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- PDB-6iz2: Crystal structure of DinB/YfiT protein DR0053 from D. radiodurans R1 -

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Basic information

Entry
Database: PDB / ID: 6iz2
TitleCrystal structure of DinB/YfiT protein DR0053 from D. radiodurans R1
ComponentsDinB/YfiT family protein
KeywordsUNKNOWN FUNCTION / damage response / four helix bundle
Function / homologyDNA damage-inducible protein DinB / DinB family / DinB/YfiT-like putative metalloenzymes / metal ion binding / ACETATE ION / Damage-inducible protein DinB
Function and homology information
Biological speciesDeinococcus radiodurans (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.069 Å
AuthorsKim, M.-K. / Zhang, J. / Zhao, L.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (Korea) Korea, Republic Of
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2019
Title: Crystal structure of the highly radiation-inducible DinB/YfiT superfamily protein DR0053 from Deinococcus radiodurans R1.
Authors: Zhang, J. / Zhao, L. / Seo, H.S. / Jung, J.H. / Choi, J.I. / Kim, M.K. / Lim, S.
History
DepositionDec 18, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 15, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 27, 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
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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DinB/YfiT family protein
B: DinB/YfiT family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,07414
Polymers39,3092
Non-polymers76612
Water3,639202
1
A: DinB/YfiT family protein
hetero molecules

A: DinB/YfiT family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,06814
Polymers39,3092
Non-polymers75912
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area4660 Å2
ΔGint-237 kcal/mol
Surface area12790 Å2
MethodPISA
2
B: DinB/YfiT family protein
hetero molecules

B: DinB/YfiT family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,08114
Polymers39,3092
Non-polymers77212
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area4360 Å2
ΔGint-270 kcal/mol
Surface area12630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.843, 109.012, 55.894
Angle α, β, γ (deg.)90.000, 89.990, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-301-

HOH

21B-402-

HOH

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Components

#1: Protein DinB/YfiT family protein


Mass: 19654.316 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422) (radioresistant)
Strain: ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422
Gene: DR_0053 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9RY97
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 202 / 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: 1.97 Å3/Da / Density % sol: 37.57 %
Crystal growTemperature: 295 K / Method: microbatch / Details: Bis-Tris pH 6.5, zinc acetate, PEG 2000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1.2827 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 20, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2827 Å / Relative weight: 1
ReflectionResolution: 2.069→50 Å / Num. obs: 18501 / % possible obs: 99.7 % / Redundancy: 6 % / Rmerge(I) obs: 0.064 / Rsym value: 0.064 / Net I/σ(I): 37.533
Reflection shellResolution: 2.07→2.11 Å / Num. unique obs: 914 / CC1/2: 0.973 / Rrim(I) all: 0.172

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIX1.14_3260refinement
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.069→39.023 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.55 / Phase error: 21.38
RfactorNum. reflection% reflection
Rfree0.2237 947 5.12 %
Rwork0.1824 --
obs0.1846 18490 99.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 117.85 Å2 / Biso mean: 35.0868 Å2 / Biso min: 10.12 Å2
Refinement stepCycle: final / Resolution: 2.069→39.023 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2266 0 21 202 2489
Biso mean--61.57 39.88 -
Num. residues----289
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.069-2.17810.27671280.18342458258699
2.1781-2.31450.23251330.182525262659100
2.3145-2.49320.2171530.185424742627100
2.4932-2.7440.24461650.197324892654100
2.744-3.1410.2917980.193225442642100
3.141-3.95670.22361240.173625252649100
3.9567-39.030.18621460.17752527267399
Refinement TLS params.Method: refined / Origin x: 35.7393 Å / Origin y: 45.0444 Å / Origin z: 13.9118 Å
111213212223313233
T0.0747 Å20.0007 Å2-0.0017 Å2-0.1452 Å2-0.0037 Å2--0.1238 Å2
L0.1472 °20.0003 °2-0.0187 °2-0.1471 °20.3008 °2--0.5313 °2
S0.0283 Å °-0.003 Å °-0.0012 Å °0.008 Å °-0.0417 Å °-0.0194 Å °-0.0164 Å °0.2769 Å °0.002 Å °
Refinement TLS groupSelection details: all

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