[English] 日本語
Yorodumi
- PDB-1a50: CRYSTAL STRUCTURE OF WILD-TYPE TRYPTOPHAN SYNTHASE COMPLEXED WITH... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1a50
TitleCRYSTAL STRUCTURE OF WILD-TYPE TRYPTOPHAN SYNTHASE COMPLEXED WITH 5-FLUOROINDOLE PROPANOL PHOSPHATE
Components(TRYPTOPHAN SYNTHASE ...) x 2
KeywordsLYASE / CARBON-OXYGEN LYASE / TRYPTOPHAN BIOSYNTHESIS / PYRIDOXAL PHOSPHATE
Function / homology
Function and homology information


tryptophan synthase / tryptophan synthase activity / tryptophan biosynthetic process / identical protein binding / cytosol / cytoplasm
Tryptophan synthase beta chain/beta chain-like / Aldolase-type TIM barrel / Pyridoxal-phosphate dependent enzyme / Tryptophan synthase alpha chain / Tryptophan synthase beta subunit-like PLP-dependent enzyme / Tryptophan synthase, alpha chain, active site / Pyridoxal-phosphate dependent enzyme / Tryptophan synthase, alpha chain / Tryptophan synthase, beta chain, conserved site / Tryptophan synthase, beta chain ...Tryptophan synthase beta chain/beta chain-like / Aldolase-type TIM barrel / Pyridoxal-phosphate dependent enzyme / Tryptophan synthase alpha chain / Tryptophan synthase beta subunit-like PLP-dependent enzyme / Tryptophan synthase, alpha chain, active site / Pyridoxal-phosphate dependent enzyme / Tryptophan synthase, alpha chain / Tryptophan synthase, beta chain, conserved site / Tryptophan synthase, beta chain / Ribulose-phosphate binding barrel / Rossmann fold - #1100 / Aldolase class I / TIM Barrel / Alpha-Beta Barrel / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Tryptophan synthase alpha chain / Tryptophan synthase beta chain
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / ISOMORPHOUS WITH PDB ENTRY 1WSY. / Resolution: 2.3 Å
AuthorsSchneider, T.R. / Gerhardt, E. / Lee, M. / Liang, P.-H. / Anderson, K.S. / Schlichting, I.
CitationJournal: Biochemistry / Year: 1998
Title: Loop closure and intersubunit communication in tryptophan synthase.
Authors: Schneider, T.R. / Gerhardt, E. / Lee, M. / Liang, P.H. / Anderson, K.S. / Schlichting, I.
Validation Report
SummaryFull reportAbout validation report
History
DepositionFeb 18, 1998-
Revision 1.0Mar 30, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: TRYPTOPHAN SYNTHASE (ALPHA CHAIN)
B: TRYPTOPHAN SYNTHASE (BETA CHAIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,1005
Polymers71,5572
Non-polymers5433
Water4,288238
1
A: TRYPTOPHAN SYNTHASE (ALPHA CHAIN)
B: TRYPTOPHAN SYNTHASE (BETA CHAIN)
hetero molecules

A: TRYPTOPHAN SYNTHASE (ALPHA CHAIN)
B: TRYPTOPHAN SYNTHASE (BETA CHAIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,20010
Polymers143,1134
Non-polymers1,0876
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Unit cell
γ
α
β
Length a, b, c (Å)182.700, 60.700, 67.500
Angle α, β, γ (deg.)90.00, 94.50, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-1369-

HOH

-
Components

-
TRYPTOPHAN SYNTHASE ... , 2 types, 2 molecules AB

#1: Protein TRYPTOPHAN SYNTHASE (ALPHA CHAIN)


Mass: 28698.797 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: INHIBITOR 5-FLUOROINDOLE PROPANOL PHOSPHATE BOUND TO THE ALPHA SITE
Source: (natural) Salmonella typhimurium (bacteria) / Cell line: CB149 / Plasmid: PSTB7 / References: UniProt: P00929, tryptophan synthase
#2: Protein TRYPTOPHAN SYNTHASE (BETA CHAIN)


Mass: 42857.805 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: INHIBITOR 5-FLUOROINDOLE PROPANOL PHOSPHATE BOUND TO THE ALPHA SITE
Source: (natural) Salmonella typhimurium (bacteria) / Cell line: CB149 / Plasmid: PSTB7 / References: UniProt: P0A2K1, tryptophan synthase

-
Non-polymers , 4 types, 241 molecules

#3: Chemical ChemComp-FIP / 5-FLUOROINDOLE PROPANOL PHOSPHATE


Mass: 273.197 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H13FNO4P
#4: Chemical ChemComp-NA / SODIUM ION / Sodium


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate / Pyridoxal phosphate


Mass: 247.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10NO6P
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 238 / 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: 2.61 Å3/Da / Density % sol: 48 %
Crystal growpH: 7.8 / Details: pH 7.8
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlenzyme1drop
250 mMBicine1drop
30.02 Mpyridoxal phosphate1drop
450 mMbicine1reservoir
51-2 mMspermine1reservoir
610 %PEG80001reservoir

-
Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1.15
DetectorType: MARRESEARCH / Detector: IMAGE PLATE AREA DETECTOR / Date: Nov 1, 1995 / Details: SYNCHROTRON
RadiationMonochromator: SYNCHROTRON / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.15 Å / Relative weight: 1
ReflectionResolution: 2.29→26.9 Å / Num. obs: 31823 / % possible obs: 95.6 % / Observed criterion σ(I): -3 / Redundancy: 2.2 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 13.4
Reflection shellResolution: 2.29→2.34 Å / Rmerge(I) obs: 0.21 / Mean I/σ(I) obs: 6.4 / % possible all: 91.6
Reflection
*PLUS
Highest resolution: 2.29 Å / Lowest resolution: 26.9 Å / Num. measured all: 66781
Reflection shell
*PLUS
% possible obs: 91.6 %

-
Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: ISOMORPHOUS WITH PDB ENTRY 1WSY.
Starting model: 1WSY

1wsy
PDB Unreleased entry


Resolution: 2.3→10 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.247 3126 10 %RANDOM
Rwork0.177 ---
Obs0.177 30327 93.8 %-
Displacement parametersBiso mean: 17.5 Å2
Refine analyzeLuzzati d res low obs: 10 Å / Luzzati sigma a obs: 0.21 Å
Refinement stepCycle: LAST / Resolution: 2.3→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4919 0 34 238 5191
Refine LS restraints
Refinement-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.006
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.3
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.53.3
X-RAY DIFFRACTIONx_mcangle_it24.1
X-RAY DIFFRACTIONx_scbond_it25.3
X-RAY DIFFRACTIONx_scangle_it2.56.9
LS refinement shellResolution: 2.3→2.34 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2893 164 -
Rwork0.2219 1337 -
Obs--91.61 %
Xplor file
Refinement-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARAM19X.PROTOPH19X.PRO
X-RAY DIFFRACTION2PARAM.IPP.NEWTOP.IPP.NEW
X-RAY DIFFRACTION3PARAM.PLP.NEWTOP.PLP.NEW
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.3 Å / Num. reflection obs: 31627 / Rfactor obs: 0.164 / Rfactor Rfree: 0.221 / Rfactor Rwork: 0.162
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS

+
About Yorodumi

-
News

-
Aug 12, 2020. New: Covid-19 info

New: Covid-19 info

  • 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. New: 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. (see PDBe EMDB page)
  • 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 at PDBe / 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. See below links for details.
  • 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

+
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.:Omokage search

Read more

-
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.

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