[English] 日本語
Yorodumi
- PDB-5e3k: Crystal structure of the ornithine aminotransferase from Toxoplas... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5e3k
TitleCrystal structure of the ornithine aminotransferase from Toxoplasma gondii ME49 in a complex with (S)-4-amino-5-fluoropentanoic acid
ComponentsAminotransferase
KeywordsTRANSFERASE / inhibitor / complex / parasite / PYRIDOXAL 5'-PHOSPHATE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


: / ornithine aminotransferase / L-ornithine transaminase activity / : / L-proline biosynthetic process / pyridoxal phosphate binding / 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) ...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
Chem-5JV / CARBONATE ION / DI(HYDROXYETHYL)ETHER / Ornithine aminotransferase
Similarity search - Component
Biological speciesToxoplasma gondii (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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: Crystal structure of the ornithine aminotransferase from Toxoplasma gondii ME49 in a complex with (S)-4-amino-5-fluoropentanoic acid
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
DepositionOct 2, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 26, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 27, 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 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Aminotransferase
B: Aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,64817
Polymers96,7882
Non-polymers1,85915
Water14,646813
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13520 Å2
ΔGint-148 kcal/mol
Surface area28660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.328, 61.524, 63.555
Angle α, β, γ (deg.)100.72, 92.96, 108.18
Int Tables number1
Space group name H-MP1

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein Aminotransferase / 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) / Gene: TGME49_269110 / Plasmid: pMCSG28 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)MAGIC / References: UniProt: S8EY38, ornithine aminotransferase

-
Non-polymers , 5 types, 828 molecules

#2: Chemical ChemComp-5JV / 4-[(E)-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)amino]pent-4-enoic acid


Mass: 344.257 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H17N2O7P
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-CO3 / CARBONATE ION


Mass: 60.009 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: CO3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 813 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.11 Å3/Da / Density % sol: 41.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.2 M AmmSO4, 0.1 M Bis-Tris, 25% PEG3350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.97913 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 23, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97913 Å / Relative weight: 1
ReflectionResolution: 1.7→30 Å / Num. obs: 84366 / % possible obs: 97.3 % / Redundancy: 3 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 20.9
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 1.9 / % possible all: 95.7

-
Processing

Software
NameVersionClassification
BLU-MAXdata collection
HKL-3000data scaling
PHASERphasing
Cootmodel building
REFMAC5.8.0124refinement
HKL-3000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4NOG

4nog


Resolution: 1.7→30 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.957 / SU B: 4.49 / SU ML: 0.076 / Cross valid method: THROUGHOUT / ESU R: 0.105 / ESU R Free: 0.106 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19601 4228 5 %RANDOM
Rwork0.15374 ---
obs0.1559 80138 96.41 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.798 Å2
Baniso -1Baniso -2Baniso -3
1--0.95 Å2-1.64 Å2-0.83 Å2
2--1.04 Å2-0.5 Å2
3---1.12 Å2
Refinement stepCycle: 1 / Resolution: 1.7→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6560 0 114 813 7487
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0196928
X-RAY DIFFRACTIONr_bond_other_d0.0020.026649
X-RAY DIFFRACTIONr_angle_refined_deg1.7491.9839394
X-RAY DIFFRACTIONr_angle_other_deg1.041315297
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.345874
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.94523.366309
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.598151174
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7391563
X-RAY DIFFRACTIONr_chiral_restr0.1080.21038
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0217871
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021554
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_it0.6721.2853457
X-RAY DIFFRACTIONr_mcbond_other0.6721.2853456
X-RAY DIFFRACTIONr_mcangle_it1.0391.9254344
X-RAY DIFFRACTIONr_mcangle_other1.0381.9264345
X-RAY DIFFRACTIONr_scbond_it1.1821.5183471
X-RAY DIFFRACTIONr_scbond_other1.1821.5183471
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.8072.25051
X-RAY DIFFRACTIONr_long_range_B_refined5.46712.3428682
X-RAY DIFFRACTIONr_long_range_B_other5.46712.3428682
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.741 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.261 256 -
Rwork0.216 5229 -
obs--84.7 %
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)
12.0251-1.1888-0.48523.71171.86427.13830.21410.26520.0666-0.2559-0.1435-0.2628-0.39170.0017-0.07060.07140.01140.04710.09470.02610.073750.020921.902149.4672
20.66870.09730.36860.4007-0.17991.14440.00290.1901-0.0255-0.1520.0023-0.0072-0.00510.079-0.00520.0880.01220.02920.0788-0.00570.056435.678913.60947.1023
30.60440.32180.03610.8861-0.07960.57540.00910.0123-0.0407-0.00230.03840.0625-0.0001-0.1282-0.04740.01750.02120.01060.06150.0080.063919.47370.876965.2252
40.33660.1910.06930.77880.16551.097-0.0080.0905-0.0759-0.22870.02320.01430.1084-0.0004-0.01520.11330.0249-0.00230.057-0.0150.057322.9451-0.016138.8511
51.6981-2.7847-0.80017.24292.20721.8176-0.01380.16550.003-0.44940.00870.0038-0.01430.03540.00510.136-0.0179-0.00290.072-0.00150.003626.03421.782529.2604
62.30370.4132-0.67360.50790.18570.4140.18420.10160.52620.062-0.10170.2333-0.044-0.0969-0.08250.11560.10490.07830.2061-0.04890.291615.253529.410769.1708
70.80610.47730.19931.12310.14380.77510.0889-0.05460.1390.1569-0.0390.074-0.27-0.0154-0.04980.17390.03360.04940.0548-0.00880.088431.032425.86471.5766
80.44950.01950.1630.4369-0.17560.72170.0260.0029-0.070.0161-0.0081-0.11730.00450.0885-0.01790.02480.02460.00440.0435-0.00640.101245.21193.698671.1971
90.8081-0.1562-0.59780.4125-0.25283.160.0092-0.12940.12760.11630.0562-0.0803-0.13160.185-0.06540.1402-0.0457-0.01720.0566-0.02530.061947.927326.149487.9864
100.78990.0327-0.3981.4790.10211.78630.0148-0.15840.05350.25140.03160.0081-0.20180.0457-0.04640.1430.0010.02360.0411-0.02250.02537.380925.021990.4374
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A18 - 32
2X-RAY DIFFRACTION2A33 - 101
3X-RAY DIFFRACTION3A102 - 334
4X-RAY DIFFRACTION4A335 - 418
5X-RAY DIFFRACTION5A419 - 439
6X-RAY DIFFRACTION6B17 - 41
7X-RAY DIFFRACTION7B42 - 101
8X-RAY DIFFRACTION8B102 - 334
9X-RAY DIFFRACTION9B335 - 366
10X-RAY DIFFRACTION10B367 - 440

+
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