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- PDB-2vf8: Crystal structure of UvrA2 from Deinococcus radiodurans -

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Basic information

Entry
Database: PDB / ID: 2vf8
TitleCrystal structure of UvrA2 from Deinococcus radiodurans
ComponentsEXCINUCLEASE ABC SUBUNIT A
KeywordsDNA BINDING PROTEIN / NUCLEOTIDE-BINDING / ZINC-BINDING DOMAIN / SOS RESPONSE / METAL-BINDING / EXCISION NUCLEASE / ZINC-FINGER / ATP-BINDING / DNA-BINDING / DNA EXCISION / ZINC / CYTOPLASM / DNA DAMAGE / DNA REPAIR / ABC PROTEIN / DNA-BINDING PROTEIN
Function / homology
Function and homology information


excinuclease repair complex / nuclease activity / nucleotide-excision repair / ATP hydrolysis activity / DNA binding / ATP binding / identical protein binding / metal ion binding / cytoplasm
Similarity search - Function
ABC transporter ATPase domain-like / ABC transporter ATPase like fold / ABC transporter ATPase like domain / UvrABC system subunit A / UvrA DNA-binding domain / UvrA DNA-binding domain / Helicase, Ruva Protein; domain 3 / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter ...ABC transporter ATPase domain-like / ABC transporter ATPase like fold / ABC transporter ATPase like domain / UvrABC system subunit A / UvrA DNA-binding domain / UvrA DNA-binding domain / Helicase, Ruva Protein; domain 3 / 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 / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / PHOSPHATE ION / UvrABC system protein A
Similarity search - Component
Biological speciesDEINOCOCCUS RADIODURANS (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsTimmins, J. / Gordon, E. / Caria, S. / Leonard, G. / Kuo, M.S. / Monchois, V. / McSweeney, S.
CitationJournal: Structure / Year: 2009
Title: Structural and Mutational Analyses of Deinococcus Radiodurans Uvra2 Provide Insight Into DNA Binding and Damage Recognition by Uvras.
Authors: Timmins, J. / Gordon, E. / Caria, S. / Leonard, G. / Acajjaoui, S. / Kuo, M.S. / Monchois, V. / Mcsweeney, S.
History
DepositionOct 31, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 16, 2008Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / 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_database_status.status_code_sf / _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_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.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_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: EXCINUCLEASE ABC SUBUNIT A
B: EXCINUCLEASE ABC SUBUNIT A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)186,16319
Polymers183,3292
Non-polymers2,83417
Water1,838102
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: EXCINUCLEASE ABC SUBUNIT A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,9388
Polymers91,6651
Non-polymers1,2737
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
B: EXCINUCLEASE ABC SUBUNIT A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,22511
Polymers91,6651
Non-polymers1,56110
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)149.632, 171.040, 204.205
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B
13A
23B
14A
24B

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PHEPHEGLUGLU5AA10 - 14010 - 140
21PHEPHEGLUGLU5BB10 - 14010 - 140
12VALVALGLYGLY4AA160 - 280160 - 280
22VALVALGLYGLY4BB160 - 280160 - 280
13LEULEULEULEU5AA295 - 485295 - 485
23LEULEULEULEU5BB295 - 485295 - 485
14ALAALAARGARG5AA500 - 842500 - 842
24ALAALAARGARG5BB500 - 842500 - 842

NCS ensembles :
ID
1
2
3
4

NCS oper: (Code: given
Matrix: (-0.249, 0.906, -0.342), (0.894, 0.08, -0.44), (-0.371, -0.416, -0.83)
Vector: -21.21179, 107.09262, 223.92561)

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein EXCINUCLEASE ABC SUBUNIT A / UVRA2


Mass: 91664.555 Da / Num. of mol.: 2 / Fragment: RESIDUES 81-922 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DEINOCOCCUS RADIODURANS (radioresistant)
Plasmid: PLX02 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9RYW8

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Non-polymers , 5 types, 119 molecules

#2: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 102 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsENGINEERED RESIDUE IN CHAIN A, GLN 826 TO ARG ENGINEERED RESIDUE IN CHAIN B, GLN 826 TO ARG

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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: 3.63 Å3/Da / Density % sol: 65.86 % / Description: NONE
Crystal growpH: 5.2
Details: 17% PEG 3000, 0.1M CITRATE PH 5.2, 125MM AMMONIUM SULPHATE AND 1MM TCEP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.2825
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2825 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 50546 / % possible obs: 96.4 % / Observed criterion σ(I): 0 / Redundancy: 4.6 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 11.2
Reflection shellResolution: 3→3.2 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 2.1 / % possible all: 98.2

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2VF7

2vf7


Resolution: 3→102.06 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.871 / SU B: 41.8 / SU ML: 0.378 / Cross valid method: THROUGHOUT / ESU R Free: 0.471 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.294 2543 5 %RANDOM
Rwork0.217 ---
obs0.221 47950 96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 67.55 Å2
Baniso -1Baniso -2Baniso -3
1--4.19 Å20 Å20 Å2
2--7.13 Å20 Å2
3----2.94 Å2
Refinement stepCycle: LAST / Resolution: 3→102.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12569 0 157 102 12828
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.02213012
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9641.98717719
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.551639
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.04923.058582
X-RAY DIFFRACTIONr_dihedral_angle_3_deg24.389152066
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.98315128
X-RAY DIFFRACTIONr_chiral_restr0.1230.21968
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.029977
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2770.27093
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3240.28654
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.20.2559
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2320.266
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2280.29
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.721.58342
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.269213100
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.48235220
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.514.54617
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

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

Ens-IDNumberTypeRms dev position (Å)Weight position
1516medium positional0.410.5
2968medium positional0.540.5
3764medium positional0.350.5
41282medium positional0.560.5
1460loose positional1.115
3719loose positional0.655
41116loose positional0.915
1516medium thermal0.992
2968medium thermal0.442
3764medium thermal0.962
41282medium thermal1.082
1460loose thermal1.8810
3719loose thermal2.2510
41116loose thermal2.2310
LS refinement shellResolution: 3→3.08 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.413 186 -
Rwork0.316 3551 -
obs--97.67 %

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