[English] 日本語
Yorodumi
- PDB-1svv: Initial Stuctural Analysis of Leishmania major Threonine Aldolase -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1svv
TitleInitial Stuctural Analysis of Leishmania major Threonine Aldolase
ComponentsTHREONINE ALDOLASE
KeywordsLYASE / structural genomics / Structural Genomics of Pathogenic Protozoa / SGPP / Protein Structure Initiative / PSI / Structural Genomics of Pathogenic Protozoa Consortium
Function / homology
Function and homology information


amino acid metabolic process / lyase activity
Similarity search - Function
Aromatic amino acid beta-eliminating lyase/threonine aldolase / Beta-eliminating lyase / 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 ...Aromatic amino acid beta-eliminating lyase/threonine aldolase / Beta-eliminating lyase / 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
Unknown ligand / Putative beta eliminating lyase / :
Similarity search - Component
Biological speciesLeishmania major (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 Å
AuthorsHol, W.G.J. / Robien, M.A. / Structural Genomics of Pathogenic Protozoa Consortium (SGPP)
CitationJournal: To be Published
Title: Initial Structural Analysis of Leishmania major Threonine Aldolase
Authors: Hol, W.G.J. / Robien, M.A. / Structural Genomics of Pathogenic Protozoa Consortium
History
DepositionMar 30, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 17, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations ...Advisory / Derived calculations / Refinement description / Version format compliance
Revision 1.3Jan 31, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Remark 400COMPOUND THE SGPP ID FOR THIS PROTEIN IS LMAJ008024AAA.
Remark 600HETEROGEN THE IDENTITY OF THE COORDINATING METAL IS UNCERTAIN AND IS LABELLED AS HET GROUP UNL, ...HETEROGEN THE IDENTITY OF THE COORDINATING METAL IS UNCERTAIN AND IS LABELLED AS HET GROUP UNL, UNKNOWN LIGAND; THE SITE WAS MODELED AS MANGANESE IN VIEW OF THE OBSERVED ANOMALOUS SIGNAL AND ELECTRON DENSITY AT THESE SITES, THE COORDINATE TEMPERATURE FACTORS, AND SIMILARITY TO SIMILAR MN LIGATION GEOMETRY; OTHER POSSIBILITIES, ESPECIALLY A PARTIAL OCCUPANCY ZN(II) WOULD BE GOOD ALTERNATIVES WHICH REMAIN UNDER INVESTIGATION.
Remark 999SEQUENCE THE SEQUENCE IS ALSO AVAILABLE THROUGH PIR ENTRY T02833.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: THREONINE ALDOLASE
B: THREONINE ALDOLASE


Theoretical massNumber of molelcules
Total (without water)79,8524
Polymers79,8522
Non-polymers02
Water2,162120
1
A: THREONINE ALDOLASE
B: THREONINE ALDOLASE

A: THREONINE ALDOLASE
B: THREONINE ALDOLASE


Theoretical massNumber of molelcules
Total (without water)159,7038
Polymers159,7034
Non-polymers04
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area14680 Å2
ΔGint-56 kcal/mol
Surface area45850 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)119.094, 119.094, 129.597
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
DetailsThe second part of the biological assembly is generated by the two fold axis: 1-y, 1-x, 1/2-z

-
Components

#1: Protein THREONINE ALDOLASE /


Mass: 39925.797 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leishmania major (eukaryote) / Gene: L4171.5 / Plasmid: PET14B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21STAR/DE3
References: UniProt: O15839, UniProt: E9AC39*PLUS, L-threonine aldolase
#2: Chemical ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 2 / Source method: obtained synthetically
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 120 / 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: 2.9 Å3/Da / Density % sol: 57 %
Crystal growTemperature: 293 K / pH: 7.5
Details: PEG8000, HEPES, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K, pH 7.50

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.9794, 0.9494, 0.9797
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Feb 26, 2004
RadiationMonochromator: DOUBLE CRYSTAL SI(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97941
20.94941
30.97971
ReflectionResolution: 2.1→19.58 Å / Num. obs: 54773 / % possible obs: 100 % / Observed criterion σ(I): 0

-
Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.1→19.17 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.944 / SU B: 4.431 / SU ML: 0.116 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / ESU R: 0.176 / ESU R Free: 0.157 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: Hydrogens have been added in the riding positions. An unidentified electron density feature remains in the final model, bounded approximately by residues Y45, G74, T76, H100, Y211, T215, ...Details: Hydrogens have been added in the riding positions. An unidentified electron density feature remains in the final model, bounded approximately by residues Y45, G74, T76, H100, Y211, T215, E223, A248 and K216. This density does not appear to closely resemble any known components of the current crystallization experiment nor the covalently modified K203 observed in the structure of 1JG8.pdb, a sequence homolog of the current entry.
RfactorNum. reflection% reflectionSelection details
Rfree0.22968 2778 5.1 %RANDOM
Rwork0.19767 ---
obs0.19927 51943 99.85 %-
all-51945 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 40.534 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.1→19.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5186 0 2 120 5308
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0215288
X-RAY DIFFRACTIONr_bond_other_d0.0020.024863
X-RAY DIFFRACTIONr_angle_refined_deg1.2661.9537169
X-RAY DIFFRACTIONr_angle_other_deg0.781311283
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6135680
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0760.2829
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025901
X-RAY DIFFRACTIONr_gen_planes_other0.0050.021024
X-RAY DIFFRACTIONr_nbd_refined0.2010.2968
X-RAY DIFFRACTIONr_nbd_other0.2270.25263
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0830.22993
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1170.2137
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.1470.23
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2120.214
X-RAY DIFFRACTIONr_symmetry_vdw_other0.270.279
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0920.27
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it1.96243382
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.19665403
X-RAY DIFFRACTIONr_scbond_it4.49861906
X-RAY DIFFRACTIONr_scangle_it6.83101766
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.212 Å / Total num. of bins used: 10 /
RfactorNum. reflection
Rfree0.308 396
Rwork0.265 7382
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)
10.59960.34950.41120.94280.52941.09890.0048-0.1280.09810.0818-0.02960.0482-0.06530.00960.02490.0818-0.02190.01080.0785-0.04710.091591.366550.278951.9711
20.70.12550.1040.51520.02171.115-0.08660.1390.2871-0.23390.02910.1373-0.49280.0570.05750.3107-0.0475-0.0650.01350.03740.15286.840365.340922.3395
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A15 - 354
2X-RAY DIFFRACTION2B15 - 356

+
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