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- PDB-6l2m: The structure of the tRNA-specific deaminase mutant from M. capricolum -

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Basic information

Entry
Database: PDB / ID: 6l2m
TitleThe structure of the tRNA-specific deaminase mutant from M. capricolum
ComponentsNucleoside deaminase family protein
KeywordsRNA BINDING PROTEIN / tRNA-specific deaminase / protein engineering
Function / homologyCytidine and deoxycytidylate deaminase zinc-binding region / APOBEC/CMP deaminase, zinc-binding / Cytidine and deoxycytidylate deaminases zinc-binding region signature. / Cytidine and deoxycytidylate deaminase domain / Cytidine and deoxycytidylate deaminases domain profile. / Cytidine deaminase-like / hydrolase activity / zinc ion binding / Nucleoside deaminase family protein
Function and homology information
Biological speciesMycoplasma capricolum subsp. capricolum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.30254929158 Å
AuthorsXie, W. / Liu, H. / Wu, S.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31870782 China
CitationJournal: Biochem.J. / Year: 2020
Title: Structure of a tRNA-specific deaminase with compromised deamination activity.
Authors: Liu, H. / Wu, S. / Ran, D. / Xie, W.
History
DepositionOct 5, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 12, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: Nucleoside deaminase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,7843
Polymers17,6831
Non-polymers1012
Water66737
1
A: Nucleoside deaminase family protein
hetero molecules

A: Nucleoside deaminase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,5686
Polymers35,3672
Non-polymers2024
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area1420 Å2
ΔGint-90 kcal/mol
Surface area15740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.589, 55.589, 109.227
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z

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Components

#1: Protein Nucleoside deaminase family protein / tRNA-specific deaminase


Mass: 17683.342 Da / Num. of mol.: 1
Mutation: I19A,K20Q,H21L,N22G,S105D,Y106P,K146A, DEL(108-110)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycoplasma capricolum subsp. capricolum (bacteria)
Gene: MCGM508_01875 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0C2W6A5
#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-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 37 / 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: 3 Å3/Da / Density % sol: 59.06 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 1.4M ammonium sulfate, 0.1M Sodium citrate pH 6.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 8, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 9158 / % possible obs: 100 % / Redundancy: 18.7 % / Biso Wilson estimate: 42.6410606465 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.105 / Net I/σ(I): 38.5
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 18.1 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 4.8 / Num. unique obs: 889 / CC1/2: 0.969 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
PHENIX1.10.1_2155refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6L2L

6l2l


Resolution: 2.30254929158→48.141486171 Å / SU ML: 0.292331904948 / Cross valid method: FREE R-VALUE / σ(F): 1.38105400115 / Phase error: 27.1589106138
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.251408846831 469 5.14310779691 %
Rwork0.198421847872 8650 -
obs0.201104412273 9119 99.7811576759 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 48.0589077702 Å2
Refinement stepCycle: LAST / Resolution: 2.30254929158→48.141486171 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1147 0 3 38 1188
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007296933155121165
X-RAY DIFFRACTIONf_angle_d0.8127263881421569
X-RAY DIFFRACTIONf_chiral_restr0.0540661923588188
X-RAY DIFFRACTIONf_plane_restr0.00428985158862200
X-RAY DIFFRACTIONf_dihedral_angle_d16.4852966091723
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3026-2.63570.2862538318491480.200394626782815X-RAY DIFFRACTION99.4629070158
2.6357-3.32060.3174239373841340.2270496603362877X-RAY DIFFRACTION99.900464499
3.3206-48.140.2269084246041870.1866038426392958X-RAY DIFFRACTION99.9682136046

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