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- PDB-6q8e: Crystal structure of branched-chain amino acid aminotransferase f... -

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Basic information

Entry
Database: PDB / ID: 6q8e
TitleCrystal structure of branched-chain amino acid aminotransferase from Thermobaculum terrenum in PMP-form
ComponentsBranched-chain-amino-acid aminotransferase
KeywordsTRANSFERASE / branched-chain / aminotransferase / PLP / PMP / transaminase / thermophlic / dimer
Function / homology
Function and homology information


L-leucine-2-oxoglutarate transaminase activity / branched-chain-amino-acid transaminase / : / L-valine-2-oxoglutarate transaminase activity / L-isoleucine-2-oxoglutarate transaminase activity / L-leucine biosynthetic process / L-valine biosynthetic process / isoleucine biosynthetic process
Similarity search - Function
Branched-chain amino acid aminotransferase I / : / D-amino Acid Aminotransferase; Chain A, domain 2 / D-amino Acid Aminotransferase, subunit A, domain 2 / 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 / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE / Branched-chain-amino-acid aminotransferase
Similarity search - Component
Biological speciesThermobaculum terrenum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.5 Å
AuthorsBoyko, K.M. / Bezsudnova, E.Y. / Nikolaeva, A.Y. / Zeifman, Y.S. / Rakitina, T.V. / Popov, V.O.
Funding support Russian Federation, 1items
OrganizationGrant numberCountry
Russian Science Foundation14-24-00172 Russian Federation
CitationJournal: Biochimie / Year: 2018
Title: Biochemical and structural insights into PLP fold type IV transaminase from Thermobaculum terrenum.
Authors: Bezsudnova, E.Y. / Boyko, K.M. / Nikolaeva, A.Y. / Zeifman, Y.S. / Rakitina, T.V. / Suplatov, D.A. / Popov, V.O.
History
DepositionDec 14, 2018Deposition site: PDBE / Processing site: PDBE
SupersessionJan 2, 2019ID: 6GKP
Revision 1.0Jan 2, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 16, 2019Group: Data collection / 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
Revision 1.2Jan 23, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 24, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
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: Branched-chain-amino-acid aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,8537
Polymers36,4271
Non-polymers4256
Water7,206400
1
A: Branched-chain-amino-acid aminotransferase
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)221,11642
Polymers218,5636
Non-polymers2,55336
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation4_556y,x,-z+11
crystal symmetry operation5_556x-y,-y,-z+11
crystal symmetry operation6_556-x,-x+y,-z+11
Buried area33730 Å2
ΔGint-441 kcal/mol
Surface area57420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)144.750, 144.750, 144.500
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-798-

HOH

21A-839-

HOH

31A-893-

HOH

41A-895-

HOH

51A-896-

HOH

61A-898-

HOH

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Components

#1: Protein Branched-chain-amino-acid aminotransferase / BCAT


Mass: 36427.219 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermobaculum terrenum (strain ATCC BAA-798 / YNP1) (bacteria)
Strain: ATCC BAA-798 / YNP1 / Gene: ilvE, Tter_1720 / Production host: Escherichia coli (E. coli)
References: UniProt: D1CCW1, branched-chain-amino-acid transaminase
#2: Chemical ChemComp-PMP / 4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE / PYRIDOXAMINE-5'-PHOSPHATE


Mass: 248.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H13N2O5P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 400 / Source method: isolated from a natural source / Formula: H2O

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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

Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Ammonium acetate 0.2M; MES 0.1M pH 6.0; PEG 3350 25%

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.9677 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 26, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 1.5→19.83 Å / Num. obs: 92398 / % possible obs: 99.9 % / Redundancy: 7.471 % / Biso Wilson estimate: 26.282 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.062 / Rrim(I) all: 0.067 / Χ2: 1.054 / Net I/σ(I): 17.04 / Num. measured all: 690288 / Scaling rejects: 6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.5-1.67.7110.6992.8312425816142161150.8290.74999.8
1.6-1.77.7660.4184.789801812625126220.930.448100
1.7-1.87.7330.2697.3276872994199410.970.288100
1.8-27.6460.14912.6311057014463144610.990.16100
2-2.56.9120.07622.5713157419054190350.9970.08299.9
2.5-37.5370.05133.863685845284500.9980.055100
3-47.3820.0441.2649993677867720.9990.04399.9
4-107.1360.03443.8733527471346980.9990.03799.7
10-505.8910.04140.6817913563040.9960.04685.4
19.83-504

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6GKR

6gkr


Resolution: 1.5→19.83 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.969 / WRfactor Rfree: 0.1781 / WRfactor Rwork: 0.1382 / FOM work R set: 0.7728 / SU B: 3.32 / SU ML: 0.048 / SU R Cruickshank DPI: 0.0474 / SU Rfree: 0.0497 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.047 / ESU R Free: 0.05 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1763 4595 5 %RANDOM
Rwork0.1399 ---
obs0.1418 87783 99.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 126.55 Å2 / Biso mean: 22.829 Å2 / Biso min: 11.26 Å2
Baniso -1Baniso -2Baniso -3
1-0.69 Å20.35 Å2-0 Å2
2--0.69 Å2-0 Å2
3----2.25 Å2
Refinement stepCycle: final / Resolution: 1.5→19.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2473 0 21 400 2894
Biso mean--21.54 39.3 -
Num. residues----304
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0132651
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172468
X-RAY DIFFRACTIONr_angle_refined_deg2.2151.6513596
X-RAY DIFFRACTIONr_angle_other_deg2.1011.5765675
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2755313
X-RAY DIFFRACTIONr_dihedral_angle_2_deg25.97119.518166
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.98215442
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4221533
X-RAY DIFFRACTIONr_chiral_restr0.1280.2342
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.022948
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02647
X-RAY DIFFRACTIONr_rigid_bond_restr4.96135119
LS refinement shellResolution: 1.5→1.539 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.397 321 -
Rwork0.388 6444 -
all-6765 -
obs--99.41 %
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)
10.4090.0856-0.0181.4227-0.16850.4791-0.01890.06730.0573-0.2079-0.0565-0.0814-0.04740.03620.07530.0443-0.003-0.00870.02790.03840.077917.248818.097355.6607
23.23142.6347-5.38254.4185-6.167410.3598-0.00890.1146-0.01330.1133-0.0677-0.0818-0.0856-0.06520.07660.0266-0.0133-0.00450.02440.02320.04515.6715.731357.637
30.56140.0502-0.22321.3808-0.13030.7087-0.02670.11820.0721-0.2895-0.0563-0.1528-0.03730.05740.0830.1477-0.0084-0.00720.14630.03790.201617.960416.866154.0444
41.5077-0.30850.53321.99621.21291.2519-0.00220.0065-0.0526-0.64410.0392-0.1719-0.3467-0.0361-0.03690.2795-0.05020.11880.14560.08210.194819.298611.924451.047
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 312
2X-RAY DIFFRACTION2A401
3X-RAY DIFFRACTION3A501 - 900
4X-RAY DIFFRACTION4A402 - 406

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