[English] 日本語
Yorodumi
- PDB-4zwm: 2.3 A resolution crystal structure of the ornithine aminotransfer... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4zwm
Title2.3 A resolution crystal structure of the ornithine aminotransferase from Toxoplasma gondii ME49
ComponentsOrnithine aminotransferase, mitochondrial, putative
KeywordsTRANSFERASE / Structural Genomics / pyridoxal 5'-phosphate (PLP)-independent aminotransferase / 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
PYRIDOXAL-5'-PHOSPHATE / Ornithine aminotransferase
Similarity search - Component
Biological speciesToxoplasma gondii ME49 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.31 Å
AuthorsFilippova, E.V. / Minasov, G. / Flores, K. / Van Le, H. / Silverman, R.B. / McLeod, R. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To Be Published
Title: 2.3 A resolution crystal structure of the ornithine aminotransferase from Toxoplasma gondii ME49
Authors: Filippova, E.V. / Minasov, G. / Flores, K. / Van Le, H. / Silverman, R.B. / McLeod, R. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionMay 19, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 3, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Derived calculations / Refinement description / Source and taxonomy
Category: entity_src_gen / pdbx_struct_oper_list / software
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Sep 27, 2023Group: 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: Ornithine aminotransferase, mitochondrial, putative
B: Ornithine aminotransferase, mitochondrial, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,43516
Polymers96,7882
Non-polymers1,64714
Water3,081171
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15620 Å2
ΔGint-305 kcal/mol
Surface area27220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.418, 60.804, 63.379
Angle α, β, γ (deg.)100.70, 92.63, 107.68
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein Ornithine aminotransferase, mitochondrial, putative


Mass: 48394.223 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Toxoplasma gondii ME49 (eukaryote) / Gene: TGME49_269110 / Plasmid: pMCSG28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)/pMagic / References: UniProt: S8EY38, ornithine aminotransferase
#2: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 171 / 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: 41.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 / 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: 0.9788 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 23, 2015
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9788 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. all: 33287 / Num. obs: 33287 / % possible obs: 96.9 % / Redundancy: 2 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 15.7
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 2.2 / % possible all: 97.2

-
Processing

Software
NameVersionClassification
BLU-MAXdata collection
HKL-2000data scaling
PHASERphasing
REFMAC5.8.0107refinement
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4NOG

4nog


Resolution: 2.31→30 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.908 / SU B: 17.568 / SU ML: 0.212 / Cross valid method: THROUGHOUT / ESU R: 0.554 / ESU R Free: 0.285 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25848 1595 4.8 %RANDOM
Rwork0.18639 ---
obs0.1899 31691 96.27 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.965 Å2
Baniso -1Baniso -2Baniso -3
1-0.8 Å2-1.02 Å2-0.77 Å2
2--0.16 Å2-1.28 Å2
3---0.48 Å2
Refinement stepCycle: 1 / Resolution: 2.31→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6546 0 90 171 6807
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0196779
X-RAY DIFFRACTIONr_bond_other_d0.0020.026487
X-RAY DIFFRACTIONr_angle_refined_deg1.5611.9829190
X-RAY DIFFRACTIONr_angle_other_deg0.98314909
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6695848
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.70423.443305
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.212151151
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0321561
X-RAY DIFFRACTIONr_chiral_restr0.0840.21026
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0217637
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021516
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_it0.8212.1823392
X-RAY DIFFRACTIONr_mcbond_other0.822.1823391
X-RAY DIFFRACTIONr_mcangle_it1.4063.2694240
X-RAY DIFFRACTIONr_mcangle_other1.4063.274241
X-RAY DIFFRACTIONr_scbond_it1.2552.3893387
X-RAY DIFFRACTIONr_scbond_other0.8982.3683340
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.5183.4934879
X-RAY DIFFRACTIONr_long_range_B_refined3.25317.5817589
X-RAY DIFFRACTIONr_long_range_B_other3.19317.5287557
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.306→2.366 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.295 115 -
Rwork0.253 2181 -
obs--89.69 %
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)
11.2124-0.12990.44620.4783-0.28490.92120.0140.24240.0889-0.1751-0.0022-0.07120.02960.0765-0.01180.07830.0080.04650.11550.02850.063738.456815.505147.4865
20.65220.2054-0.00610.8249-0.0550.3856-0.027-0.0009-0.0165-0.00640.02830.05710.0069-0.0388-0.00130.04850.04080.01130.11040.0070.103719.34130.844165.2901
31.2288-0.4913-0.38425.55991.30661.8286-0.14830.2438-0.0402-0.50540.12260.35160.1526-0.29320.02560.1998-0.0623-0.05480.12080.01360.02916.74220.932237.591
42.24860.164-0.20221.6265-0.51462.0625-0.14750.1398-0.1381-0.45470.1180.00010.30110.03390.02940.2434-0.0440.02740.12280.00290.014127.4856-0.208936.6878
53.00330.4841-1.45191.81120.51351.0250.2270.05330.53030.2705-0.07950.3492-0.008-0.0646-0.14760.07770.04380.06410.1066-0.00730.171416.106725.456671.8277
60.6469-0.0181-0.38280.90280.04480.75310.04110.10080.15410.0725-0.08530.0217-0.04770.01170.04420.07190.02620.01480.0990.01570.11737.272123.172964.2687
70.50030.1216-0.00250.6032-0.31870.5434-0.0034-0.0152-0.02080.0307-0.0013-0.0458-0.01630.04780.00470.06780.02390.01060.1065-0.0010.107545.48542.849573.1618
81.61140.2119-0.47241.9580.14693.0060.0081-0.1363-0.02210.4896-0.0529-0.0097-0.26330.14990.04490.2473-0.01970.02170.0212-0.00660.036140.753225.520489.597
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A18 - 101
2X-RAY DIFFRACTION2A102 - 334
3X-RAY DIFFRACTION3A335 - 370
4X-RAY DIFFRACTION4A371 - 439
5X-RAY DIFFRACTION5B17 - 53
6X-RAY DIFFRACTION6B54 - 124
7X-RAY DIFFRACTION7B125 - 334
8X-RAY DIFFRACTION8B335 - 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