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- PDB-7mfp: crystal structure of the L136 aminotransferase K185A from acantha... -

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Basic information

Entry
Database: PDB / ID: 7mfp
Titlecrystal structure of the L136 aminotransferase K185A from acanthamoeba polyphaga mimivirus in the presence of the UDP-viosamine external aldimine
ComponentsL136 aminotransferase
KeywordsTRANSFERASE / mimivirus / aminotransferase / viosamine
Function / homologyDegT/DnrJ/EryC1/StrS aminotransferase / DegT/DnrJ/EryC1/StrS aminotransferase family / polysaccharide biosynthetic process / transaminase activity / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / pyridoxal phosphate binding / Chem-Z7P / Uncharacterized protein L136
Function and homology information
Biological speciesAcanthamoeba polyphaga mimivirus
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsSeltzner, C.A. / 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
Revision 1.3Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)164,73824
Polymers160,9234
Non-polymers3,81620
Water24,3921354
1
A: L136 aminotransferase
B: L136 aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,30711
Polymers80,4612
Non-polymers1,8469
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6100 Å2
ΔGint-54 kcal/mol
Surface area25320 Å2
MethodPISA
2
C: L136 aminotransferase
D: L136 aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,43113
Polymers80,4612
Non-polymers1,97011
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6290 Å2
ΔGint-50 kcal/mol
Surface area24890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.033, 108.548, 145.514
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
L136 aminotransferase


Mass: 40230.652 Da / Num. of mol.: 4 / Mutation: K185A
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 , 5 types, 1374 molecules

#2: Chemical
ChemComp-Z7P / (2R,3R,4S,5S,6R)-3,4-dihydroxy-5-[(E)-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)amino]-6-methyloxan-2-yl [(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxyoxolan-2-yl]methyl dihydrogen diphosphate (non-preferred name)


Mass: 778.444 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C23H33N4O20P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1354 / 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: 2.23 Å3/Da / Density % sol: 44.94 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: protein incubated with 1 mM PLP and 5 mM UDP-viosamine 18-22% PEG-3350, 2% MPD, 100 mM MES

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: BRUKER D8 QUEST / Wavelength: 1.54178 Å
DetectorType: Bruker PHOTON II / Detector: PIXEL / Date: Sep 19, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. obs: 123055 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8 % / Rsym value: 0.084 / Net I/σ(I): 15.4
Reflection shellResolution: 1.85→1.9 Å / Redundancy: 3 % / Mean I/σ(I) obs: 4 / Num. unique obs: 9180 / Rsym value: 0.443 / % possible all: 99.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0253refinement
SAINTdata reduction
SADABSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7mfo

7mfo


Resolution: 1.85→29.723 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.918 / SU B: 3.386 / SU ML: 0.098 / Cross valid method: FREE R-VALUE / ESU R: 0.143 / ESU R Free: 0.136
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2187 6181 5.023 %
Rwork0.1718 116878 -
all0.174 --
obs-123059 99.751 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 12.803 Å2
Baniso -1Baniso -2Baniso -3
1--0.015 Å20 Å20 Å2
2---0.003 Å20 Å2
3---0.017 Å2
Refinement stepCycle: LAST / Resolution: 1.85→29.723 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11213 0 234 1354 12801
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01311708
X-RAY DIFFRACTIONr_bond_other_d0.0010.01710599
X-RAY DIFFRACTIONr_angle_refined_deg1.6131.66115877
X-RAY DIFFRACTIONr_angle_other_deg1.3661.58824700
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.95551406
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.43423.689610
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.713151993
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.4621549
X-RAY DIFFRACTIONr_chiral_restr0.0790.21547
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212972
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022407
X-RAY DIFFRACTIONr_nbd_refined0.2120.22412
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1770.210435
X-RAY DIFFRACTIONr_nbtor_refined0.1720.25735
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0780.25152
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1930.21131
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1660.24
X-RAY DIFFRACTIONr_metal_ion_refined0.2580.25
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2220.218
X-RAY DIFFRACTIONr_nbd_other0.1880.275
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2140.247
X-RAY DIFFRACTIONr_mcbond_it1.0491.2095621
X-RAY DIFFRACTIONr_mcbond_other1.0481.2095620
X-RAY DIFFRACTIONr_mcangle_it1.6841.8087022
X-RAY DIFFRACTIONr_mcangle_other1.6841.8087023
X-RAY DIFFRACTIONr_scbond_it1.5471.3776087
X-RAY DIFFRACTIONr_scbond_other1.5471.3786088
X-RAY DIFFRACTIONr_scangle_it2.4991.9838853
X-RAY DIFFRACTIONr_scangle_other2.4991.9838854
X-RAY DIFFRACTIONr_lrange_it4.18814.89413910
X-RAY DIFFRACTIONr_lrange_other4.18814.89613911
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.8980.3314590.318525X-RAY DIFFRACTION99.3256
1.898-1.950.3054190.2578323X-RAY DIFFRACTION99.5219
1.95-2.0060.2634590.2258033X-RAY DIFFRACTION99.5662
2.006-2.0680.2594080.2117919X-RAY DIFFRACTION99.6887
2.068-2.1360.2273880.1837660X-RAY DIFFRACTION99.8511
2.136-2.2110.2174320.1737390X-RAY DIFFRACTION99.8341
2.211-2.2940.2243520.1687177X-RAY DIFFRACTION99.8144
2.294-2.3880.2183370.1596915X-RAY DIFFRACTION99.8073
2.388-2.4940.2293670.1616613X-RAY DIFFRACTION99.9141
2.494-2.6150.213270.1536337X-RAY DIFFRACTION99.8502
2.615-2.7570.2183220.1486040X-RAY DIFFRACTION99.9529
2.757-2.9240.1993090.155729X-RAY DIFFRACTION99.8842
2.924-3.1250.2013030.1525381X-RAY DIFFRACTION99.9297
3.125-3.3750.2072480.1555063X-RAY DIFFRACTION99.9812
3.375-3.6970.2072410.1584640X-RAY DIFFRACTION99.959
3.697-4.1330.1732380.1364225X-RAY DIFFRACTION99.9105
4.133-4.770.1521840.1213756X-RAY DIFFRACTION99.9493
4.77-5.8380.1791700.1433196X-RAY DIFFRACTION99.9406
5.838-8.2370.191350.1352525X-RAY DIFFRACTION99.9624
8.237-290.177830.1591431X-RAY DIFFRACTION97.0513

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