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- PDB-7wrx: Structure of Deinococcus radiodurans HerA-ADP complex -

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Basic information

Entry
Database: PDB / ID: 7wrx
TitleStructure of Deinococcus radiodurans HerA-ADP complex
ComponentsHerA
KeywordsTRANSLOCASE / hexamer / ATPase / RecA-like / helicase
Function / homology: / nucleotide binding / P-loop containing nucleoside triphosphate hydrolase / metal ion binding / ADENOSINE-5'-DIPHOSPHATE / Helicase HerA central domain-containing protein
Function and homology information
Biological speciesDeinococcus radiodurans (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.40003560509 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
Revision 1.2Nov 29, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: HerA
A: HerA
B: HerA
C: HerA
D: HerA
E: HerA
F: HerA
G: HerA
I: HerA
J: HerA
K: HerA
L: HerA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)814,60526
Polymers809,43012
Non-polymers5,17514
Water00
1
H: HerA
G: HerA
I: HerA
J: HerA
K: HerA
L: HerA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)407,30213
Polymers404,7156
Non-polymers2,5887
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area32490 Å2
ΔGint-126 kcal/mol
Surface area129130 Å2
MethodPISA
2
A: HerA
B: HerA
C: HerA
D: HerA
E: HerA
F: HerA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)407,30213
Polymers404,7156
Non-polymers2,5887
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area33590 Å2
ΔGint-122 kcal/mol
Surface area127810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.011, 202.869, 411.852
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein
HerA


Mass: 67452.461 Da / Num. of mol.: 12
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
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
Has ligand of interestY

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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: 2.72 Å3/Da / Density % sol: 54.85 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.8 / Details: 0.2 M MgCl2, 0.1 M HEPES (pH 7.8), 14% PEG 3350

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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: 3.39→102.9 Å / Num. obs: 120020 / % possible obs: 97.5 % / Redundancy: 5.4 % / Biso Wilson estimate: 72 Å2 / Rrim(I) all: 0.157 / Net I/σ(I): 7.8
Reflection shellResolution: 3.39→3.46 Å / Num. unique obs: 5712 / Rrim(I) all: 0.618

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Processing

Software
NameVersionClassification
Cootmodel building
PHENIX1.11.1_2575refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7WRW

7wrw


Resolution: 3.40003560509→9.99988280767 Å / SU ML: 0.478000504202 / Cross valid method: FREE R-VALUE / σ(F): 1.33473620971 / Phase error: 30.443582993
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.290776296642 5820 5.06421635168 %
Rwork0.275648835352 109104 -
obs0.276419459316 114924 97.5618866515 %
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: 3.40003560509→9.99988280767 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms54976 0 326 0 55302
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084845432818356463
X-RAY DIFFRACTIONf_angle_d1.2388690912876691
X-RAY DIFFRACTIONf_chiral_restr0.08006593813048529
X-RAY DIFFRACTIONf_plane_restr0.0066371968349410176
X-RAY DIFFRACTIONf_dihedral_angle_d20.721405599421095
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.400036-3.43710.3840352744082080.3574893312663489X-RAY DIFFRACTION94.1910828025
3.4371-3.47590.3645850257621770.3551482325453599X-RAY DIFFRACTION98.6673634701
3.4759-3.51650.3941673102631870.3454812755173675X-RAY DIFFRACTION98.1698017285
3.5165-3.5590.3396154178572060.3332609469963602X-RAY DIFFRACTION98.0937660999
3.559-3.60370.3581616708541920.3388860083613586X-RAY DIFFRACTION98.2063945932
3.6037-3.65070.3831624105452000.329517205373604X-RAY DIFFRACTION96.4014191586
3.6507-3.70020.3435112318791860.3251489139143535X-RAY DIFFRACTION96.3241004401
3.7002-3.75260.3175753798971870.3093882385263653X-RAY DIFFRACTION97.8593272171
3.7526-3.8080.3387741282752020.3114854743833662X-RAY DIFFRACTION99.0007686395
3.808-3.86690.3094866838051910.3092642985363627X-RAY DIFFRACTION98.860693941
3.8669-3.92960.3308362313532010.3116998798973698X-RAY DIFFRACTION98.7088607595
3.9296-3.99660.3249875850891860.3074162765013622X-RAY DIFFRACTION98.6272986273
3.9966-4.06840.3252422650232070.2950359449633684X-RAY DIFFRACTION98.7312864755
4.0684-4.14560.2898601095371970.2829874424943647X-RAY DIFFRACTION98.6652977413
4.1456-4.22910.2973384186752030.2817533736613668X-RAY DIFFRACTION98.6242038217
4.2291-4.31970.3095784615511960.2758360265193632X-RAY DIFFRACTION98.4061696658
4.3197-4.41860.2826663562552130.2756840504243670X-RAY DIFFRACTION98.5032978184
4.4186-4.52730.2706808298611970.2540331343625X-RAY DIFFRACTION98.4797732543
4.5273-4.64750.2800488229281990.2604895241963664X-RAY DIFFRACTION98.0456852792
4.6475-4.78150.2787977013831800.2592346086853664X-RAY DIFFRACTION97.9612640163
4.7815-4.93260.2821574419451650.2585894025633649X-RAY DIFFRACTION97.4450689831
4.9326-5.10470.2764356635861930.2646101773293636X-RAY DIFFRACTION96.7652261815
5.1047-5.30360.2545536629891860.2499758523393638X-RAY DIFFRACTION96.6144517433
5.3036-5.53780.2905893641861930.2836063942753519X-RAY DIFFRACTION94.4048830112
5.5378-5.81960.3093347545471910.2860273489363649X-RAY DIFFRACTION97.26443769
5.8196-6.16930.2818508311961680.2800975804823717X-RAY DIFFRACTION97.6375973863
6.1693-6.62170.3024245981962000.258485619393686X-RAY DIFFRACTION97.5646497615
6.6217-7.24510.2573915898072050.2423008155143642X-RAY DIFFRACTION96.5127947817
7.2451-80.264972834612070.230370539263688X-RAY DIFFRACTION96.8423669816
8-9.99980.1677030971431970.1610413079573674X-RAY DIFFRACTION95.5330700888
Refinement TLS params.Method: refined / Origin x: 118.595548331 Å / Origin y: 217.924978034 Å / Origin z: 147.962379689 Å
111213212223313233
T0.57476436982 Å20.0111342256749 Å2-0.00884818771687 Å2-0.577493801791 Å2-0.0136692669087 Å2--0.57749696535 Å2
L-0.0181573734039 °2-0.000139192508507 °20.0437525376285 °2--0.0200998760608 °2-0.0467825376472 °2--0.410960750151 °2
S0.0119124752131 Å °-0.0066949898102 Å °0.00818155090767 Å °0.00103988011682 Å °0.0197767349346 Å °0.0285688452316 Å °-0.0464248094597 Å °-0.0522845910442 Å °-0.0327483138188 Å °
Refinement TLS groupSelection details: all

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