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- PDB-7dry: Crystal structure of Aspergillus oryzae Rib2 deaminase -

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Basic information

Entry
Database: PDB / ID: 7dry
TitleCrystal structure of Aspergillus oryzae Rib2 deaminase
ComponentsCMP/dCMP-type deaminase domain-containing protein
KeywordsBIOSYNTHETIC PROTEIN / deaminase / CDA fold / 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
CMP/dCMP-type deaminase domain-containing protein
Similarity search - Component
Biological speciesAspergillus oryzae RIB40 (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.44 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)26,3264
Polymers26,0681
Non-polymers2583
Water4,035224
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area410 Å2
ΔGint-59 kcal/mol
Surface area8840 Å2
Unit cell
Length a, b, c (Å)87.410, 87.410, 60.660
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

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


Mass: 26068.477 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus oryzae RIB40 (mold) / Strain: RIB 40 / 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 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 224 / 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: 2.22 Å3/Da / Density % sol: 44.65 %
Crystal growTemperature: 288 K / Method: vapor diffusion
Details: 1.5 M ammonium sulfate and 0.1 M sodium acetate pH 4.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 0.9762 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Jun 5, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.44→30 Å / Num. obs: 43068 / % possible obs: 99.9 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.042 / Net I/σ(I): 33.8
Reflection shellResolution: 1.44→1.49 Å / Rmerge(I) obs: 0.746 / Num. unique obs: 4217

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 1.44→21.85 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 18.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1979 2098 5.06 %RANDOM
Rwork0.1715 39390 --
obs0.1728 41488 96.37 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 77.24 Å2 / Biso mean: 23.1639 Å2 / Biso min: 7.73 Å2
Refinement stepCycle: final / Resolution: 1.44→21.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1446 0 11 224 1681
Biso mean--40.68 36.72 -
Num. residues----186
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.44-1.470.2299930.21071588168160
1.47-1.510.23061170.21752383250089
1.51-1.550.22061530.20192631278499
1.55-1.60.22791410.189526892830100
1.6-1.650.18911480.184326842832100
1.65-1.710.22751590.18626752834100
1.71-1.780.21011440.189226972841100
1.78-1.860.18711440.175226972841100
1.86-1.950.21211360.184927072843100
1.95-2.080.1871390.164827212860100
2.08-2.240.19411630.167226992862100
2.24-2.460.2011510.167127122863100
2.46-2.820.19911520.173427672919100
2.82-3.550.18951160.158228322948100
3.55-21.850.18581420.16132908305099
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)
13.84623.0742-3.19197.0282-5.2936.1877-0.1786-0.0863-0.2655-0.3159-0.0056-0.29490.40770.07310.18270.0963-0.00660.00940.1319-0.05250.12542.050215.57012.5871
23.25592.15611.2874.77062.4642.7141-0.21160.01610.7646-0.20730.0764-0.0723-0.85090.36660.18530.1952-0.1056-0.02310.1925-0.03760.249347.863731.86294.0262
32.13230.3329-0.26492.9147-1.12232.2002-0.0321-0.0678-0.165-0.03640.07220.02710.15810.0106-0.04980.0726-0.0110.01120.0763-0.02870.0932.928118.60935.6106
42.9342-0.91380.50711.2599-0.76212.29850.0517-0.23120.00080.10950.0397-0.0282-0.0369-0.0146-0.07670.0986-0.02360.02490.0751-0.02050.106430.590528.26435.8536
52.1296-0.47210.95884.6687-1.6032.2104-0.1332-0.29850.18230.48770.19510.2837-0.5983-0.4034-0.03770.18130.02680.05530.1429-0.0240.168622.179130.947710.1572
60.32960.4593-0.65541.852-0.8791.3045-0.0071-0.1509-0.14960.09630.12710.29350.0731-0.1267-0.10280.1066-0.02890.02850.09650.02140.163425.263415.105210.9447
72.3348-0.0074-0.00762.8289-0.10121.52370.0196-0.33610.21630.31890.05560.1566-0.23760.0461-0.05650.1797-0.01970.02590.1557-0.03630.096533.91825.361516.4547
81.78890.74840.5323.43030.48150.74950.0988-0.64120.05120.8584-0.1296-0.4241-0.16860.1632-0.08750.2472-0.0959-0.04830.3342-0.06950.207248.066225.071416.7294
97.7436-1.4595-3.4914.59941.29566.8095-0.1272-0.64250.11820.81520.1458-0.2049-0.06440.21230.02710.2441-0.0131-0.02590.18460.01290.103139.883717.945720.0193
104.6485-1.25590.20193.668-1.80753.40660.0595-0.0050.20450.199-0.0965-0.2799-0.26410.5939-0.00450.1112-0.0758-0.00090.2676-0.06390.13654.392624.86046.3282
116.78823.0794-3.25996.9354-1.58466.58650.2907-0.3722-0.25061.1665-0.5549-0.6642-0.36140.78030.23060.3602-0.1557-0.09210.4748-0.05250.252259.076323.966211.6385
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 18 )A3 - 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 73 )A62 - 73
5X-RAY DIFFRACTION5chain 'A' and (resid 74 through 83 )A74 - 83
6X-RAY DIFFRACTION6chain 'A' and (resid 84 through 97 )A84 - 97
7X-RAY DIFFRACTION7chain 'A' and (resid 98 through 132 )A98 - 132
8X-RAY DIFFRACTION8chain 'A' and (resid 133 through 144 )A133 - 144
9X-RAY DIFFRACTION9chain 'A' and (resid 145 through 163 )A145 - 163
10X-RAY DIFFRACTION10chain 'A' and (resid 164 through 177 )A164 - 177
11X-RAY DIFFRACTION11chain 'A' and (resid 178 through 188 )A178 - 188

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