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- PDB-5cm0: Crystal structure of branched-chain aminotransferase from thermop... -

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Basic information

Entry
Database: PDB / ID: 5cm0
TitleCrystal structure of branched-chain aminotransferase from thermophilic archaea Geoglobus acetivorans
ComponentsBranched-chain transaminase
KeywordsTRANSFERASE / aminotransferase / branched-chain / PLP / BCAT / Geoglobus acetivorans
Function / homology
Function and homology information


L-valine-2-oxoglutarate transaminase activity / L-isoleucine-2-oxoglutarate transaminase activity / branched-chain-amino-acid transaminase / L-leucine biosynthetic process / L-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 / Branched-chain-amino-acid aminotransferase-like, N-terminal / Aminotransferase class IV / Aminotransferase-like, PLP-dependent enzymes ...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 / 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 / D-amino Acid Aminotransferase; Chain A, domain 1 / Alpha-Beta Barrel / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
PYRIDOXAL-5'-PHOSPHATE / Branched-chain-amino-acid aminotransferase
Similarity search - Component
Biological speciesGeoglobus acetivorans (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 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 Fund Russian Federation
ERA-IB ("Thermogene") 7th EU Framework Programme
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
DepositionJul 16, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Sep 14, 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_special_symmetry
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

Downloads & links

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Assembly

Deposited unit
A: Branched-chain transaminase
B: Branched-chain transaminase
C: Branched-chain transaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,8988
Polymers97,9723
Non-polymers9265
Water11,277626
1
A: Branched-chain transaminase
B: Branched-chain transaminase
C: Branched-chain transaminase
hetero molecules

A: Branched-chain transaminase
B: Branched-chain transaminase
C: Branched-chain transaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)197,79516
Polymers195,9446
Non-polymers1,85110
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554x-y,-y,-z-2/31
Buried area29580 Å2
ΔGint-153 kcal/mol
Surface area53530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.650, 117.650, 135.980
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11B-597-

HOH

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Components

#1: Protein Branched-chain transaminase


Mass: 32657.373 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


Mass: 247.142 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: C8H10NO6P
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 626 / 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: 2.78 Å3/Da / Density % sol: 55.83 %
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: 1.9→58.83 Å / Num. obs: 85638 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 19.8 % / Biso Wilson estimate: 36.772 Å2 / Rmerge F obs: 1 / Rmerge(I) obs: 0.066 / Rrim(I) all: 0.068 / Χ2: 1.021 / Net I/σ(I): 31.75 / Num. measured all: 1696134
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.9-20.9290.7714.0223020512122119490.79298.6
2-2.10.9720.4676.72191595993799260.47999.9
2.1-2.40.9930.23713.5442644020879208080.24399.7
2.4-2.630.9980.12523.9520143010160101510.12899.9
2.63-2.810.9990.09233.3121538584958490.095100
2.81-3.030.9990.07242.96109827536753670.074100
3.03-3.320.9990.05454.2196204509150700.05599.6
3.32-3.7110.04271.5193005461546120.04399.9
3.71-4.2710.03582.9277565401640120.03699.9
4.27-5.210.03188.1262302345834500.03199.8
5.2-7.2410.0388.5655101274927490.031100
7.24-8010.02310030922169916950.02399.8
803

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
REFMAC5.8.0124refinement
HKL-2000data reduction
XSCALEdata scaling
MOLREPphasing
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2EIY

2eiy


Resolution: 1.9→101.89 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.963 / SU B: 2.835 / SU ML: 0.081 / Cross valid method: THROUGHOUT / ESU R: 0.11 / ESU R Free: 0.109 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1879 4226 4.9 %RANDOM
Rwork0.15143 ---
obs0.1533 81410 99.64 %-
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 mean: 37.672 Å2
Baniso -1Baniso -2Baniso -3
1-0.48 Å20.24 Å2-0 Å2
2--0.48 Å20 Å2
3----1.56 Å2
Refinement stepCycle: LAST / Resolution: 1.9→101.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6624 0 12 626 7262
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0196791
X-RAY DIFFRACTIONr_bond_other_d0.0020.026548
X-RAY DIFFRACTIONr_angle_refined_deg1.9881.9859216
X-RAY DIFFRACTIONr_angle_other_deg1.144315011
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5955843
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.67224.129310
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.69151122
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2021550
X-RAY DIFFRACTIONr_chiral_restr0.1360.21049
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0217694
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021515
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_it3.3843.5673392
X-RAY DIFFRACTIONr_mcbond_other3.3843.5663391
X-RAY DIFFRACTIONr_mcangle_it4.1635.3234227
X-RAY DIFFRACTIONr_mcangle_other4.1635.3244228
X-RAY DIFFRACTIONr_scbond_it4.2353.933399
X-RAY DIFFRACTIONr_scbond_other4.2353.933399
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.8025.7484987
X-RAY DIFFRACTIONr_long_range_B_refined7.27629.8748093
X-RAY DIFFRACTIONr_long_range_B_other7.27629.8798094
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.295 315 -
Rwork0.291 5791 -
obs--97.59 %

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