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- PDB-1d9z: CRYSTAL STRUCTURE OF THE DNA REPAIR PROTEIN UVRB IN COMPLEX WITH ATP -

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Basic information

Entry
Database: PDB / ID: 1d9z
TitleCRYSTAL STRUCTURE OF THE DNA REPAIR PROTEIN UVRB IN COMPLEX WITH ATP
ComponentsEXCINUCLEASE UVRABC COMPONENT UVRB
KeywordsGENE REGULATION / ATP-bound protein / EXCINUCLEASE
Function / homology
Function and homology information


excinuclease ABC activity / excinuclease repair complex / SOS response / nucleotide-excision repair / ATP hydrolysis activity / DNA binding / ATP binding / cytoplasm
Similarity search - Function
Helix Hairpins - #240 / UvrB, YAD/RRR-motif-containing domain / Ultra-violet resistance protein B / Penicillin-binding protein 1b fold / Penicillin-binding protein 1b domain / UvrABC system, subunit B / UVR domain superfamily / UvrB/uvrC motif / UvrB, interaction domain / UvrB interaction domain ...Helix Hairpins - #240 / UvrB, YAD/RRR-motif-containing domain / Ultra-violet resistance protein B / Penicillin-binding protein 1b fold / Penicillin-binding protein 1b domain / UvrABC system, subunit B / UVR domain superfamily / UvrB/uvrC motif / UvrB, interaction domain / UvrB interaction domain / UVR domain / UVR domain profile. / Helicase/UvrB, N-terminal / Type III restriction enzyme, res subunit / Helix Hairpins / Helix non-globular / Special / Helicase conserved C-terminal domain / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / UvrABC system protein B
Similarity search - Component
Biological speciesBacillus caldotenax (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.15 Å
AuthorsTheis, K. / Chen, P.J. / Skorvaga, M. / Van Houten, B. / Kisker, C.
Citation
Journal: EMBO J. / Year: 1999
Title: Crystal structure of UvrB, a DNA helicase adapted for nucleotide excision repair.
Authors: Theis, K. / Chen, P.J. / Skorvaga, M. / Van Houten, B. / Kisker, C.
#1: Journal: Embo J. / Year: 1999
Title: Strand opening by the UvrA2B complex allows dynamic recognition of DNA damage
Authors: Zou, Y. / Van Houten, B.
History
DepositionOct 30, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 3, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_sheet / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_sheet.number_strands / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: EXCINUCLEASE UVRABC COMPONENT UVRB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,0925
Polymers75,4301
Non-polymers6624
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)153.443, 153.443, 80.741
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein EXCINUCLEASE UVRABC COMPONENT UVRB


Mass: 75429.875 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus caldotenax (bacteria) / Plasmid: PTYB1 / Production host: Escherichia coli (E. coli) / References: UniProt: P56981
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM

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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

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
13.6466.18
2
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2951vapor diffusion98 mg/ml UvrB, 500 mM NaCl, 14-18% PEG 6000, 10 mM ZnCl2, 100 mM Bicine pH 9, pH 9.0, VAPOR DIFFUSION, temperature 295K
2952soaking95 mM ATP 5 mM MgCl2 500 mM NaCl, 14-18% PEG 6000, 10 mM ZnCl2, 100 mM Bicine pH 9, pH 9.0, Soaking, temperature 295K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
18 mg/mlprotein1drop
2500 mM1dropNaCl
320 mMTris-HCl1drop
41 mMdithiothreitol1drop
50.1 mMEDTA1drop
60.03 %dodecylmaltoside1drop
714-18 %PEG60001dropor PEG20000
810 mM1dropZnCl2
9100 mMBicine1drop
1020 %PEG60001reservoir
11500 mM1reservoirNaCl
12100 mMTris-HCl1reservoir

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X26C / Wavelength: 1.1
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 9, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 3.15→20 Å / Num. all: 19075 / Num. obs: 19075 / % possible obs: 100 % / Observed criterion σ(F): -1000 / Observed criterion σ(I): -3 / Redundancy: 6 % / Biso Wilson estimate: 76 Å2 / Rmerge(I) obs: 0.14 / Net I/σ(I): 17.7
Reflection shellResolution: 3.15→3.32 Å / Redundancy: 7 % / Rmerge(I) obs: 0.48 / Num. unique all: 2669 / % possible all: 100
Reflection
*PLUS
Reflection shell
*PLUS
% possible obs: 100 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 3.6

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Processing

Software
NameClassification
REFMACrefinement
X-PLORrefinement
MAR345data collection
SCALEPACKdata scaling
RefinementResolution: 3.15→20 Å / σ(F): -1000 / σ(I): -1000 / Stereochemistry target values: Engh & Huber / Details: maximum likelyhood
RfactorNum. reflection% reflectionSelection details
Rfree0.335 954 -random
Rwork0.262 ---
all-19075 --
obs-19075 100 %-
Refinement stepCycle: LAST / Resolution: 3.15→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4632 0 34 0 4666
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.009
X-RAY DIFFRACTIONr_angle_d0.031
Software
*PLUS
Name: 'REFMAC AND XPLOR' / Classification: refinement
Refinement
*PLUS
Lowest resolution: 20 Å / Rfactor obs: 0.262
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDType
X-RAY DIFFRACTIONp_bond_d
X-RAY DIFFRACTIONp_angle_d

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