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- PDB-1t5l: Crystal structure of the DNA repair protein UvrB point mutant Y96... -

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Basic information

Entry
Database: PDB / ID: 1t5l
TitleCrystal structure of the DNA repair protein UvrB point mutant Y96A revealing a novel fold for domain 2
ComponentsUvrABC system protein B
KeywordsDNA excision repair / DNA damage / DNA repair / Nucleotide Excision Repair / UvrB / UvrA / UvrC / NER / Mfd / TRCF
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 / Penicillin-binding protein 1b fold / Penicillin-binding protein 1b domain / UvrB, YAD/RRR-motif-containing domain / Ultra-violet resistance protein B / UvrABC system, subunit B / UVR domain superfamily / UvrB/uvrC motif / UvrB, interaction domain / UvrB interaction domain ...Helix Hairpins - #240 / Penicillin-binding protein 1b fold / Penicillin-binding protein 1b domain / UvrB, YAD/RRR-motif-containing domain / Ultra-violet resistance protein B / 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 / Helicase conserved C-terminal domain / Special / 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 / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
UvrABC system protein B
Similarity search - Component
Biological speciesBacillus caldotenax (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsTruglio, J.J. / Croteau, D.L. / Skorvaga, M. / DellaVecchia, M.J. / Theis, K. / Mandavilli, B.S. / Van Houten, B. / Kisker, C.
CitationJournal: Embo J. / Year: 2004
Title: Interactions between UvrA and UvrB: the role of UvrB's domain 2 in nucleotide excision repair
Authors: Truglio, J.J. / Croteau, D.L. / Skorvaga, M. / DellaVecchia, M.J. / Theis, K. / Mandavilli, B.S. / Van Houten, B. / Kisker, C.
History
DepositionMay 4, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 22, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999AUTHORS INFORMED THAT THE SEQUENCE THEY PROVIDED IS CORRECT AND THAT THE SEQUENCE IN THE SWISS PROT ...AUTHORS INFORMED THAT THE SEQUENCE THEY PROVIDED IS CORRECT AND THAT THE SEQUENCE IN THE SWISS PROT ENTRY IS INCORRECT.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: UvrABC system protein B
B: UvrABC system protein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)151,2516
Polymers150,9902
Non-polymers2624
Water3,531196
1
A: UvrABC system protein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,6263
Polymers75,4951
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: UvrABC system protein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,6263
Polymers75,4951
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)150.815, 150.815, 159.832
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31A
41B
12A
22B
13A
23B
14A
24B
15A
25B

NCS domain segments:

Refine code: 4

Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111GLYGLYVALVALAA3 - 903 - 90
211GLYGLYVALVALBB3 - 903 - 90
321PHEPHELEULEUAA131 - 157131 - 157
421PHEPHELEULEUBB131 - 157131 - 157
112PROPROPROPROAA245 - 414245 - 414
212PROPROPROPROBB245 - 414245 - 414
113SERSERASPASPAA91 - 11791 - 117
213SERSERASPASPBB91 - 11791 - 117
114VALVALPHEPHEAA158 - 244158 - 244
214VALVALPHEPHEBB158 - 244158 - 244
115THRTHRVALVALAA415 - 595415 - 595
215THRTHRVALVALBB415 - 595415 - 595

NCS ensembles :
ID
1
2
3
4
5

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Components

#1: Protein UvrABC system protein B / UvrB protein / Excinuclease ABC subunit B


Mass: 75494.906 Da / Num. of mol.: 2 / Mutation: Y96A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus caldotenax (bacteria) / Gene: UVRB / Production host: Escherichia coli (E. coli) / References: UniProt: P56981
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 196 / Source method: isolated from a natural source / Formula: H2O

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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: 3.47 Å3/Da / Density % sol: 60 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG 6000, Tris, ZnCl2, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X26C / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.6→30 Å / Num. obs: 61397

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
COMOphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→25 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.895 / SU B: 11.316 / SU ML: 0.236 / Cross valid method: THROUGHOUT / ESU R: 0.405 / ESU R Free: 0.304 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.28674 3277 5.1 %RANDOM
Rwork0.22962 ---
obs0.23252 61362 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 36.744 Å2
Baniso -1Baniso -2Baniso -3
1-1.82 Å20.91 Å20 Å2
2--1.82 Å20 Å2
3----2.73 Å2
Refinement stepCycle: LAST / Resolution: 2.6→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9612 0 4 196 9812
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0219774
X-RAY DIFFRACTIONr_angle_refined_deg1.8681.96813208
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.58451188
X-RAY DIFFRACTIONr_chiral_restr0.130.21486
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.027432
X-RAY DIFFRACTIONr_nbd_refined0.2390.24294
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1710.2385
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2080.266
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1330.213
X-RAY DIFFRACTIONr_mcbond_it0.8991.55926
X-RAY DIFFRACTIONr_mcangle_it1.73529624
X-RAY DIFFRACTIONr_scbond_it2.62933848
X-RAY DIFFRACTIONr_scangle_it4.5224.53584
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Refine-ID: X-RAY DIFFRACTION

Ens-IDNumberTypeRms dev position (Å)Weight position
1900medium positional0.290.5
21392medium positional0.310.5
3226medium positional0.480.5
4720medium positional0.490.5
51452medium positional0.310.5
1900medium thermal0.92
21392medium thermal2.072
3226medium thermal0.672
4720medium thermal0.572
51452medium thermal1.152
LS refinement shellResolution: 2.602→2.669 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.398 252
Rwork0.337 4421

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