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- PDB-3pih: T. maritima UvrA in complex with fluorescein-modified DNA -

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Basic information

Entry
Database: PDB / ID: 3pih
TitleT. maritima UvrA in complex with fluorescein-modified DNA
Components
  • DNA (32-MER)
  • UvrABC system protein A
KeywordsHYDROLASE/DNA / hydrolase / ABC ATPase / DNA repair / nucleotide excision repair / UvrB / HYDROLASE-DNA complex
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, A domain / ATP-grasp fold, subdomain 1 / Dna Ligase; domain 1 / ABC transporter-like, conserved site / ABC transporters family signature. ...UvrA, interaction domain / UvrA interaction domain / UvrABC system subunit A / UvrA DNA-binding domain / UvrA DNA-binding domain / ATP-grasp fold, A domain / ATP-grasp fold, subdomain 1 / Dna Ligase; domain 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. / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PYROPHOSPHATE / DNA / DNA (> 10) / UvrABC system protein A
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsJaciuk, M. / Nowak, E. / Nowotny, M.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2011
Title: Structure of UvrA nucleotide excision repair protein in complex with modified DNA.
Authors: Jaciuk, M. / Nowak, E. / Skowronek, K. / Tanska, A. / Nowotny, M.
History
DepositionNov 6, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 19, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Sep 6, 2023Group: 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_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / 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.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _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: UvrABC system protein A
D: DNA (32-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,5127
Polymers112,9602
Non-polymers5525
Water43224
1
A: UvrABC system protein A
D: DNA (32-MER)
hetero molecules

A: UvrABC system protein A
D: DNA (32-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)227,02414
Polymers225,9194
Non-polymers1,10410
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Buried area9370 Å2
ΔGint-65 kcal/mol
Surface area81370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.510, 107.510, 108.256
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number77
Space group name H-MP42

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Components

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


Mass: 103118.367 Da / Num. of mol.: 1
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: DNA chain DNA (32-MER)


Mass: 9841.340 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthetic DNA oligo
#3: Chemical ChemComp-PPV / PYROPHOSPHATE / Pyrophosphate


Mass: 177.975 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: H4O7P2
#4: Chemical ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 24 / 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: 2.77 Å3/Da / Density % sol: 55.58 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 49-52% MPD, 0.1-0.2 M ammonium phosphate and 0.1 M Tris pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 12, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. all: 26300 / Num. obs: 19081 / % possible obs: 72.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.4 % / Rmerge(I) obs: 0.061
Reflection shellResolution: 2.9→2.95 Å / Rmerge(I) obs: 0.412 / Mean I/σ(I) obs: 2.1 / % possible all: 62.7

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Processing

Software
NameVersionClassification
MAR345data collection
PHASERphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2R6F

2r6f


Resolution: 2.9→48.08 Å / SU ML: 0.44 / σ(F): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2651 1275 5.03 %random
Rwork0.198 ---
obs0.2014 -92.48 %-
Solvent computationShrinkage radii: 1.06 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 46.751 Å2 / ksol: 0.272 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--3.9588 Å2-0 Å20 Å2
2---3.9588 Å2-0 Å2
3---7.9176 Å2
Refinement stepCycle: LAST / Resolution: 2.9→48.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6395 653 21 24 7093
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0067247
X-RAY DIFFRACTIONf_angle_d1.0469951
X-RAY DIFFRACTIONf_dihedral_angle_d18.6042735
X-RAY DIFFRACTIONf_chiral_restr0.0631147
X-RAY DIFFRACTIONf_plane_restr0.0041174
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-3.01620.3927930.25231755X-RAY DIFFRACTION61
3.0162-3.15340.33511400.26292362X-RAY DIFFRACTION83
3.1534-3.31960.3551420.23172716X-RAY DIFFRACTION94
3.3196-3.52750.31011750.21332777X-RAY DIFFRACTION97
3.5275-3.79980.30991400.18572853X-RAY DIFFRACTION98
3.7998-4.1820.25471350.17432866X-RAY DIFFRACTION99
4.182-4.78670.23291450.16082900X-RAY DIFFRACTION100
4.7867-6.02880.26361540.20822893X-RAY DIFFRACTION100
6.0288-48.08650.20811510.20182936X-RAY DIFFRACTION99

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