[English] 日本語
Yorodumi
- PDB-1ax4: TRYPTOPHANASE FROM PROTEUS VULGARIS -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1ax4
TitleTRYPTOPHANASE FROM PROTEUS VULGARIS
ComponentsTRYPTOPHANASE
KeywordsTRYPTOPHAN BIOSYNTHESIS / TRYPTOPHAN INDOLE-LYASE / PYRIDOXAL 5'-PHOSPHATE / MONOVALENT CATION BINDING SITE
Function / homology
Function and homology information


tryptophanase activity / tryptophanase
Similarity search - Function
Tryptophanase / Beta-eliminating lyase family / Tryptophanase, conserved site / Beta-eliminating lyases pyridoxal-phosphate attachment site. / 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) ...Tryptophanase / Beta-eliminating lyase family / Tryptophanase, conserved site / Beta-eliminating lyases pyridoxal-phosphate attachment site. / 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
Biological speciesProteus vulgaris (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsIsupov, M.N. / Antson, A.A. / Dodson, E.J. / Dodson, G.G. / Dementieva, I.S. / Zakomirdina, L.N. / Wilson, K.S. / Dauter, Z. / Lebedev, A.A. / Harutyunyan, E.H.
Citation
#1: Journal: Biochemistry of Vitamin B6 and Pqq / Year: 1994
Title: X-Ray Study of Tryptophanase at 2.1 Angstrom Resolution
Authors: Isupov, M. / Dementieva, I. / Zakomirdina, L. / Wilson, K.S. / Dauter, Z. / Antson, A.A. / Dodson, G.G. / Harutyunyan, E.H.
#2: Journal: J.Mol.Biol. / Year: 1994
Title: Crystallization and Preliminary X-Ray Investigation of Holotryptophanases from Escherichia Coli and Proteus Vulgaris
Authors: Dementieva, I.S. / Zakomirdina, L.N. / Sinitzina, N.I. / Antson, A.A. / Wilson, K.S. / Isupov, M.N. / Lebedev, A.A. / Harutyunyan, E.H.
History
DepositionOct 28, 1997Processing site: BNL
Revision 1.0Jan 28, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 2, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: database_2 / diffrn_source ...database_2 / diffrn_source / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _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: TRYPTOPHANASE
B: TRYPTOPHANASE
C: TRYPTOPHANASE
D: TRYPTOPHANASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)211,3058
Polymers211,1484
Non-polymers1564
Water16,934940
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18180 Å2
ΔGint-86 kcal/mol
Surface area58440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.990, 118.230, 153.680
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.01, -0.212, 0.977), (-0.214, -0.955, -0.205), (0.977, -0.208, -0.055)-46.10084, 127.67617, 75.14806
2given(-0.009, 0.263, -0.965), (0.229, -0.939, -0.257), (-0.973, -0.223, -0.052)43.11463, 129.55736, 76.94052
3given(-1, -0.018, 0.002), (-0.015, 0.887, 0.462), (-0.01, 0.462, -0.887)2.05439, -21.19797, 86.3586

-
Components

#1: Protein
TRYPTOPHANASE / TRYPTOPHAN INDOLE-LYASE


Mass: 52787.102 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: PYRIDOXAL 5'-DEPENDENT ENZYME, REQUIRES MONOVALENT CATIONS FOR ACTIVITY, DEGRADES L-TRYPTOPHAN TO INDOLE, PYRUVATE AND AMMONIA
Source: (gene. exp.) Proteus vulgaris (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P28796, tryptophanase
#2: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 940 / 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: 2.49 Å3/Da / Density % sol: 51 %
Crystal growpH: 7.8
Details: 27 % PEG 4000, 0.1 M POTASSIUM PHOSPHATE BUFFER PH 7.8, 0.25 MM PYRIDOXAL 5'-PHOSPHATE, 5MM DTT, 0.1 M CSCL.
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
10.25 mMPLP1reservoir
25 mMdithiothreitol1reservoir
30.1 M1reservoirCsCl
40.1 Mpotassium phosphate1reservoir
527 %PEG40001reservoir

-
Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.95
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 1, 1994
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95 Å / Relative weight: 1
ReflectionResolution: 2.1→18 Å / Num. obs: 397510 / % possible obs: 97.6 % / Redundancy: 3.33 % / Rmerge(I) obs: 0.098 / Rsym value: 0.098 / Net I/σ(I): 11
Reflection shellResolution: 2.1→2.17 Å / Redundancy: 2.49 % / Rmerge(I) obs: 0.273 / Mean I/σ(I) obs: 3.2 / Rsym value: 0.273 / % possible all: 97.3
Reflection
*PLUS
Num. obs: 117863 / Num. measured all: 397510
Reflection shell
*PLUS
% possible obs: 97.3 %

-
Processing

Software
NameClassification
AMoREphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: TYROSINE PHENOL LYASE, PDB ENTRY 1TPL

1tpl


Resolution: 2.1→18 Å / Cross valid method: FREE R
RfactorNum. reflection% reflectionSelection details
Rfree0.22749 2364 2 %RANDOM
Rwork0.18688 ---
obs-115498 97.6 %-
Refinement stepCycle: LAST / Resolution: 2.1→18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14772 0 64 941 15777
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Num. reflection all: 117863 / Rfactor obs: 0.187
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0120.02
X-RAY DIFFRACTIONp_angle_d0.030.04
X-RAY DIFFRACTIONp_dihedral_angle_d
X-RAY DIFFRACTIONp_dihedral_angle_deg4.17
X-RAY DIFFRACTIONp_planar_d0.0340.05
X-RAY DIFFRACTIONp_plane_restr0.0210.02
X-RAY DIFFRACTIONp_chiral_restr0.1180.15
X-RAY DIFFRACTIONp_mcbond_it2.84
X-RAY DIFFRACTIONp_scbond_it5.78
X-RAY DIFFRACTIONp_mcangle_it3.76
X-RAY DIFFRACTIONp_scangle_it7.710

+
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