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- PDB-7mfo: X-ray structure of the L136 Aminotransferase from Acanthamoeba po... -

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Basic information

Entry
Database: PDB / ID: 7mfo
TitleX-ray structure of the L136 Aminotransferase from Acanthamoeba polyphaga mimivirus in the presence of TDP and PMP
ComponentsL136 aminotransferase
KeywordsTRANSFERASE / mimivirus / aminotransferase / viosamine
Function / homologyDegT/DnrJ/EryC1/StrS aminotransferase / DegT/DnrJ/EryC1/StrS aminotransferase family / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / 4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE / PHOSPHATE ION / THYMIDINE-5'-DIPHOSPHATE / Uncharacterized protein L136
Function and homology information
Biological speciesAcanthamoeba polyphaga mimivirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 Å
AuthorsFerek, J.D. / Thoden, J.B. / Holden, H.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM134643 United States
CitationJournal: Protein Sci. / Year: 2021
Title: Characterization of an aminotransferase from Acanthamoeba polyphaga Mimivirus.
Authors: Seltzner, C.A. / Ferek, J.D. / Thoden, J.B. / Holden, H.M.
History
DepositionApr 10, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 28, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 14, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Sep 1, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: L136 aminotransferase
B: L136 aminotransferase
C: L136 aminotransferase
D: L136 aminotransferase
E: L136 aminotransferase
F: L136 aminotransferase
G: L136 aminotransferase
H: L136 aminotransferase
I: L136 aminotransferase
J: L136 aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)410,01840
Polymers402,88810
Non-polymers7,13130
Water52,4962914
1
A: L136 aminotransferase
B: L136 aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,19511
Polymers80,5782
Non-polymers1,6179
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8050 Å2
ΔGint-54 kcal/mol
Surface area24960 Å2
MethodPISA
2
C: L136 aminotransferase
D: L136 aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,9407
Polymers80,5782
Non-polymers1,3635
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7290 Å2
ΔGint-34 kcal/mol
Surface area25170 Å2
MethodPISA
3
E: L136 aminotransferase
F: L136 aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,0028
Polymers80,5782
Non-polymers1,4256
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7380 Å2
ΔGint-33 kcal/mol
Surface area25570 Å2
MethodPISA
4
G: L136 aminotransferase
H: L136 aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,8786
Polymers80,5782
Non-polymers1,3014
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7040 Å2
ΔGint-41 kcal/mol
Surface area25210 Å2
MethodPISA
5
I: L136 aminotransferase
J: L136 aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,0028
Polymers80,5782
Non-polymers1,4256
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7090 Å2
ΔGint-35 kcal/mol
Surface area25280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.885, 126.875, 206.365
Angle α, β, γ (deg.)90.000, 90.890, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 10 molecules ABCDEFGHIJ

#1: Protein
L136 aminotransferase


Mass: 40288.754 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acanthamoeba polyphaga mimivirus / Gene: MIMI_L136 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5UPL1

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Non-polymers , 6 types, 2944 molecules

#2: Chemical
ChemComp-PMP / 4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE / PYRIDOXAMINE-5'-PHOSPHATE


Mass: 248.173 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C8H13N2O5P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Chemical
ChemComp-TYD / THYMIDINE-5'-DIPHOSPHATE / Thymidine diphosphate


Mass: 402.188 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C10H16N2O11P2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2914 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.43 Å3/Da / Density % sol: 49.44 %
Crystal growTemperature: 293 K / Method: microbatch / pH: 7.5
Details: protein incubated with 1 mM PLP and 5 mM TDP-4-aminoquinovose. 11-14% PEG-8000, 200 mM KCl, 100 mM HEPES

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Jun 23, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 397722 / % possible obs: 94.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Rsym value: 0.055 / Net I/σ(I): 36.2
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 2.9 % / Mean I/σ(I) obs: 5 / Num. unique obs: 18360 / Rsym value: 0.194 / % possible all: 87.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 1.7→33.78 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.938 / SU B: 2.372 / SU ML: 0.078 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.113 / ESU R Free: 0.113 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2215 19828 5 %RANDOM
Rwork0.1819 ---
obs0.1839 377894 94.23 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 102.23 Å2 / Biso mean: 24.036 Å2 / Biso min: 10.09 Å2
Baniso -1Baniso -2Baniso -3
1-2.12 Å20 Å2-0.32 Å2
2---0.64 Å20 Å2
3----1.46 Å2
Refinement stepCycle: final / Resolution: 1.7→33.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms28003 0 448 2914 31365
Biso mean--34.73 31.16 -
Num. residues----3508
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01329123
X-RAY DIFFRACTIONr_bond_other_d0.0010.01726493
X-RAY DIFFRACTIONr_angle_refined_deg1.6191.63539484
X-RAY DIFFRACTIONr_angle_other_deg1.4111.57561690
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.81753516
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.64223.7051514
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.912154982
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.41115120
X-RAY DIFFRACTIONr_chiral_restr0.0830.23826
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0232343
X-RAY DIFFRACTIONr_gen_planes_other0.0010.025978
LS refinement shellResolution: 1.7→1.744 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.265 1385 -
Rwork0.235 25596 -
all-26981 -
obs--86.64 %

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