[English] 日本語
Yorodumi
- PDB-1gbn: HUMAN ORNITHINE AMINOTRANSFERASE COMPLEXED WITH THE NEUROTOXIN GA... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1gbn
TitleHUMAN ORNITHINE AMINOTRANSFERASE COMPLEXED WITH THE NEUROTOXIN GABACULINE
ComponentsORNITHINE AMINOTRANSFERASE
KeywordsTRANSFERASE / ORNITHINE AMINOTRANSFERASE / UREA CYCLE / PYRIDOXAL-5'-PHOSPHATE
Function / homology
Function and homology information


arginine catabolic process to proline via ornithine / ornithine aminotransferase activity / ornithine aminotransferase / arginine catabolic process to glutamate / L-proline biosynthetic process / Glutamate and glutamine metabolism / visual perception / pyridoxal phosphate binding / mitochondrial matrix / mitochondrion ...arginine catabolic process to proline via ornithine / ornithine aminotransferase activity / ornithine aminotransferase / arginine catabolic process to glutamate / L-proline biosynthetic process / Glutamate and glutamine metabolism / visual perception / pyridoxal phosphate binding / mitochondrial matrix / mitochondrion / nucleoplasm / identical protein binding / cytoplasm
Similarity search - Function
Ornithine aminotransferase / : / Aminotransferases class-III pyridoxal-phosphate attachment site. / Aminotransferase class-III / Aminotransferase class-III / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain ...Ornithine aminotransferase / : / Aminotransferases class-III pyridoxal-phosphate attachment site. / Aminotransferase class-III / Aminotransferase class-III / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
3-AMINOBENZOIC ACID / GABACULINE / PYRIDOXAL-5'-PHOSPHATE / Ornithine aminotransferase, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsShah, S.A. / Shen, B.W. / Brunger, A.T.
CitationJournal: Structure / Year: 1997
Title: Human ornithine aminotransferase complexed with L-canaline and gabaculine: structural basis for substrate recognition.
Authors: Shah, S.A. / Shen, B.W. / Brunger, A.T.
History
DepositionMay 29, 1997Processing site: BNL
Revision 1.0Jun 3, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 9, 2023Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ORNITHINE AMINOTRANSFERASE
B: ORNITHINE AMINOTRANSFERASE
C: ORNITHINE AMINOTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,2799
Polymers134,1183
Non-polymers1,1616
Water5,927329
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: ORNITHINE AMINOTRANSFERASE
B: ORNITHINE AMINOTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,1856
Polymers89,4122
Non-polymers7734
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12290 Å2
ΔGint-52 kcal/mol
Surface area24800 Å2
MethodPISA
3
C: ORNITHINE AMINOTRANSFERASE
hetero molecules

C: ORNITHINE AMINOTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,1896
Polymers89,4122
Non-polymers7774
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area12320 Å2
ΔGint-50 kcal/mol
Surface area24830 Å2
MethodPISA
4
C: ORNITHINE AMINOTRANSFERASE
hetero molecules

A: ORNITHINE AMINOTRANSFERASE
B: ORNITHINE AMINOTRANSFERASE
C: ORNITHINE AMINOTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)180,37412
Polymers178,8254
Non-polymers1,5498
Water724
TypeNameSymmetry operationNumber
crystal symmetry operation4_555y,x,-z1
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)115.013, 115.013, 185.753
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.905265, 0.049533, -0.421949), (0.048561, -0.998735, -0.013059), (-0.422062, -0.008668, -0.906526)7.61656, 73.34723, 43.01362
2given(-0.440738, 0.789615, 0.426917), (-0.872489, -0.488624, 0.003011), (0.21098, -0.371153, 0.904286)-2.00252, 80.59359, -6.71558

-
Components

#1: Protein ORNITHINE AMINOTRANSFERASE /


Mass: 44706.156 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: BOUND INHIBITOR GABACULINE / Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P04181, ornithine aminotransferase
#2: Chemical ChemComp-GAB / 3-AMINOBENZOIC ACID / GABACULINE / 3-Aminobenzoic acid


Mass: 137.136 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H7NO2
#3: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate / Pyridoxal phosphate


Mass: 247.142 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H10NO6P
#4: Chemical ChemComp-GBC / GABACULINE / Gabaculine


Mass: 141.168 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H11NO2 / Comment: inhibitor, neurotoxin*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 329 / 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: 2.64 Å3/Da / Density % sol: 50.1 %
Crystal growpH: 6.5 / Details: pH 6.5
Crystal grow
*PLUS
pH: 7.8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110-20 mg/mlprotein1drop
250 mMTris-HCl1drop
30.01 MPLP1drop
410-15 %PEG60001reservoir
550-200 mM1reservoirNaCl

-
Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.9417
DetectorType: PRINCETON 2K / Detector: CCD / Date: Oct 10, 1995 / Details: DUEL SLITS
RadiationMonochromator: CRYSTAL / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9417 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 57010 / % possible obs: 90 % / Observed criterion σ(I): 2 / Redundancy: 4.6 % / Biso Wilson estimate: 14.3 Å2 / Rmerge(I) obs: 0.064 / Rsym value: 0.064 / Net I/σ(I): 16.2
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.17 / Mean I/σ(I) obs: 5.9 / Rsym value: 0.17 / % possible all: 80.1
Reflection
*PLUS
% possible obs: 89.9 %
Reflection shell
*PLUS
Lowest resolution: 2.4 Å / % possible obs: 80.1 % / Redundancy: 2.6 % / Rmerge(I) obs: 0.171

-
Processing

Software
NameVersionClassification
X-PLOR3.851model building
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.851phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1OAT

1oat


Resolution: 2.3→50 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 470426.53 / Data cutoff low absF: 0.0001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.235 5275 10.1 %RANDOM
Rwork0.209 ---
obs0.209 52216 81.9 %-
Displacement parametersBiso mean: 22 Å2
Baniso -1Baniso -2Baniso -3
1-1.3 Å20.12 Å20 Å2
2--1.3 Å20 Å2
3----2.6 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.32 Å0.29 Å
Refinement stepCycle: LAST / Resolution: 2.3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9450 0 75 329 9854
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.4
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d23.6
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.25
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.421.5
X-RAY DIFFRACTIONx_mcangle_it2.232
X-RAY DIFFRACTIONx_scbond_it2.342
X-RAY DIFFRACTIONx_scangle_it3.342.5
Refine LS restraints NCSRms dev Biso : 1.618 Å2 / Rms dev position: 0.1647 Å
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.294 705 10.1 %
Rwork0.265 6270 -
obs--66.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2PARAM.PLP
X-RAY DIFFRACTION3PARAM.GABACULINE
X-RAY DIFFRACTION4PARAM.PATCH
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Num. reflection obs: 52218 / Rfactor obs: 0.206
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_deg1.32
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23.6
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.25
LS refinement shell
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 2.4 Å / Num. reflection Rfree: 70 / % reflection Rfree: 10 % / Num. reflection Rwork: 5123

+
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://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