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- PDB-7wrw: Structure of Deinococcus radiodurans HerA -

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Basic information

Entry
Database: PDB / ID: 7wrw
TitleStructure of Deinococcus radiodurans HerA
ComponentsHerA
KeywordsTRANSLOCASE / hexamer / ATPase / RecA-like / helicase
Function / homology: / nucleotide binding / P-loop containing nucleoside triphosphate hydrolase / metal ion binding / Helicase HerA central domain-containing protein
Function and homology information
Biological speciesDeinococcus radiodurans (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.00008283281 Å
AuthorsCheng, K.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32100017 China
CitationJournal: Bmc Biol. / Year: 2023
Title: Structural and DNA end resection study of the bacterial NurA-HerA complex.
Authors: Yang, J. / Sun, Y. / Wang, Y. / Hao, W. / Cheng, K.
History
DepositionJan 27, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 1, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 16, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: HerA
C: HerA
F: HerA
D: HerA
E: HerA
A: HerA


Theoretical massNumber of molelcules
Total (without water)404,7156
Polymers404,7156
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area27220 Å2
ΔGint-100 kcal/mol
Surface area130030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)279.030, 279.030, 105.680
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z

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Components

#1: Protein
HerA


Mass: 67452.461 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Deinococcus radiodurans (radioresistant)
Strain: ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422
Gene: DR_0837 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9RW32

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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: 2.93 Å3/Da / Density % sol: 58.08 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1M HEPES (pH7.5), 1.3M NaAc

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 20, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→49.41 Å / Num. obs: 94205 / % possible obs: 99.8 % / Redundancy: 6.2 % / Biso Wilson estimate: 79 Å2 / Rrim(I) all: 0.083 / Net I/σ(I): 16.4
Reflection shellResolution: 3→3.05 Å / Num. unique obs: 4621 / Rrim(I) all: 0.835

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
autoPROCdata processing
Cootmodel building
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 3.00008283281→9.99747115467 Å / SU ML: 0.376541397477 / Cross valid method: FREE R-VALUE / σ(F): 1.34352208559 / Phase error: 26.1563760267
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.245596815319 4632 5.06019358081 %
Rwork0.224971716881 86906 -
obs0.22600367168 91538 99.848380728 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 70 Å2
Refinement stepCycle: LAST / Resolution: 3.00008283281→9.99747115467 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms27153 0 0 0 27153
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.010175599331627716
X-RAY DIFFRACTIONf_angle_d1.2789561741537623
X-RAY DIFFRACTIONf_chiral_restr0.1144314724864211
X-RAY DIFFRACTIONf_plane_restr0.007225427090655007
X-RAY DIFFRACTIONf_dihedral_angle_d20.642218054110353
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0001-3.03320.394785214881350.3437216590912886X-RAY DIFFRACTION98.5966057441
3.0332-3.06790.3425956772021710.3201265811972857X-RAY DIFFRACTION99.8351467194
3.0679-3.10420.3496808228341430.3163019484452910X-RAY DIFFRACTION99.9018324607
3.1042-3.14230.3335490007451500.31159307082851X-RAY DIFFRACTION100
3.1423-3.18230.3069782094671580.2974378387682884X-RAY DIFFRACTION99.9671376931
3.1823-3.22450.2948875783171340.2920826881932904X-RAY DIFFRACTION100
3.2245-3.2690.3346822017971940.2915687944822851X-RAY DIFFRACTION99.9343616672
3.269-3.3160.3000813258431750.2964251850762875X-RAY DIFFRACTION99.8690242305
3.316-3.36590.3099063085391530.2785953804442848X-RAY DIFFRACTION99.9333999334
3.3659-3.41890.324953969841440.2722091314122916X-RAY DIFFRACTION99.9673309376
3.4189-3.47540.2747719861911530.2728601924962901X-RAY DIFFRACTION99.9018645731
3.4754-3.53590.2678308171521540.2663685721552890X-RAY DIFFRACTION99.9671592775
3.5359-3.60080.2731774499241600.2600996059022861X-RAY DIFFRACTION100
3.6008-3.67070.2685632859381710.2543791001382896X-RAY DIFFRACTION99.8697492673
3.6707-3.74640.3062354526311610.2409866436162857X-RAY DIFFRACTION99.9006951341
3.7464-3.82880.2411044036371560.2371940326842900X-RAY DIFFRACTION99.9019287349
3.8288-3.91890.2574461900211880.2319143008482881X-RAY DIFFRACTION99.8698340384
3.9189-4.01820.2609095155711300.2325809677712900X-RAY DIFFRACTION100
4.0182-4.12830.2292998256421630.2226993371792879X-RAY DIFFRACTION100
4.1283-4.25160.2373287927371680.2162668094722916X-RAY DIFFRACTION100
4.2516-4.39110.2130193416271530.1979268215162903X-RAY DIFFRACTION99.9019287349
4.3911-4.55090.1987775794361510.1975649663122884X-RAY DIFFRACTION99.8355263158
4.5509-4.73690.2203766763871730.1942599261062899X-RAY DIFFRACTION99.8699609883
4.7369-4.95750.2156544514541430.1913398387592891X-RAY DIFFRACTION99.9012183075
4.9575-5.2260.2472270409861520.2068466175892929X-RAY DIFFRACTION99.935128122
5.226-5.56410.255817588571320.2284112731712953X-RAY DIFFRACTION99.7736093144
5.5641-6.01110.2453210782461280.2337789548862920X-RAY DIFFRACTION99.9672023614
6.0111-6.64840.2481085002321430.2176221477612953X-RAY DIFFRACTION99.6138996139
6.6484-7.68670.216998455891480.1981065921832939X-RAY DIFFRACTION99.7415185784
7.6867-9.99740.1512995585661480.1507938645952972X-RAY DIFFRACTION99.6486745449
Refinement TLS params.Method: refined / Origin x: 193.238422484 Å / Origin y: 47.2725973369 Å / Origin z: 110.795745146 Å
111213212223313233
T0.630395061855 Å2-0.0526591531401 Å2-0.029524087124 Å2-0.456750844474 Å20.110458529743 Å2--0.5658829219 Å2
L0.344588239731 °2-0.0551114463963 °20.0513037274102 °2-0.486579710852 °2-0.141068660999 °2--0.468462632744 °2
S-0.0313226727074 Å °-0.0269337591633 Å °0.0328211392839 Å °0.139220237767 Å °-0.0856140121075 Å °-0.222377621936 Å °-0.151812595724 Å °0.173486245422 Å °0.11302003678 Å °
Refinement TLS groupSelection details: all

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