY DIFFRACTIONr_chiral_restr0.0850.2434
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213270
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02685
X-RAY DIFFRACTIONr_mcbond_it2.2662.3161412
X-RAY DIFFRACTIONr_mcbond_other2.2422.3151410
X-RAY DIFFRACTIONr_mcangle_it2.9353.4821772
X-RAY DIFFRACTIONr_rigid_bond_restr1.34135583
X-RAY DIFFRACTIONr_sphericity_free31.8285236
X-RAY DIFFRACTIONr_sphericity_bonded12.87755574
LS refinement shellResolution: 1.419→1.456 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.255 238 -
Rwork0.221 4559 -
all-4797 -
obs--99.34 %

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