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- PDB-7ds1: Crystal structure of Aspergillus oryzae Rib2 deaminase in complex... -

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Basic information

Entry
Database: PDB / ID: 7ds1
TitleCrystal structure of Aspergillus oryzae Rib2 deaminase in complex with DARIPP (C-terminal deletion mutant at pH 6.5)
ComponentsCMP/dCMP-type deaminase domain-containing protein
KeywordsBIOSYNTHETIC PROTEIN / deaminase / riboflavin
Function / homology
Function and homology information


nucleobase-containing compound metabolic process / catalytic activity / metal ion binding
Similarity search - Function
Invertebrate-AID/APOBEC-deaminase / Cytidine Deaminase, domain 2 / Cytidine Deaminase; domain 2 / Cytidine and deoxycytidylate deaminase domain / Cytidine and deoxycytidylate deaminases domain profile. / Cytidine deaminase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-HJL / CMP/dCMP-type deaminase domain-containing protein
Similarity search - Component
Biological speciesAspergillus oryzae RIB40 (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.58 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)22,4433
Polymers22,0221
Non-polymers4212
Water3,243180
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area9100 Å2
Unit cell
Length a, b, c (Å)59.320, 90.778, 40.833
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-HJL / [(2~{R},3~{S},4~{S})-5-[[2,5-bis(azanyl)-6-oxidanylidene-1~{H}-pyrimidin-4-yl]amino]-2,3,4-tris(oxidanyl)pentyl] dihydrogen phosphate


Mass: 355.242 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H18N5O8P / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 180 / Source method: isolated from a natural source / Formula: H2O
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: 2.5 Å3/Da / Density % sol: 50.72 %
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: 1.58→31.54 Å / Num. obs: 31013 / % possible obs: 100 % / Redundancy: 4.8 % / Biso Wilson estimate: 13.76 Å2 / Rmerge(I) obs: 0.045 / Net I/σ(I): 19.7
Reflection shellResolution: 1.58→1.64 Å / Rmerge(I) obs: 0.622 / Num. unique obs: 3056

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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: 1.58→31.54 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 18.7 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.2078 1538 5.03 %RANDOM
Rwork0.1827 29066 --
obs0.1839 30604 98.8 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 63.28 Å2 / Biso mean: 20.1704 Å2 / Biso min: 7.55 Å2
Refinement stepCycle: final / Resolution: 1.58→31.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1428 0 24 180 1632
Biso mean--16.93 29.86 -
Num. residues----183
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.58-1.630.2591350.22452330246589
1.63-1.690.2711280.20772572270099
1.69-1.760.23711430.209126412784100
1.76-1.840.25191340.186526312765100
1.84-1.930.20471010.180426922793100
1.93-2.050.20631430.181526502793100
2.05-2.210.19061580.176526342792100
2.21-2.440.17851550.173826482803100
2.44-2.790.21761590.190526752834100
2.79-3.510.22291400.184227332873100
3.51-31.540.18521420.170128603002100
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)
13.23810.3261-1.68951.96990.00152.5184-0.08880.30960.1311-0.11350.10160.25790.1146-0.2759-0.04550.1021-0.0065-0.01940.11940.01860.1215-11.61136.0828-7.5005
25.8739-0.03980.79335.3313-1.09936.2682-0.02710.4648-0.2483-0.42210.17340.22850.0571-0.1904-0.15760.2171-0.0389-0.02330.2331-0.0570.1201-15.037722.8242-18.4056
32.2346-0.56070.67281.5590.30332.2303-0.11120.4444-0.2518-0.33950.123-0.32480.02050.186-0.01880.13520.00230.04640.1732-0.0190.10781.661629.0089-9.7068
42.2935-0.39230.61931.4788-0.1821.3136-0.0907-0.1755-0.1570.06970.032-0.08160.0652-0.01470.05770.08440.00770.0260.09320.0080.08711.591427.1842.7309
52.58241.26050.12473.1355-0.14312.92120.0398-0.16460.12430.1517-0.02870.12190.0522-0.0771-0.02250.06420.01660.01940.0843-0.0230.0953-7.191532.26651.8822
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 133 through 163 )A133 - 163
2X-RAY DIFFRACTION2chain 'A' and (resid 164 through 189 )A164 - 189
3X-RAY DIFFRACTION3chain 'A' and (resid 3 through 45 )A3 - 45
4X-RAY DIFFRACTION4chain 'A' and (resid 46 through 97 )A46 - 97
5X-RAY DIFFRACTION5chain 'A' and (resid 98 through 132 )A98 - 132

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