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- PDB-8isc: Crystal structure of MV in complex with LLP -

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Basic information

Entry
Database: PDB / ID: 8isc
TitleCrystal structure of MV in complex with LLP
ComponentsBranched chain amino acid: 2-keto-4-methylthiobutyrate aminotransferase
KeywordsTRANSFERASE / complex
Function / homology
Function and homology information


carboxylic acid biosynthetic process / Transferases; Transferring nitrogenous groups; Transaminases / transaminase activity
Similarity search - Function
: / Branched-chain-amino-acid aminotransferase-like, N-terminal / Aminotransferase class IV / Aminotransferase-like, PLP-dependent enzymes / Branched-chain-amino-acid aminotransferase-like, C-terminal / Amino-transferase class IV
Similarity search - Domain/homology
Branched chain amino acid: 2-keto-4-methylthiobutyrate aminotransferase
Similarity search - Component
Biological speciesMycolicibacterium vanbaalenii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.27 Å
AuthorsLi, Q. / Zhu, Y.M. / Gao, J. / Wei, H.L. / Han, X. / Liu, W.D. / Sun, Y.X.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Iscience / Year: 2024
Title: Protein engineering of transaminase facilitating enzyme cascade reaction for the biosynthesis of azasugars.
Authors: Zhu, Y. / Chen, P. / Dong, Q. / Li, Q. / Liu, D. / Liu, T. / Liu, W. / Sun, Y.
History
DepositionMar 20, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jan 24, 2024Provider: repository / Type: Initial release
Revision 1.1Aug 6, 2025Group: Database references / Structure summary
Category: citation / citation_author ...citation / citation_author / pdbx_entry_details / pdbx_modification_feature
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Branched chain amino acid: 2-keto-4-methylthiobutyrate aminotransferase
B: Branched chain amino acid: 2-keto-4-methylthiobutyrate aminotransferase
C: Branched chain amino acid: 2-keto-4-methylthiobutyrate aminotransferase
D: Branched chain amino acid: 2-keto-4-methylthiobutyrate aminotransferase


Theoretical massNumber of molelcules
Total (without water)147,5294
Polymers147,5294
Non-polymers00
Water20,8251156
1
A: Branched chain amino acid: 2-keto-4-methylthiobutyrate aminotransferase
C: Branched chain amino acid: 2-keto-4-methylthiobutyrate aminotransferase
D: Branched chain amino acid: 2-keto-4-methylthiobutyrate aminotransferase

B: Branched chain amino acid: 2-keto-4-methylthiobutyrate aminotransferase


Theoretical massNumber of molelcules
Total (without water)147,5294
Polymers147,5294
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-x,y-1/2,-z1
Buried area12340 Å2
ΔGint-47 kcal/mol
Surface area45790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.950, 112.850, 92.244
Angle α, β, γ (deg.)90.00, 112.37, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Branched chain amino acid: 2-keto-4-methylthiobutyrate aminotransferase


Mass: 36882.352 Da / Num. of mol.: 4
Mutation: H69K,S105P,S121M,K142P,K145R,H152N,L162I,A168E,R215G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycolicibacterium vanbaalenii (strain DSM 7251 / JCM 13017 / BCRC 16820 / KCTC 9966 / NRRL B-24157 / PYR-1) (bacteria)
Gene: Mvan_4516 / Production host: Escherichia coli (E. coli)
References: UniProt: A1TDP1, Transferases; Transferring nitrogenous groups; Transaminases
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1156 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.66 Å3/Da / Density % sol: 53.71 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.2 M lithium sulfate,0.1 M Tris 8.5,1.26 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Mar 25, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.27→50 Å / Num. obs: 66664 / % possible obs: 95 % / Redundancy: 5.4 % / CC1/2: 0.991 / CC star: 0.998 / Rmerge(I) obs: 0.122 / Rpim(I) all: 0.059 / Rrim(I) all: 0.136 / Χ2: 2.329 / Net I/σ(I): 11.3 / Num. measured all: 358730
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.27-2.3550.45568650.9090.9760.2240.5091.74397.9
2.35-2.455.40.32869660.9250.980.1570.3651.8399.8
2.45-2.565.50.26669610.9520.9880.1270.2961.89999.7
2.56-2.695.50.21869970.9710.9930.1030.2432.01399.5
2.69-2.865.60.17768920.980.9950.0830.1962.299.4
2.86-3.085.60.13969920.9870.9970.0650.1542.47899.4
3.08-3.395.40.10169530.9920.9980.0490.1132.63499.3
3.39-3.884.70.08645680.9930.9980.0440.0972.87265
3.88-4.894.90.05764580.9950.9990.0290.0642.9191.9
4.89-505.90.05670120.9970.9990.0260.0622.93797.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACTdata extraction
Aimlessdata scaling
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.27→39.93 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.885 / SU B: 6.375 / SU ML: 0.156 / Cross valid method: THROUGHOUT / ESU R: 0.344 / ESU R Free: 0.245 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24828 3335 5 %RANDOM
Rwork0.18987 ---
obs0.19283 63136 94.11 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.411 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å2-0 Å2-0 Å2
2--0.01 Å2-0 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 2.27→39.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9925 0 0 1156 11081
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01310156
X-RAY DIFFRACTIONr_bond_other_d0.0010.0179471
X-RAY DIFFRACTIONr_angle_refined_deg1.5821.64913835
X-RAY DIFFRACTIONr_angle_other_deg1.2521.57921815
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.39951276
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.06521.67527
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.58151577
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5891576
X-RAY DIFFRACTIONr_chiral_restr0.0670.21347
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211580
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022292
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3531.9155116
X-RAY DIFFRACTIONr_mcbond_other1.3521.9155115
X-RAY DIFFRACTIONr_mcangle_it2.092.8686388
X-RAY DIFFRACTIONr_mcangle_other2.092.8696389
X-RAY DIFFRACTIONr_scbond_it1.7462.1295040
X-RAY DIFFRACTIONr_scbond_other1.7462.1295040
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.8273.1047447
X-RAY DIFFRACTIONr_long_range_B_refined4.61723.06111687
X-RAY DIFFRACTIONr_long_range_B_other4.3422.68111355
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.272→2.331 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.405 228 -
Rwork0.318 4310 -
obs--87.34 %

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