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- PDB-7ds0: Crystal structure of Aspergillus oryzae Rib2 deaminase (C-termina... -

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Basic information

Entry
Database: PDB / ID: 7ds0
TitleCrystal structure of Aspergillus oryzae Rib2 deaminase (C-terminal deletion mutant) at pH 6.5
ComponentsCMP/dCMP-type deaminase domain-containing protein
KeywordsBIOSYNTHETIC PROTEIN / deaminase / riboflavin
Function / homologyInvertebrate-AID/APOBEC-deaminase / diaminohydroxyphosphoribosylaminopyrimidine deaminase activity / Cytidine and deoxycytidylate deaminase domain / Cytidine and deoxycytidylate deaminases domain profile. / Cytidine deaminase-like / nucleobase-containing compound metabolic process / metal ion binding / CMP/dCMP-type deaminase domain-containing protein
Function and homology information
Biological speciesAspergillus oryzae RIB40 (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.69 Å
AuthorsChen, S.C. / Liaw, S.H. / Hsu, C.H.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, Taiwan) Taiwan
CitationJournal: Iucrj / Year: 2021
Title: Crystal structures of Aspergillus oryzae Rib2 deaminase: the functional mechanism involved in riboflavin biosynthesis.
Authors: Chen, S.C. / Ye, L.C. / Yen, T.M. / Zhu, R.X. / Li, C.Y. / Chang, S.C. / Liaw, S.H. / Hsu, C.H.
History
DepositionDec 30, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 14, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CMP/dCMP-type deaminase domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,1833
Polymers22,0221
Non-polymers1612
Water2,576143
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area100 Å2
ΔGint-38 kcal/mol
Surface area8870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.486, 90.905, 40.800
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein CMP/dCMP-type deaminase domain-containing protein


Mass: 22021.980 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: C-terminal deletion mutant / Source: (gene. exp.) Aspergillus oryzae RIB40 (mold) / Strain: RIB40 / Gene: AO090026000280 / Production host: Escherichia coli (E. coli) / References: UniProt: Q2UFA9
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 143 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.46 Å3/Da / Density % sol: 50.05 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop
Details: 0.1 M MES pH 6.5, 0.2 M ammonium sulfate and 30% PEG 5000 MME

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 1 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Nov 1, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.69→30 Å / Num. obs: 25024 / % possible obs: 99.8 % / Redundancy: 6.6 % / Biso Wilson estimate: 13.86 Å2 / Rmerge(I) obs: 0.089 / Net I/σ(I): 27.1
Reflection shellResolution: 1.7→1.76 Å / Rmerge(I) obs: 0.726 / Num. unique obs: 2438

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHENIX1.17.1_3660refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.69→26.91 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 19.69 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.2087 1142 4.83 %RANDOM
Rwork0.1927 22525 --
obs0.1934 23667 93.87 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 67.58 Å2 / Biso mean: 21.6006 Å2 / Biso min: 6.78 Å2
Refinement stepCycle: final / Resolution: 1.69→26.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1415 0 6 143 1564
Biso mean--19.3 31.18 -
Num. residues----181
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.69-1.760.2368930.20831956204966
1.76-1.860.24271240.2232672279690
1.86-1.970.24561550.20282844299997
1.97-2.130.21491560.19122901305798
2.13-2.340.19611400.188129773117100
2.34-2.680.22011560.193229913147100
2.68-3.370.20961640.197430303194100
3.37-26.910.18581540.18133154330899
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.3563-0.0874-0.53732.533-0.28290.7772-0.0858-0.5160.3360.6586-0.0308-0.3135-0.00010.1886-0.07570.27780.0403-0.1770.2315-0.12110.157230.771218.666513.3278
22.9136-1.0497-1.20850.39930.27281.75570.2140.29331.3566-0.29880.35660.713-0.7458-0.5167-0.28370.30380.08750.00210.2060.03980.554218.746529.37248.9264
32.32341.202-0.75291.2990.72352.0592-0.1556-0.25160.21740.2890.1161-0.48930.01060.1850.07930.10960.0115-0.07410.1085-0.01440.112533.264115.59324.4213
41.13990.4219-0.50312.0441-0.20911.2522-0.11550.14710.0558-0.11930.0376-0.189-0.1321-0.04220.07570.092-0.0095-0.03790.11120.00330.109731.873315.6366-4.8833
52.8787-1.4470.22953.0579-0.50531.6883-0.02390.1574-0.0251-0.06180.0116-0.0292-0.0091-0.0912-0.00890.0766-0.0049-0.03520.0932-0.0210.090621.926513.0218-1.908
61.2527-1.1413-0.22253.35352.215.6773-0.2119-0.3132-0.22520.35170.16610.384-0.1149-0.33610.030.13050.03580.01880.13840.02030.137618.0848.84387.3068
72.78181.27760.23044.406-1.83433.267-0.1937-0.68580.44721.04760.51780.4886-0.0939-0.59760.2160.39120.17740.04710.3847-0.07250.180114.299122.479318.5958
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 18 )A4 - 18
2X-RAY DIFFRACTION2chain 'A' and (resid 19 through 28 )A19 - 28
3X-RAY DIFFRACTION3chain 'A' and (resid 29 through 61 )A29 - 61
4X-RAY DIFFRACTION4chain 'A' and (resid 62 through 97 )A62 - 97
5X-RAY DIFFRACTION5chain 'A' and (resid 98 through 132 )A98 - 132
6X-RAY DIFFRACTION6chain 'A' and (resid 133 through 163 )A133 - 163
7X-RAY DIFFRACTION7chain 'A' and (resid 164 through 189 )A164 - 189

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