[English] 日本語
Yorodumi
- PDB-2hhf: X-ray crystal structure of oxidized human mitochondrial branched ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2hhf
TitleX-ray crystal structure of oxidized human mitochondrial branched chain aminotransferase (hBCATm)
Components(Branched-chain-amino-acid aminotransferase, mitochondrial) x 2
KeywordsTRANSFERASE / D-aminoacid aminotransferase-like PLP-dependent enzymes
Function / homology
Function and homology information


regulation of hormone levels / isoleucine catabolic process / L-leucine:2-oxoglutarate aminotransferase activity / branched-chain-amino-acid transaminase / L-leucine transaminase activity / L-valine transaminase activity / L-isoleucine transaminase activity / branched-chain amino acid biosynthetic process / branched-chain-amino-acid transaminase activity / Branched-chain amino acid catabolism ...regulation of hormone levels / isoleucine catabolic process / L-leucine:2-oxoglutarate aminotransferase activity / branched-chain-amino-acid transaminase / L-leucine transaminase activity / L-valine transaminase activity / L-isoleucine transaminase activity / branched-chain amino acid biosynthetic process / branched-chain-amino-acid transaminase activity / Branched-chain amino acid catabolism / L-leucine biosynthetic process / valine biosynthetic process / amino acid biosynthetic process / cellular response to leukemia inhibitory factor / lipid metabolic process / mitochondrial matrix / mitochondrion / nucleoplasm
Similarity search - Function
Branched-chain amino acid aminotransferase II / Branched-chain aminotransferase / 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 II / Branched-chain aminotransferase / 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, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsYennawar, N.H. / Hutson, S.M.
Citation
Journal: J.Biol.Chem. / Year: 2006
Title: Human Mitochondrial Branched Chain Aminotransferase Isozyme: STRUCTURAL ROLE OF THE CXXC CENTER IN CATALYSIS.
Authors: Yennawar, N.H. / Islam, M.M. / Conway, M. / Wallin, R. / Hutson, S.M.
#1: Journal: J.BIOL.CHEM. / Year: 1998
Title: Overexpression and characterization of the human mitochondrial and cytosolic branched-chain aminotransferases.
Authors: Davoodi, J. / Drown, P.M. / Bledsoe, R.K. / Wallin, R. / Reinhart, G.D. / Hutson, S.M.
#2: Journal: Biochim.Biophys.Acta / Year: 1997
Title: Cloning of the rat and human mitochondrial branched chain aminotransferases (BCATm).
Authors: Bledsoe, R.K. / Dawson, P.A. / Hutson, S.M.
History
DepositionJun 28, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 24, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 15, 2023Group: Data collection / Derived calculations / Category: chem_comp_atom / chem_comp_bond / struct_conn
Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2 / _struct_conn.pdbx_leaving_atom_flag

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Branched-chain-amino-acid aminotransferase, mitochondrial
B: Branched-chain-amino-acid aminotransferase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,5995
Polymers82,8662
Non-polymers7333
Water3,711206
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6310 Å2
ΔGint-19 kcal/mol
Surface area27160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.123, 104.183, 58.264
Angle α, β, γ (deg.)90.00, 100.72, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Branched-chain-amino-acid aminotransferase, mitochondrial / BCATm / Placental protein 18 / PP18 / MITOCHONDRIAL BRANCHED CHAIN AMINOTRANSFERASE


Mass: 41450.023 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: In this entity, residue 141 in chain A is a modified Tyrosine, TYO. The authors state that Tyrosine 141 has undergone radiation damage in the presence of the oxidizing agent hydrogen peroxide to form TYO.
Source: (gene. exp.) Homo sapiens (human) / Gene: BCAT2, BCATM, ECA40 / Plasmid: PET-28A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21de3
References: UniProt: O15382, branched-chain-amino-acid transaminase
#2: Protein Branched-chain-amino-acid aminotransferase, mitochondrial / BCATm / Placental protein 18 / PP18 / MITOCHONDRIAL BRANCHED CHAIN AMINOTRANSFERASE


