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- PDB-6n9l: Crystal structure of T. maritima UvrA d117-399 with ADP -

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Basic information

Entry
Database: PDB / ID: 6n9l
TitleCrystal structure of T. maritima UvrA d117-399 with ADP
ComponentsUvrABC system protein A
KeywordsDNA BINDING PROTEIN / UvrA / Nucleotide Excision Repair / NER / ADP / hydrolase / DNA damage repair
Function / homology
Function and homology information


excinuclease ABC activity / excinuclease repair complex / SOS response / nucleotide-excision repair / ATP hydrolysis activity / DNA binding / zinc ion binding / ATP binding / cytoplasm
Similarity search - Function
UvrA, interaction domain / UvrA interaction domain / UvrABC system subunit A / UvrA DNA-binding domain / UvrA DNA-binding domain / ATP-grasp fold, subdomain 1 / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter / ABC transporter-like, ATP-binding domain ...UvrA, interaction domain / UvrA interaction domain / UvrABC system subunit A / UvrA DNA-binding domain / UvrA DNA-binding domain / ATP-grasp fold, subdomain 1 / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / UvrABC system protein A
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.01 Å
AuthorsHartley, S. / Case, B. / Osuga, M. / Hingorani, M.M. / Jeruzalmi, D.
Funding support United States, 2items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)MCB# 1330528 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R15 GM114743 United States
CitationJournal: Nucleic Acids Res. / Year: 2019
Title: The ATPase mechanism of UvrA2 reveals the distinct roles of proximal and distal ATPase sites in nucleotide excision repair.
Authors: Case, B.C. / Hartley, S. / Osuga, M. / Jeruzalmi, D. / Hingorani, M.M.
History
DepositionDec 3, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 1, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 3, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: UvrABC system protein A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,2504
Polymers71,3301
Non-polymers9203
Water7,764431
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1440 Å2
ΔGint-12 kcal/mol
Surface area26800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)143.134, 81.379, 90.416
Angle α, β, γ (deg.)90.00, 125.30, 90.00
Int Tables number5
Space group name H-MC121
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein UvrABC system protein A / UvrA protein / Excinuclease ABC subunit A


Mass: 71329.703 Da / Num. of mol.: 1 / Mutation: d117-399
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: uvrA, TM_0480 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9WYV0
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 431 / 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: 3.02 Å3/Da / Density % sol: 59.21 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / Details: 100 mM HEPES-NaOH, pH 7.5 and 22w/v PEG 3350 / PH range: 7.0-7.5

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Data collection

Diffraction
IDMean temperature (K)Crystal-IDSerial crystal experiment
198.21N
21001N
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSSRL BL12-210.97946
SYNCHROTRONAPS 21-ID-E20.97918
Detector
TypeIDDetectorDate
DECTRIS PILATUS 6M1PIXELMar 20, 2016
DECTRIS EIGER X 16M2PIXELJun 28, 2018
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si(111)SINGLE WAVELENGTHMx-ray1
2Si(111)SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.979461
20.979181
ReflectionResolution: 2.01→38.049 Å / Num. obs: 51809 / % possible obs: 91.81 % / Redundancy: 3.9 % / CC1/2: 0.994 / Net I/σ(I): 8.42
Reflection shellResolution: 2.01→2.082 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 1.09 / Num. unique obs: 4575 / CC1/2: 0.525 / % possible all: 81.93

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3UX8

3ux8


Resolution: 2.01→38.049 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 21.08
RfactorNum. reflection% reflection
Rfree0.2013 1141 2.2 %
Rwork0.1694 --
obs0.1701 51809 91.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.01→38.049 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4881 0 55 431 5367
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0095011
X-RAY DIFFRACTIONf_angle_d1.0766777
X-RAY DIFFRACTIONf_dihedral_angle_d10.4673052
X-RAY DIFFRACTIONf_chiral_restr0.065789
X-RAY DIFFRACTIONf_plane_restr0.006862
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.01-2.10150.25811340.24995612X-RAY DIFFRACTION82
2.1015-2.21230.26641230.21335802X-RAY DIFFRACTION84
2.2123-2.35090.24241370.18956193X-RAY DIFFRACTION90
2.3509-2.53240.20591490.17826376X-RAY DIFFRACTION93
2.5324-2.78710.22921380.17436443X-RAY DIFFRACTION93
2.7871-3.19020.21211520.16996627X-RAY DIFFRACTION96
3.1902-4.01870.16911510.15236761X-RAY DIFFRACTION98
4.0187-38.0560.18091570.1536854X-RAY DIFFRACTION97
Refinement TLS params.Method: refined / Origin x: 21.7381 Å / Origin y: 3.0624 Å / Origin z: 25.9285 Å
111213212223313233
T0.1438 Å20.0078 Å20.0015 Å2-0.123 Å20.022 Å2--0.1334 Å2
L0.5692 °20.0623 °20.0767 °2-0.6217 °20.1356 °2--0.5207 °2
S-0.0089 Å °0.0296 Å °-0.0073 Å °-0.0137 Å °0.0195 Å °0.0367 Å °0.0363 Å °-0.0172 Å °-0.0001 Å °
Refinement TLS groupSelection details: all

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