[English] 日本語
Yorodumi
- PDB-5eqc: Structure of the ornithine aminotransferase from Toxoplasma gondi... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5eqc
TitleStructure of the ornithine aminotransferase from Toxoplasma gondii crystallized in presence of oxidized glutathione reveals partial occupancy of PLP at the protein active site
ComponentsOrnithine aminotransferase, mitochondrial
KeywordsTRANSFERASE / PLP / gabaculine / parasite / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


ornithine aminotransferase activity / ornithine aminotransferase / L-proline biosynthetic process / pyridoxal phosphate binding
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
beta-D-glucopyranose / BETA-MERCAPTOETHANOL / alpha-D-glucopyranose / DI(HYDROXYETHYL)ETHER / PYRIDOXAL-5'-PHOSPHATE / Ornithine aminotransferase
Similarity search - Component
Biological speciesToxoplasma gondii (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsFilippova, E.V. / Minasov, G. / Flores, K. / Le, H.V. / Silverman, R.B. / McLeod, R.L. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To Be Published
Title: Structure of the ornithine aminotransferase from Toxoplasma gondii crystallized in presence of oxidized glutathione reveals partial occupancy of PLP at the protein active site
Authors: Filippova, E.V. / Minasov, G. / Flores, K. / Le, H.V. / Silverman, R.B. / McLeod, R.L. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionNov 12, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 24, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_oper_list / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_oper_list.symmetry_operation
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Ornithine aminotransferase, mitochondrial
B: Ornithine aminotransferase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,01816
Polymers96,7882
Non-polymers2,22914
Water7,891438
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16300 Å2
ΔGint-49 kcal/mol
Surface area28000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.406, 109.406, 109.883
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein Ornithine aminotransferase, mitochondrial /


Mass: 48394.223 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Toxoplasma gondii (eukaryote) / Strain: ME49 / Gene: TGME49_269110 / Plasmid: pMCSG28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)/pMagic / References: UniProt: S8EY38, ornithine aminotransferase

-
Sugars , 2 types, 5 molecules

#2: Sugar ChemComp-GLC / alpha-D-glucopyranose / alpha-D-glucose / D-glucose / glucose / Glucose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-glucopyranoseCOMMON NAMEGMML 1.0
a-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Sugar
ChemComp-BGC / beta-D-glucopyranose / beta-D-glucose / D-glucose / glucose / Glucose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranoseCOMMON NAMEGMML 1.0
b-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0

-
Non-polymers , 6 types, 447 molecules

#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate / Pyridoxal phosphate


Mass: 247.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10NO6P
#7: Chemical ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER / Bis-tris methane


Mass: 209.240 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H19NO5 / Comment: pH buffer*YM
#8: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL / 2-Mercaptoethanol


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 438 / 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: 3.4 Å3/Da / Density % sol: 63.79 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Na Thiocyanate, 20% PEG3350, 0.5 mM oxidized glutathione

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 13, 2015
RadiationMonochromator: beryllium lenses / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.2→30 Å / Num. obs: 65316 / % possible obs: 100 % / Redundancy: 8.3 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 23.4
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 8.2 % / Rmerge(I) obs: 0.7 / Mean I/σ(I) obs: 3.3 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.8.0131refinement
BLU-MAXdata collection
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4NOG

4nog


Resolution: 2.2→30 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.955 / SU B: 7.508 / SU ML: 0.097 / Cross valid method: THROUGHOUT / ESU R: 0.151 / ESU R Free: 0.138 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.181 3219 4.9 %RANDOM
Rwork0.145 ---
obs0.146 62063 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.35 Å2
Baniso -1Baniso -2Baniso -3
1--1.09 Å20 Å20 Å2
2---1.09 Å20 Å2
3---2.17 Å2
Refinement stepCycle: LAST / Resolution: 2.2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6579 0 140 438 7157
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0196917
X-RAY DIFFRACTIONr_bond_other_d0.0020.026672
X-RAY DIFFRACTIONr_angle_refined_deg1.9151.9899355
X-RAY DIFFRACTIONr_angle_other_deg1.067315363
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2245863
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.21423.399306
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.75151175
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8721562
X-RAY DIFFRACTIONr_chiral_restr0.1310.21046
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0217761
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021537
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_it1.2352.2253434
X-RAY DIFFRACTIONr_mcbond_other1.2342.2243433
X-RAY DIFFRACTIONr_mcangle_it1.9883.3274303
X-RAY DIFFRACTIONr_mcangle_other1.9883.3284304
X-RAY DIFFRACTIONr_scbond_it2.292.683483
X-RAY DIFFRACTIONr_scbond_other2.292.683483
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.513.885053
X-RAY DIFFRACTIONr_long_range_B_refined6.09919.0917968
X-RAY DIFFRACTIONr_long_range_B_other6.09919.0947968
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.26 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.225 203 -
Rwork0.178 4575 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.76160.2482-0.02030.4937-0.0580.4038-0.00820.09210.00420.00450.0320.05370.05060.0171-0.02390.07320.00740.00050.08990.0250.1624134.2032119.552-19.8222
20.77420.1341-0.21430.394-0.2930.58560.0446-0.13640.01410.195-0.0934-0.0887-0.08230.17570.04880.1477-0.0117-0.04140.08030.02660.1181147.0683121.98427.7425
32.97381.17450.54031.60020.88931.8301-0.0322-0.2419-0.1120.3549-0.07160.10490.135-0.02550.10380.23130.005-0.00590.05140.05230.0963138.7411112.980217.2906
40.87640.10380.32780.8103-0.25590.31170.0179-0.04620.08720.2535-0.00970.0319-0.0882-0.0227-0.00820.1679-0.00740.01350.0596-0.01730.1492137.5995126.62096.0634
50.3238-0.0274-0.13262.3402-0.40070.56630.0146-0.01280.01570.02050.0370.1680.0673-0.0033-0.05170.06780.00510.0230.07520.02110.1647123.4008104.3124-4.5569
60.88620.3759-0.38451.0669-0.39431.4615-0.04460.11020.29490.19810.013-0.0012-0.22210.06820.03160.1503-0.0311-0.01890.03420.02440.2326141.6832146.2672-4.6359
70.38120.01840.10320.378-0.17350.70880.00140.0461-0.04860.0346-0.061-0.08670.04670.20540.05950.03810.0105-0.00580.15040.0450.1778157.0598120.084-8.8486
81.5069-0.1282-0.84375.00310.10281.7154-0.0954-0.0562-0.0210.20630.02-0.2614-0.01040.55840.07540.019-0.0185-0.02570.29830.05870.1814171.2502126.9433-13.1025
90.62760.3906-0.04560.6671-0.36040.4922-0.01890.03480.0219-0.004-0.0078-0.08340.05110.16130.02670.05740.00670.01460.17060.03490.1638155.9281122.8953-16.433
101.2545-0.1152-0.25652.02540.86531.58340.0356-0.01060.37650.04230.0404-0.2866-0.11610.3104-0.0760.0539-0.0827-0.00890.14350.0270.256163.4944149.9197-12.0794
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A17 - 102
2X-RAY DIFFRACTION2A103 - 209
3X-RAY DIFFRACTION3A210 - 248
4X-RAY DIFFRACTION4A249 - 334
5X-RAY DIFFRACTION5A335 - 441
6X-RAY DIFFRACTION6B18 - 87
7X-RAY DIFFRACTION7B88 - 219
8X-RAY DIFFRACTION8B220 - 248
9X-RAY DIFFRACTION9B249 - 333
10X-RAY DIFFRACTION10B334 - 441

+
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