[English] 日本語
Yorodumi
- PDB-2qve: Crystal Structure of SgTAM bound to mechanism based inhibitor -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2qve
TitleCrystal Structure of SgTAM bound to mechanism based inhibitor
ComponentsTyrosine Aminomutase
KeywordsTRANSFERASE / MIO / Aminomutase / enediyne
Function / homology
Function and homology information


tyrosine 2,3-aminomutase / L-tyrosine 2,3-aminomutase activity / tyrosine ammonia-lyase / tyrosine ammonia-lyase activity / histidine ammonia-lyase activity / toxin biosynthetic process / L-histidine catabolic process / antibiotic biosynthetic process
Similarity search - Function
Tyrosine 2,3-aminomutase, putative / Phenylalanine/histidine ammonia-lyases, active site / Phenylalanine and histidine ammonia-lyases signature. / Aromatic amino acid lyase / Aromatic amino acid lyase / Fumarase/aspartase (N-terminal domain) / Fumarase/aspartase (Central domain) / Fumarase C; Chain A, domain 2 / Fumarase C; Chain B, domain 1 / Fumarase/histidase, N-terminal ...Tyrosine 2,3-aminomutase, putative / Phenylalanine/histidine ammonia-lyases, active site / Phenylalanine and histidine ammonia-lyases signature. / Aromatic amino acid lyase / Aromatic amino acid lyase / Fumarase/aspartase (N-terminal domain) / Fumarase/aspartase (Central domain) / Fumarase C; Chain A, domain 2 / Fumarase C; Chain B, domain 1 / Fumarase/histidase, N-terminal / L-Aspartase-like / Up-down Bundle / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-247 / MIO-dependent tyrosine 2,3-aminomutase
Similarity search - Component
Biological speciesStreptomyces globisporus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsChristianson, C.V. / Montavon, T.J. / Bruner, S.D.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2008
Title: Design and characterization of mechanism-based inhibitors for the tyrosine aminomutase SgTAM
Authors: Montavon, T.J. / Christianson, C.V. / Festin, G.M. / Shen, B. / Bruner, S.D.
History
DepositionAug 8, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 22, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 16, 2011Group: Atomic model
Revision 1.3Oct 25, 2017Group: Refinement description / Category: software
Revision 1.4Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.location / _software.name / _software.type / _struct_conn.pdbx_leaving_atom_flag
Revision 1.5Aug 30, 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 / 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 / _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
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / pdbx_validate_torsion / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Tyrosine Aminomutase
B: Tyrosine Aminomutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,3414
Polymers113,9072
Non-polymers4342
Water7,512417
1
A: Tyrosine Aminomutase
B: Tyrosine Aminomutase
hetero molecules

A: Tyrosine Aminomutase
B: Tyrosine Aminomutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)228,6828
Polymers227,8134
Non-polymers8694
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area35710 Å2
ΔGint-150 kcal/mol
Surface area54220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.435, 145.863, 75.048
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-1164-

HOH

21B-1196-

HOH

DetailsThe biological unit is the tetramer which is generated by the two fold axix: -x, -y, z (2_555)

-
Components

#1: Protein Tyrosine Aminomutase / E.C.5.4.3.6 / Putative ammonia lyase/transferase


Mass: 56953.340 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces globisporus (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: Q8GMG0, tyrosine 2,3-aminomutase
#2: Chemical ChemComp-247 / (3R)-3-amino-2,2-difluoro-3-(4-hydroxyphenyl)propanoic acid


Mass: 217.169 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H9F2NO3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 417 / 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: 2.22 Å3/Da / Density % sol: 44.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 4.2 M Sodium Formate, 100 mM TMAO, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X26C / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 3, 2007 / Details: mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→25 Å / Num. all: 69074 / Num. obs: 67948 / % possible obs: 99.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 4.7 % / Rmerge(I) obs: 0.097 / Χ2: 2.903 / Net I/σ(I): 10.2
Reflection shellResolution: 2→2.07 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.668 / Mean I/σ(I) obs: 3.1 / Num. unique all: 6758 / Χ2: 5.315 / % possible all: 99.1

-
Processing

Software
NameVersionClassificationNB
CNSrefinement
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3data extraction
CBASSdata collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
DENZOdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2OHY

2ohy


Resolution: 2→25 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflection
Rfree0.224 6542 9.4 %
Rwork0.194 --
all-69021 -
obs-64732 93.5 %
Solvent computationBsol: 66.804 Å2
Displacement parametersBiso mean: 30.2 Å2
Baniso -1Baniso -2Baniso -3
1--4.427 Å20 Å20 Å2
2--7.992 Å20 Å2
3----3.565 Å2
Refinement stepCycle: LAST / Resolution: 2→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8014 0 30 417 8461
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_mcbond_it1.1731.5
X-RAY DIFFRACTIONc_scbond_it1.9332
X-RAY DIFFRACTIONc_mcangle_it1.7392
X-RAY DIFFRACTIONc_scangle_it2.7592.5
LS refinement shell
Resolution (Å)Rfactor RworkRefine-IDNum. reflection obs% reflection obs (%)
2-2.070.66X-RAY DIFFRACTION675899.1
2.07-2.150.45X-RAY DIFFRACTION680399.6
2.25-2.370.27X-RAY DIFFRACTION683899.8
2.52-2.710.18X-RAY DIFFRACTION6885100
2.99-3.420.078X-RAY DIFFRACTION6931100
4.3-250.042X-RAY DIFFRACTION726399.7
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1btyr.param
X-RAY DIFFRACTION2protein_rep_MDO_7.param
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.param

+
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://pdbjlvh1.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