[English] 日本語
Yorodumi
- PDB-2rh9: Tryptophan synthase complexed with IGP, internal aldimine, pH 9.0 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2rh9
TitleTryptophan synthase complexed with IGP, internal aldimine, pH 9.0
Components(Tryptophan synthase ...) x 2
KeywordsLYASE / AROMATIC AMINO ACID BIOSYNTHESIS / TRYPTOPHAN BIOSYNTHESIS / CARBON-OXYGEN LYASE / AMINOACID BIOSYNTHESIS / ALLOSTERIC ENZYME / PYRIDOXAL PHOSPHATE / Amino-acid biosynthesis
Function / homology
Function and homology information


tryptophan synthase / tryptophan synthase activity / tryptophan biosynthetic process / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Tryptophan synthase, alpha chain / Tryptophan synthase, alpha chain, active site / Tryptophan synthase alpha chain / Tryptophan synthase alpha chain signature. / Tryptophan synthase, beta chain, conserved site / Tryptophan synthase, beta chain / Tryptophan synthase beta chain/beta chain-like / Tryptophan synthase beta chain pyridoxal-phosphate attachment site. / Rossmann fold - #1100 / Pyridoxal-phosphate dependent enzyme ...Tryptophan synthase, alpha chain / Tryptophan synthase, alpha chain, active site / Tryptophan synthase alpha chain / Tryptophan synthase alpha chain signature. / Tryptophan synthase, beta chain, conserved site / Tryptophan synthase, beta chain / Tryptophan synthase beta chain/beta chain-like / Tryptophan synthase beta chain pyridoxal-phosphate attachment site. / Rossmann fold - #1100 / Pyridoxal-phosphate dependent enzyme / Tryptophan synthase beta subunit-like PLP-dependent enzyme / Pyridoxal-phosphate dependent enzyme / Ribulose-phosphate binding barrel / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
INDOLE-3-GLYCEROL PHOSPHATE / PYRIDOXAL-5'-PHOSPHATE / Tryptophan synthase alpha chain / Tryptophan synthase beta chain
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.7 Å
AuthorsKulik, V. / Barends, T.R.M. / Schlichting, I.
CitationJournal: To be Published
Title: Tryptophan synthase complexed with IGP, internal aldimine, pH 9.0.
Authors: Kulik, V. / Barends, T.R.M. / Schlichting, I.
History
DepositionOct 8, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 6, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance

-
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)72,1755
Polymers71,6182
Non-polymers5573
Water8,701483
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)144,35010
Polymers143,2354
Non-polymers1,1156
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area10950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)183.071, 59.281, 67.345
Angle α, β, γ (deg.)90.00, 94.67, 90.00
Int Tables number5
Space group name H-MC121

-
Components

-
Tryptophan synthase ... , 2 types, 2 molecules AB

#1: Protein Tryptophan synthase alpha chain


Mass: 28698.797 Da / Num. of mol.: 1 / Fragment: tryptophan synthase, alpha chain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Gene: trpA, STM1727 / Plasmid: pSTB7 / Production host: Escherichia coli (E. coli) / Strain (production host): CB149 / References: UniProt: P00929, tryptophan synthase
#2: Protein Tryptophan synthase beta chain


Mass: 42918.879 Da / Num. of mol.: 1 / Fragment: tryptophan synthase, beta chain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Gene: trpB, STM1726 / Plasmid: pSTB7 / Production host: Escherichia coli (E. coli) / Strain (production host): CB149 / References: UniProt: P0A2K1, tryptophan synthase

-
Non-polymers , 4 types, 486 molecules

#3: Chemical ChemComp-IGP / INDOLE-3-GLYCEROL PHOSPHATE


Mass: 287.206 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H14NO6P
#4: Chemical ChemComp-NA / SODIUM ION


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.: 483 / 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: 2.54 Å3/Da / Density % sol: 51.63 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9
Details: Protein: 50 mM Bicine pH 7.8, 10 mM Na-EDTA, 1 mM DTE, 20 uM PLP. Reservoir: 50 mM Bicine pH 7.8, 5 mM DTE, 5 mM Na-EDTA, 0.1 M PLP, 2 mM Spermine, 2 mM NaN3, 8-12% PEG 8000. Crystal soaked ...Details: Protein: 50 mM Bicine pH 7.8, 10 mM Na-EDTA, 1 mM DTE, 20 uM PLP. Reservoir: 50 mM Bicine pH 7.8, 5 mM DTE, 5 mM Na-EDTA, 0.1 M PLP, 2 mM Spermine, 2 mM NaN3, 8-12% PEG 8000. Crystal soaked in 15% PEG 8000, 20% Glycerol, 23 mM IGP, pH controlled at pH 9.0 before flash-cooling, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.93 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 30, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93 Å / Relative weight: 1
ReflectionResolution: 1.7→55 Å / Num. all: 77139 / Num. obs: 77139 / % possible obs: 97.3 % / Observed criterion σ(I): -3 / Redundancy: 2.4 % / Biso Wilson estimate: 19.8 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 10.01
Reflection shellResolution: 1.7→1.8 Å / Rmerge(I) obs: 0.313 / Mean I/σ(I) obs: 2.46 / Num. unique all: 12104 / % possible all: 97.1

-
Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
ADSCQuantumdata collection
XDSdata reduction
XSCALEdata scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.7→43.73 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.951 / SU B: 2.066 / SU ML: 0.068 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.097 / ESU R Free: 0.095 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. Program CNS has also been used in refinement
RfactorNum. reflection% reflectionSelection details
Rfree0.20044 3922 5.1 %RANDOM
Rwork0.17194 ---
all0.17338 73246 --
obs0.17338 73246 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.991 Å2
Baniso -1Baniso -2Baniso -3
1--0.8 Å20 Å2-0.41 Å2
2--2.19 Å20 Å2
3----1.46 Å2
Refinement stepCycle: LAST / Resolution: 1.7→43.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4895 0 35 483 5413
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0225082
X-RAY DIFFRACTIONr_bond_other_d0.0010.024660
X-RAY DIFFRACTIONr_angle_refined_deg1.4261.9796888
X-RAY DIFFRACTIONr_angle_other_deg0.924310841
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4075650
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.4824.11219
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.28115836
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2461532
X-RAY DIFFRACTIONr_chiral_restr0.0750.2762
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025720
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02993
X-RAY DIFFRACTIONr_nbd_refined0.2190.21028
X-RAY DIFFRACTIONr_nbd_other0.1850.24620
X-RAY DIFFRACTIONr_nbtor_refined0.1770.22476
X-RAY DIFFRACTIONr_nbtor_other0.0840.22725
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1310.2378
X-RAY DIFFRACTIONr_metal_ion_refined0.0980.23
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1350.27
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2270.258
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1150.211
X-RAY DIFFRACTIONr_mcbond_it0.7141.53236
X-RAY DIFFRACTIONr_mcbond_other0.181.51332
X-RAY DIFFRACTIONr_mcangle_it1.30825164
X-RAY DIFFRACTIONr_scbond_it2.0931877
X-RAY DIFFRACTIONr_scangle_it3.4524.51724
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.243 296
Rwork0.239 5384

+
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