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- PDB-3ux8: Crystal structure of UvrA -

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Basic information

Entry
Database: PDB / ID: 3ux8
TitleCrystal structure of UvrA
ComponentsExcinuclease ABC, A subunit
KeywordsDNA BINDING PROTEIN / UvrA / nucleotide excision repair / DNA repair / ABC ATPase / DNA
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 / identical protein 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 / UvrABC system protein A
Similarity search - Component
Biological speciesGeobacillus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsSamuels, M.A. / Pakotiprapha, D. / Jeruzalmi, D.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2012
Title: Structure and mechanism of the UvrA-UvrB DNA damage sensor.
Authors: Pakotiprapha, D. / Samuels, M. / Shen, K. / Hu, J.H. / Jeruzalmi, D.
History
DepositionDec 4, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 8, 2012Provider: repository / Type: Initial release
Revision 1.1May 9, 2012Group: Database references
Revision 1.2May 7, 2014Group: Other
Revision 1.3Aug 16, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.4Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / 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.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_ref_seq_dif.details / _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 ABC, A subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,2153
Polymers73,7221
Non-polymers4932
Water3,603200
1
A: Excinuclease ABC, A subunit
hetero molecules

A: Excinuclease ABC, A subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)148,4296
Polymers147,4442
Non-polymers9854
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area3170 Å2
ΔGint-17 kcal/mol
Surface area46610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.653, 51.330, 112.395
Angle α, β, γ (deg.)90.00, 97.27, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Excinuclease ABC, A subunit


Mass: 73721.961 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus (bacteria) / Strain: Y412MC52 / Gene: GYMC52_3203, uvrA / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) pLysS / References: UniProt: E8SW61, UniProt: A0A0E0TG05*PLUS
#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.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 200 / 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: 2.5 Å3/Da / Density % sol: 50.74 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 9
Details: BICINE, PEG 20,000, 1,4-dioxane, pH 9.0, vapor diffusion, hanging drop, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97919 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97919 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 42002 / % possible obs: 98.6 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.056 / Χ2: 1.177 / Net I/σ(I): 15.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.1-2.183.30.441691.908198.8
2.18-2.263.30.28341691.263199.1
2.26-2.373.40.21841981.712199.2
2.37-2.493.40.1742261.063199.5
2.49-2.653.40.1342141.041199.6
2.65-2.853.40.09242290.954199.5
2.85-3.143.30.06542380.947199.8
3.14-3.593.30.04642340.973199.5
3.59-4.523.30.0442380.911198.6
4.52-503.30.0340870.998192.8

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 45.88 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å37.13 Å
Translation2.5 Å37.13 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.1.4phasing
REFMAC5.6.0117refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→37.08 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.918 / Occupancy max: 1 / Occupancy min: 1 / SU B: 9.719 / SU ML: 0.123 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.219 / ESU R Free: 0.185 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT; U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2453 2026 5 %RANDOM
Rwork0.2105 ---
obs0.2122 40344 94.43 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 95.38 Å2 / Biso mean: 38.0648 Å2 / Biso min: 19.67 Å2
Baniso -1Baniso -2Baniso -3
1--0.62 Å20 Å21.08 Å2
2--0.23 Å20 Å2
3---0.67 Å2
Refinement stepCycle: LAST / Resolution: 2.1→37.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4338 0 28 200 4566
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0194429
X-RAY DIFFRACTIONr_angle_refined_deg1.2571.9865985
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.345558
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.59323.367196
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.44215782
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6031543
X-RAY DIFFRACTIONr_chiral_restr0.0810.2687
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213296
LS refinement shellResolution: 2.103→2.158 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.275 136 -
Rwork0.232 2414 -
all-2550 -
obs--83.58 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.4292-0.1505-0.39650.79620.04112.273-0.04540.1314-0.1899-0.10770.0835-0.0870.21850.1824-0.03820.0930.014-0.00110.055-0.0360.054664.39336.88117.76
22.4815-0.3009-0.40661.25840.38122.00640.04180.04640.0609-0.0048-0.02480.12590.0319-0.1458-0.0170.0036-0.0087-0.00730.03210.02610.043842.03647.36936.463
33.9518-1.4608-1.7441.9661.77865.50550.07910.78490.1189-0.3571-0.22780.1588-0.3614-0.59460.14870.16780.0494-0.0370.29640.06410.088545.15548.4838.963
43.20141.41050.60771.749-0.10851.3983-0.01250.05640.3295-0.0478-0.05230.0196-0.05630.08940.06480.02180.01730.02370.04080.0220.085374.1861.19740.986
50000000000000000.22290.0136-0.01080.25430.06970.17782.01869.35330.357
621.87191.43295.827528.9592-3.50962.07770.6538-0.2439-0.3571-0.8158-0.36621.11230.2953-0.0258-0.28760.21830.0236-0.02020.20960.01140.149837.93852.54920.655
70.76920.0860.03160.210.05990.43150.00510.0270.01910.00190.01590.01470.04620.0169-0.02090.1555-0.0006-0.00770.11040.04540.093357.76147.76333.029
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 88
2X-RAY DIFFRACTION1A504 - 591
3X-RAY DIFFRACTION2A609 - 687
4X-RAY DIFFRACTION2A843 - 949
5X-RAY DIFFRACTION3A89 - 105
6X-RAY DIFFRACTION3A433 - 503
7X-RAY DIFFRACTION4A688 - 842
8X-RAY DIFFRACTION5A1001
9X-RAY DIFFRACTION6A1002
10X-RAY DIFFRACTION7A1101 - 1300

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