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- PDB-5e25: Crystal structure of branched-chain aminotransferase from thermop... -

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Basic information

Entry
Database: PDB / ID: 5.0E+25
TitleCrystal structure of branched-chain aminotransferase from thermophilic archaea Geoglobus acetivorans complexed with alpha-ketoglutarate
Componentsbranched-chain aminotransferase
KeywordsTRANSFERASE / aminotransferase / branched-chain / PLP / BCAT / Geoglobus acetivorans / alpha-ketoglutarate / complex
Function / homology
Function and homology information


L-leucine:2-oxoglutarate aminotransferase activity / branched-chain-amino-acid transaminase / L-leucine transaminase activity / L-valine transaminase activity / L-isoleucine transaminase activity / L-leucine biosynthetic process / valine biosynthetic process / isoleucine biosynthetic process
Similarity search - Function
Branched-chain amino acid aminotransferase I / Aminotransferase, class IV, conserved site / Aminotransferases class-IV signature. / Aminotransferase class 4, branched-chain amino acid transferase, N-terminal domain / D-amino Acid Aminotransferase; Chain A, domain 2 / D-amino Acid Aminotransferase, subunit A, domain 2 / Aminotransferase class IV / Aminotransferase-like, PLP-dependent enzymes / Branched-chain-amino-acid aminotransferase-like, N-terminal / Branched-chain-amino-acid aminotransferase-like, C-terminal ...Branched-chain amino acid aminotransferase I / Aminotransferase, class IV, conserved site / Aminotransferases class-IV signature. / Aminotransferase class 4, branched-chain amino acid transferase, N-terminal domain / D-amino Acid Aminotransferase; Chain A, domain 2 / D-amino Acid Aminotransferase, subunit A, domain 2 / Aminotransferase class IV / Aminotransferase-like, PLP-dependent enzymes / Branched-chain-amino-acid aminotransferase-like, N-terminal / Branched-chain-amino-acid aminotransferase-like, C-terminal / Amino-transferase class IV / D-amino Acid Aminotransferase; Chain A, domain 1 / Alpha-Beta Barrel / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
2-OXOGLUTARIC ACID / PYRIDOXAL-5'-PHOSPHATE / Branched-chain-amino-acid aminotransferase
Similarity search - Component
Biological speciesGeoglobus acetivorans (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å
AuthorsBoyko, K.M. / Nikolaeva, A.Y. / Stekhanova, T.N. / Mardanov, A.V. / Rakitin, A.L. / Ravin, N.V. / Popov, V.O.
Funding support Russian Federation, 2items
OrganizationGrant numberCountry
Russian Scientific Foundation14-24-00172 Russian Federation
ERA-NET Scheme of the 7th EU Framework Programme"THERMOGENE"
CitationJournal: Front Bioeng Biotechnol / Year: 2019
Title: Thermostable Branched-Chain Amino Acid Transaminases From the Archaea Geoglobus acetivorans and Archaeoglobus fulgidus : Biochemical and Structural Characterization.
Authors: Isupov, M.N. / Boyko, K.M. / Sutter, J.M. / James, P. / Sayer, C. / Schmidt, M. / Schonheit, P. / Nikolaeva, A.Y. / Stekhanova, T.N. / Mardanov, A.V. / Ravin, N.V. / Bezsudnova, E.Y. / ...Authors: Isupov, M.N. / Boyko, K.M. / Sutter, J.M. / James, P. / Sayer, C. / Schmidt, M. / Schonheit, P. / Nikolaeva, A.Y. / Stekhanova, T.N. / Mardanov, A.V. / Ravin, N.V. / Bezsudnova, E.Y. / Popov, V.O. / Littlechild, J.A.
History
DepositionSep 30, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Oct 5, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 15, 2017Group: Structure summary
Revision 1.2Mar 31, 2021Group: Database references / Derived calculations / Structure summary
Category: citation / citation_author ...citation / citation_author / entity / pdbx_struct_sheet_hbond / struct_conf / struct_sheet / struct_sheet_order / struct_sheet_range
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._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 / _entity.pdbx_ec
Revision 1.3Jan 10, 2024Group: 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: branched-chain aminotransferase
B: branched-chain aminotransferase
C: branched-chain aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,4667
Polymers97,5793
Non-polymers8884
Water9,152508
1
A: branched-chain aminotransferase
C: branched-chain aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,6935
Polymers65,0522
Non-polymers6403
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6360 Å2
ΔGint-35 kcal/mol
Surface area21540 Å2
MethodPISA
2
B: branched-chain aminotransferase
hetero molecules

B: branched-chain aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,5474
Polymers65,0522
Non-polymers4942
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554x-y,-y,-z-2/31
Buried area5880 Å2
ΔGint-39 kcal/mol
Surface area22220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.310, 117.310, 135.310
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11B-552-

HOH

21C-564-

HOH

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Components

#1: Protein branched-chain aminotransferase


Mass: 32526.182 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geoglobus acetivorans (archaea) / Gene: GACE_1900 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0A7GJ30
#2: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate / Pyridoxal phosphate


Mass: 247.142 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C8H10NO6P
#3: Chemical ChemComp-AKG / 2-OXOGLUTARIC ACID / Α-Ketoglutaric acid


Mass: 146.098 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C5H6O5
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 508 / 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

CrystalDensity Matthews: 2.75 Å3/Da / Density % sol: 55.25 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6 / Details: 0.2M CaCl2, 0.1M Na acetate, 20% isopropanol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 15, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→67.66 Å / Num. obs: 55018 / % possible obs: 99.9 % / Redundancy: 17.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.129 / Rpim(I) all: 0.031 / Net I/σ(I): 15.1 / Num. measured all: 974881 / Scaling rejects: 67
Reflection shell

Diffraction-ID: 1 / Redundancy: 18.4 % / Rejects: 0

Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
2.2-2.260.6554.98199244570.9260.15699.8
9.33-67.660.07334.1150568190.9980.01799.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
REFMAC5.8.0131refinement
HKL-2000data collection
Aimless0.1.27data scaling
PDB_EXTRACT3.15data extraction
BALBESphasing
iMOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2EIY

2eiy


Resolution: 2.2→58.65 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.94 / WRfactor Rfree: 0.208 / WRfactor Rwork: 0.1495 / FOM work R set: 0.8664 / SU B: 4.779 / SU ML: 0.12 / SU R Cruickshank DPI: 0.1898 / SU Rfree: 0.1749 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.19 / ESU R Free: 0.175 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2085 2646 4.8 %RANDOM
Rwork0.1497 ---
obs0.1525 52335 99.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 119.01 Å2 / Biso mean: 37.773 Å2 / Biso min: 15.28 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20.02 Å2-0 Å2
2--0.03 Å20 Å2
3----0.1 Å2
Refinement stepCycle: final / Resolution: 2.2→58.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6765 0 10 508 7283
Biso mean--48.89 41.08 -
Num. residues----864
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0196975
X-RAY DIFFRACTIONr_angle_refined_deg2.1111.9869460
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0675860
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.624.19327
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.194151177
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1841552
X-RAY DIFFRACTIONr_chiral_restr0.1720.21059
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0215306
X-RAY DIFFRACTIONr_mcbond_it3.4293.6813453
X-RAY DIFFRACTIONr_mcangle_it4.6195.4974309
X-RAY DIFFRACTIONr_scbond_it4.5473.873522
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.273 188 -
Rwork0.197 3833 -
all-4021 -
obs--99.98 %

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