[English] 日本語
Yorodumi
- PDB-5cm0: Crystal structure of branched-chain aminotransferase from thermop... -

+
Open data


ID or keywords:

Loading...

-
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-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
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
Phasing

PhasingMethod: molecular replacement

-
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 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more