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- PDB-1qoj: Crystal Structure of E.coli UvrB C-terminal domain, and a model f... -

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Basic information

Entry
Database: PDB / ID: 1qoj
TitleCrystal Structure of E.coli UvrB C-terminal domain, and a model for UvrB-UvrC interaction.
ComponentsUVRBUvrABC endonuclease
KeywordsDNA EXCISION REPAIR / NUCLEOTIDE EXCISION REPAIR / UVRB PROTEIN / UVRB-C INTERACTION
Function / homology
Function and homology information


: / excinuclease ABC activity / excinuclease repair complex / nucleotide-excision repair, DNA damage recognition / nucleotide-excision repair, preincision complex assembly / SOS response / nucleotide-excision repair / response to radiation / ATP hydrolysis activity / DNA binding ...: / excinuclease ABC activity / excinuclease repair complex / nucleotide-excision repair, DNA damage recognition / nucleotide-excision repair, preincision complex assembly / SOS response / nucleotide-excision repair / response to radiation / ATP hydrolysis activity / DNA binding / ATP binding / identical protein binding / cytoplasm
Similarity search - Function
UVR domain / UvrB, YAD/RRR-motif-containing domain / Ultra-violet resistance protein B / UvrABC system, subunit B / DNA Excision Repair, Uvrb; Chain A / UVR domain superfamily / UvrB/uvrC motif / UvrB, interaction domain / UvrB interaction domain / UVR domain ...UVR domain / UvrB, YAD/RRR-motif-containing domain / Ultra-violet resistance protein B / UvrABC system, subunit B / DNA Excision Repair, Uvrb; Chain A / 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 / Helicase conserved C-terminal domain / Few Secondary Structures / Irregular / 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 nucleoside triphosphate hydrolase
Similarity search - Domain/homology
UvrABC system protein B / UvrABC system protein B
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3 Å
AuthorsSohi, M. / Alexandrovich, A. / Moolenaar, G. / Visse, R. / Goosen, N. / Vernede, X. / Fontecilla-Camps, J. / Champness, J. / Sanderson, M.R.
CitationJournal: FEBS Lett. / Year: 2000
Title: Crystal Structure of E.Coli Uvrb C-Terminal Domain, and a Model for Uvrb-Uvrc Interaction
Authors: Sohi, M. / Alexandrovich, A. / Moolenaar, G. / Visse, R. / Goosen, N. / Vernede, X. / Fontecilla-Camps, J. / Champness, J. / Sanderson, M.R.
History
DepositionNov 10, 1999Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 10, 2000Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 6, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_conn
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: UVRB
B: UVRB


Theoretical massNumber of molelcules
Total (without water)15,3722
Polymers15,3722
Non-polymers00
Water0
1
A: UVRB
B: UVRB

A: UVRB
B: UVRB


Theoretical massNumber of molelcules
Total (without water)30,7444
Polymers30,7444
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_675-x+1,-y+2,z1
Buried area2180 Å2
ΔGint-21.5 kcal/mol
Surface area13360 Å2
MethodPQS
Unit cell
Length a, b, c (Å)84.810, 84.810, 53.190
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number171
Space group name H-MP62
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.95228, 0.29719, 0.06957), (0.2917, -0.95322, 0.07923), (0.08986, -0.05515, -0.99443)
Vector: -14.65653, 93.7687, 9.34176)

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Components

#1: Protein UVRB / UvrABC endonuclease


Mass: 7685.937 Da / Num. of mol.: 2 / Fragment: C-TERMINAL DOMAIN / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: PP3398 / References: UniProt: P07025, UniProt: P0A8F8*PLUS

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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: 3.71 Å3/Da / Density % sol: 75 %
Crystal growMethod: vapor diffusion / pH: 8.5
Details: BY VAPOUR DIFFUSION 3UL PROTEIN SOLUTION: 2MG/ML UVRB DOMAIN, 20MM TRIS-CL PH7.0, 150MM NACL 0.1% NAN3 + 3UL WELL SOLUTION 0.5ML WELL SOLUTION: 35% SAT. AMMONIUM SULPHATE 100MM TRIS-CL PH8.8, 0.1% NAN3, pH 8.50
Crystal grow
*PLUS
Temperature: 5 ℃ / pH: 7 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
12 mg/mlprotein1drop
220 mMTris-HCl1drop
3150 mM1dropNaCl
40.1 %1dropNaN3
535 %satammonium sulfate1reservoir
6100 mMTris-HCl1reservoir
70.1 %1reservoirNaN3

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.8856, 0.9788, 0.9789
DetectorType: MARRESEARCH / Detector: CCD / Date: May 15, 1999
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.88561
20.97881
30.97891
ReflectionResolution: 3→20 Å / Num. obs: 4450 / % possible obs: 100 % / Redundancy: 3.86 % / Rmerge(I) obs: 0.102
Reflection shellResolution: 3→3.11 Å / Redundancy: 3.71 % / Rmerge(I) obs: 0.511 / Mean I/σ(I) obs: 2.75 / % possible all: 100
Reflection
*PLUS
% possible obs: 100 % / Num. measured all: 65208

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
SHELXL-97phasing
SOLVEphasing
SHELXL-97refinement
RefinementMethod to determine structure: MAD / Resolution: 3→20 Å / Num. parameters: 3031 / Num. restraintsaints: 3887 / Cross valid method: THROUGHOUT / σ(F): 4 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
obs0.3266 -100 %-
all-8435 --
Rfree---RANDOM
Refine analyzeNum. disordered residues: 0
Refinement stepCycle: LAST / Resolution: 3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms713 0 0 0 713
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.006
X-RAY DIFFRACTIONs_angle_d0.022
X-RAY DIFFRACTIONs_similar_dist
X-RAY DIFFRACTIONs_from_restr_planes
X-RAY DIFFRACTIONs_zero_chiral_vol
X-RAY DIFFRACTIONs_non_zero_chiral_vol
X-RAY DIFFRACTIONs_anti_bump_dis_restr
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt
X-RAY DIFFRACTIONs_similar_adp_cmpnt
X-RAY DIFFRACTIONs_approx_iso_adps
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
Num. reflection obs: 6381 / σ(F): 4 / Num. reflection Rfree: 327 / % reflection Rfree: 5 % / Rfactor all: 0.286
Solvent computation
*PLUS
Displacement parameters
*PLUS

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