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- PDB-2vf7: Crystal structure of UvrA2 from Deinococcus radiodurans -

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Basic information

Entry
Database: PDB / ID: 2vf7
TitleCrystal structure of UvrA2 from Deinococcus radiodurans
ComponentsEXCINUCLEASE ABC, SUBUNIT A.
KeywordsDNA BINDING PROTEIN / DNA-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 / UvrABC system protein A
Similarity search - Component
Biological speciesDEINOCOCCUS RADIODURANS (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 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 1.3Jul 12, 2017Group: Derived calculations / Category: pdbx_struct_conn_angle / struct_conn
Revision 1.4Jun 6, 2018Group: Data collection / Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_oper_list / pdbx_struct_sheet_hbond / struct_conf / struct_sheet / struct_sheet_order / struct_sheet_range / struct_site / struct_site_gen
Item: _citation.page_last / _citation.pdbx_database_id_DOI ..._citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name / _pdbx_struct_assembly.method_details / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type / _pdbx_struct_oper_list.vector[1] / _pdbx_struct_oper_list.vector[3] / _pdbx_struct_sheet_hbond.range_1_auth_atom_id / _pdbx_struct_sheet_hbond.range_1_auth_comp_id / _pdbx_struct_sheet_hbond.range_1_auth_seq_id / _pdbx_struct_sheet_hbond.range_1_label_atom_id / _pdbx_struct_sheet_hbond.range_1_label_comp_id / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_auth_atom_id / _pdbx_struct_sheet_hbond.range_2_auth_comp_id / _pdbx_struct_sheet_hbond.range_2_auth_seq_id / _pdbx_struct_sheet_hbond.range_2_label_atom_id / _pdbx_struct_sheet_hbond.range_2_label_comp_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _pdbx_struct_sheet_hbond.sheet_id / _struct_conf.beg_auth_comp_id / _struct_conf.beg_auth_seq_id / _struct_conf.beg_label_comp_id / _struct_conf.beg_label_seq_id / _struct_conf.pdbx_PDB_helix_id / _struct_conf.pdbx_PDB_helix_length / _struct_sheet.id / _struct_sheet_order.sheet_id / _struct_sheet_range.sheet_id / _struct_site.details / _struct_site.id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id / _struct_site.pdbx_num_residues / _struct_site_gen.auth_asym_id / _struct_site_gen.auth_comp_id / _struct_site_gen.auth_seq_id / _struct_site_gen.label_asym_id / _struct_site_gen.label_comp_id / _struct_site_gen.label_seq_id / _struct_site_gen.pdbx_num_res / _struct_site_gen.site_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.
C: EXCINUCLEASE ABC, SUBUNIT A.
hetero molecules


Theoretical massNumber of molelcules
Total (without water)277,97416
Polymers274,9943
Non-polymers2,98013
Water10,755597
1
A: EXCINUCLEASE ABC, SUBUNIT A.
B: EXCINUCLEASE ABC, SUBUNIT A.
hetero molecules


Theoretical massNumber of molelcules
Total (without water)185,30010
Polymers183,3292
Non-polymers1,9708
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: EXCINUCLEASE ABC, SUBUNIT A.
hetero molecules

C: EXCINUCLEASE ABC, SUBUNIT A.
hetero molecules


Theoretical massNumber of molelcules
Total (without water)185,34812
Polymers183,3292
Non-polymers2,01910
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_658-x+1,y,-z+31
3
A: EXCINUCLEASE ABC, SUBUNIT A.
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,6505
Polymers91,6651
Non-polymers9854
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
B: EXCINUCLEASE ABC, SUBUNIT A.
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,6505
Polymers91,6651
Non-polymers9854
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
C: EXCINUCLEASE ABC, SUBUNIT A.
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,6746
Polymers91,6651
Non-polymers1,0105
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)271.710, 111.670, 103.290
Angle α, β, γ (deg.)90.00, 100.80, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11C-1049-

HOH

21C-1069-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
12A
22B
32C
13A
23B
33C
14A
24B
34C

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1116A11 - 130
2116B11 - 130
3116C11 - 130
1124A150 - 280
2124B150 - 280
3124C150 - 280
1136A300 - 495
2136B300 - 495
3136C300 - 495
1146A496 - 842
2146B496 - 842
3146C496 - 842

NCS ensembles :
ID
1
2
3
4

NCS oper:
IDCodeMatrixVector
1given(0.249, -0.952, 0.178), (-0.896, -0.296, -0.33), (0.367, -0.077, -0.927)163.01366, 163.06448, 214.57796
2given(0.6, 0.528, 0.601), (0.486, -0.837, 0.25), (0.636, 0.142, -0.759)-73.31448, 116.08421, 95.2169

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Components

#1: Protein EXCINUCLEASE ABC, SUBUNIT A. / UVRA2


Mass: 91664.555 Da / Num. of mol.: 3 / 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
#2: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 6 / 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.: 6 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 597 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, GLN 826 TO ARG ENGINEERED RESIDUE IN CHAIN B, GLN 826 TO ARG ...ENGINEERED RESIDUE IN CHAIN A, GLN 826 TO ARG ENGINEERED RESIDUE IN CHAIN B, GLN 826 TO ARG ENGINEERED RESIDUE IN CHAIN C, 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: 2.82 Å3/Da / Density % sol: 55.99 % / Description: NONE
Crystal growpH: 5.2 / Details: 17% PEG 3000, 0.1M CITRATE PH 5.2, 1MM TCEP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.98
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.3→47.3 Å / Num. obs: 123364 / % possible obs: 92.1 % / Observed criterion σ(I): 0 / Redundancy: 2.1 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 7.1
Reflection shellResolution: 2.3→2.4 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 1.1 / % possible all: 62.1

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
XDSdata reduction
XDSdata scaling
SHARPphasing
RefinementMethod to determine structure: MAD
Starting model: NONE

Resolution: 2.3→40 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.897 / SU B: 20.977 / SU ML: 0.264 / Cross valid method: THROUGHOUT / ESU R: 0.351 / ESU R Free: 0.281 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.295 6448 5 %RANDOM
Rwork0.219 ---
obs0.223 121316 95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 57.33 Å2
Baniso -1Baniso -2Baniso -3
1--0.64 Å20 Å20.33 Å2
2--1.04 Å20 Å2
3----0.27 Å2
Refinement stepCycle: LAST / Resolution: 2.3→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18711 0 169 597 19477
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.02219321
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5361.98326296
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.16252443
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.16122.912862
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.454153092
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.51415195
X-RAY DIFFRACTIONr_chiral_restr0.1060.22932
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0214830
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2210.28414
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3030.212696
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1750.2741
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0960.21
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2130.280
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1670.212
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4981.512440
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.864219483
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.23337716
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.9854.56809
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

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
21A1030medium positional0.650.5
22B1030medium positional0.750.5
23C1030medium positional0.740.5
11A901loose positional1.035
12B901loose positional0.745
13C901loose positional0.755
31A1519loose positional0.795
32B1519loose positional0.765
33C1519loose positional0.765
41A2418loose positional0.675
42B2418loose positional0.695
43C2418loose positional0.815
21A1030medium thermal0.572
22B1030medium thermal0.722
23C1030medium thermal0.562
11A901loose thermal1.7510
12B901loose thermal2.2910
13C901loose thermal1.6710
31A1519loose thermal2.0410
32B1519loose thermal2.410
33C1519loose thermal1.9310
41A2418loose thermal2.2410
42B2418loose thermal2.2410
43C2418loose thermal2.110
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.388 333 -
Rwork0.289 6085 -
obs--65.18 %

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