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

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Basic information

Entry
Database: PDB / ID: 7drz
TitleCrystal structure of Aspergillus oryzae Rib2 deaminase (C-terminal deletion mutant) at pH 4.6
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: 1.7 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)22,0872
Polymers22,0221
Non-polymers651
Water2,306128
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 area8860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.093, 87.093, 61.215
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-528-

HOH

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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 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 128 / 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: 2.81 Å3/Da / Density % sol: 56.15 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop
Details: 2 M sodium chloride 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: Jul 12, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.7→30 Å / Num. obs: 26416 / % possible obs: 100 % / Redundancy: 11.3 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 21.7
Reflection shellResolution: 1.7→1.76 Å / Rmerge(I) obs: 0.78 / Num. unique obs: 2577

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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: 1.7→25.12 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 18.93 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.2107 1292 4.91 %RANDOM
Rwork0.1954 25025 --
obs0.1961 26317 99.55 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 62.52 Å2 / Biso mean: 19.7504 Å2 / Biso min: 4.85 Å2
Refinement stepCycle: final / Resolution: 1.7→25.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1446 0 1 128 1575
Biso mean--12.55 28.73 -
Num. residues----186
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7-1.770.26151230.2252671279497
1.77-1.850.23181570.211627182875100
1.85-1.950.22441590.202527252884100
1.95-2.070.17541370.178427432880100
2.07-2.230.20711150.18527992914100
2.23-2.450.18441480.188127762924100
2.45-2.810.18851460.201128042950100
2.81-3.530.22491430.20228252968100
3.53-25.120.21861640.190129643128100
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)
10.13310.0310.01350.0726-0.04380.2462-0.03690.0457-0.0567-0.0884-0.0496-0.17460.00850.1702-0.13130.0659-0.01910.00390.1002-0.02170.110244.205821.99543.373
20.00010.0570.00930.0785-0.01420.0388-0.07940.0724-0.22720.06740.18990.10620.10620.1620.13350.0731-0.05470.0521-0.03570.01640.204829.9649.17847.4135
30.1564-0.14920.04610.125-0.14120.18710.0137-0.05390.01720.13260.0184-0.0392-0.0307-0.00140.04270.0634-0.01370.00780.0539-0.00950.079733.598428.00854.7223
40.03630.00670.00950.0559-0.03310.0525-0.1298-0.07390.13420.1980.07130.2065-0.1393-0.1357-0.00550.15180.04480.04220.1203-0.00880.141122.124431.00510.166
50.12620.06590.0620.08720.14730.25420.0129-0.0961-0.2090.060.10420.1640.0989-0.03410.10920.0846-0.01680.04460.09130.06010.194126.41315.965910.7165
60.0110.0143-0.00050.06180.0530.03310.0428-0.1870.12060.1328-0.0365-0.0859-0.30990.20640.00770.2101-0.0289-0.01050.1467-0.05910.112341.235530.907216.1516
70.46-0.1303-0.00920.6969-0.01090.1877-0.1095-0.4278-0.11410.48930.1451-0.0005-0.05640.04820.02790.1614-0.00270.02950.1626-0.01220.092835.202623.135316.9148
80.40.4056-0.03560.65370.06190.34490.0097-0.3014-0.23820.52750.0936-0.3843-0.0365-0.03160.09810.28250.05760.02840.23790.02190.029539.948717.846720.1006
90.2131-0.0001-0.04050.0903-0.06990.16890.0112-0.0172-0.06160.0751-0.1747-0.24190.04020.4096-0.05730.0565-0.0569-0.0170.1845-0.03880.109154.410624.68526.4463
100.2405-0.01550.06180.09670.00580.02120.15780.08130.05230.1388-0.0383-0.2741-0.05920.08620.0540.0079-0.2576-0.29120.1787-0.1385-0.05659.172423.752211.6788
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 28 )A3 - 28
2X-RAY DIFFRACTION2chain 'A' and (resid 29 through 45 )A29 - 45
3X-RAY DIFFRACTION3chain 'A' and (resid 46 through 73 )A46 - 73
4X-RAY DIFFRACTION4chain 'A' and (resid 74 through 83 )A74 - 83
5X-RAY DIFFRACTION5chain 'A' and (resid 84 through 97 )A84 - 97
6X-RAY DIFFRACTION6chain 'A' and (resid 98 through 111 )A98 - 111
7X-RAY DIFFRACTION7chain 'A' and (resid 112 through 144 )A112 - 144
8X-RAY DIFFRACTION8chain 'A' and (resid 145 through 163 )A145 - 163
9X-RAY DIFFRACTION9chain 'A' and (resid 164 through 177 )A164 - 177
10X-RAY DIFFRACTION10chain 'A' and (resid 178 through 188 )A178 - 188

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