Mass: 41416.012 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: In this entity, residue 641 is TYR. The authors state that the tyrosine of the second monomer (Chain B) is not modified.
Source: (gene. exp.) Homo sapiens (human) / Gene: BCAT2, BCATM, ECA40 / Plasmid: PET-28A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21de3 / References: UniProt: O15382
#3: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10NO6P
#4: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 206 / 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: 2.09 Å3/Da / Density % sol: 41.17 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Peg1500, Hepes, pH 7.0, H2O2, VAPOR DIFFUSION, HANGING DROP, temperature 294K

-
Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.91609 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 1, 2002 / Details: Si(111)
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91609 Å / Relative weight: 1
ReflectionResolution: 1.8→30 Å / Num. all: 63136 / Num. obs: 58070 / % possible obs: 92 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.077 / Χ2: 1.057 / Net I/σ(I): 9
Reflection shellResolution: 1.8→1.83 Å / Rmerge(I) obs: 0.483 / Num. unique all: 2757 / Χ2: 0.941 / % possible all: 86.9

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT2data extraction
ADSCQUANTUMdata collection
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1EKF

1ekf


Resolution: 1.8→30 Å / FOM work R set: 0.79 / σ(F): 2 / Stereochemistry target values: Engh & Huber
Details: Due to a feature in the refinement program, the structure was refined with OXT on one or more residues that is not the terminal residue of the sequence. In all these instances the OXT was ...Details: Due to a feature in the refinement program, the structure was refined with OXT on one or more residues that is not the terminal residue of the sequence. In all these instances the OXT was changed to N of the next residue.
RfactorNum. reflection% reflectionSelection details
Rfree0.283 2886 4.6 %RANDOM
Rwork0.252 ---
obs0.283 57920 91.8 %-
all-63068 --
Solvent computationBsol: 15.948 Å2
Displacement parametersBiso mean: 24.072 Å2
Baniso -1Baniso -2Baniso -3
1-6.899 Å20 Å2-0.539 Å2
2---8.598 Å20 Å2
3---1.698 Å2
Refinement stepCycle: LAST / Resolution: 1.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5684 0 45 206 5935
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.014
X-RAY DIFFRACTIONc_angle_deg2.066
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 50

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs
1.8-1.810.324570.31310071064
1.81-1.820.388440.31410651109
1.82-1.840.308520.30210661118
1.84-1.850.282610.29510541115
1.85-1.860.326640.29210461110
1.86-1.880.366710.30410461117
1.88-1.890.314500.30610911141
1.89-1.910.283450.28310581103
1.91-1.920.299550.28910671122
1.92-1.940.386660.29810551121
1.94-1.960.354550.28210751130
1.96-1.970.307540.27710351089
1.97-1.990.272480.28211051153
1.99-2.010.336500.27610641114
2.01-2.030.334510.27510741125
2.03-2.050.32640.26210721136
2.05-2.070.342470.27310851132
2.07-2.090.3490.27510921141
2.09-2.110.328550.25610601115
2.11-2.130.296580.2710971155
2.13-2.160.327510.2611001151
2.16-2.180.31710.26210551126
2.18-2.210.296660.26310841150
2.21-2.240.317640.24710891153
2.24-2.270.297650.25710661131
2.27-2.30.317620.26511181180
2.3-2.330.305700.26310861156
2.33-2.370.325550.2511111166
2.37-2.40.293510.27411241175
2.4-2.440.382680.28711291197
2.44-2.480.258630.25611181181
2.48-2.530.312630.24911381201
2.53-2.580.241530.26411091162
2.58-2.630.391570.26811851242
2.63-2.690.284500.26711401190
2.69-2.750.304470.25611901237
2.75-2.820.377560.26911431199
2.82-2.90.297630.25812151278
2.9-2.980.271480.24811821230
2.98-3.080.235570.24311881245
3.08-3.190.251540.24711461200
3.19-3.310.25710.23511721243
3.31-3.470.268600.23311341194
3.47-3.650.249700.24411301200
3.65-3.880.25690.23211281197
3.88-4.170.283540.23610581112
4.17-4.590.236500.22210411091
4.59-5.250.237680.2210681136
5.25-6.610.296580.24111721230
6.61-300.203560.21811011157
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein.param
X-RAY DIFFRACTION2water_rep.param
X-RAY DIFFRACTION3acy+glyc.par
X-RAY DIFFRACTION4epe_xplor_par.txt

+
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