[English] 日本語
Yorodumi
- PDB-6xrh: Salmonella typhimurium tryptophan synthase complexed with oxindol... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6xrh
TitleSalmonella typhimurium tryptophan synthase complexed with oxindolyl-L-alanine and D-glycerol-3-phosphate
Components(Tryptophan synthase ...) x 2
KeywordsLYASE / multi-enzyme complex / allosteric enzyme product complex
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. / Pyridoxal-phosphate dependent enzyme / Tryptophan synthase beta subunit-like PLP-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. / Pyridoxal-phosphate dependent enzyme / Tryptophan synthase beta subunit-like PLP-dependent enzyme / Pyridoxal-phosphate dependent enzyme / Ribulose-phosphate binding barrel / Aldolase-type TIM barrel
Similarity search - Domain/homology
SN-GLYCEROL-1-PHOSPHATE / Chem-VCP / Chem-VCS / Tryptophan synthase alpha chain / Tryptophan synthase alpha chain / Tryptophan synthase beta chain
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.44 Å
AuthorsPhillips, R.S.
CitationJournal: Biochemistry / Year: 2021
Title: Structural Basis of the Stereochemistry of Inhibition of Tryptophan Synthase by Tryptophan and Derivatives.
Authors: Phillips, R.S. / Harris, A.P.
History
DepositionJul 12, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 3, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
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)73,80520
Polymers71,6182
Non-polymers2,18818
Water13,061725
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)147,61140
Polymers143,2354
Non-polymers4,37536
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Unit cell
Length a, b, c (Å)184.180, 58.200, 67.190
Angle α, β, γ (deg.)90.000, 95.339, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11B-612-

HOH

21B-932-

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 genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Gene: trpA, DD95_04145 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A0D6FWC1, UniProt: P00929*PLUS, tryptophan synthase
#2: Protein Tryptophan synthase beta chain


Mass: 42918.879 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Gene: trpB / Production host: Escherichia coli (E. coli) / References: UniProt: P0A2K1, tryptophan synthase

-
Non-polymers , 6 types, 743 molecules

#3: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical ChemComp-1GP / SN-GLYCEROL-1-PHOSPHATE


Mass: 172.074 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H9O6P
#5: Chemical ChemComp-VCP / (E)-N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)-3-[(3S)-2-oxo-2,3-dihydro-1H-indol-3-yl]-L-alanine


Mass: 449.351 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H20N3O8P / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-VCS / 4-[(E)-({1-carboxy-2-[(3S)-2-oxo-2,3-dihydro-1H-indol-3-yl]ethan-1-id-1-yl}iminio)methyl]-2-methyl-5-[(phosphonooxy)methyl]pyridin-1-ium-3-olate


Mass: 449.351 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H20N3O8P
#7: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 725 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 50.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: 0.05 M Bicine-Na, pH 7.8, 1 mM EDTA, 0.1 mM PLP, 1 mM DTT, and 1 mM spermine tetrahydrochloride, containing 10-12% PEG 3350 and 6-10% glycerol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 25, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.436→45.85 Å / Num. obs: 75381 / % possible obs: 88.4 % / Redundancy: 5.7 % / Biso Wilson estimate: 14.98 Å2 / CC1/2: 0.996 / CC star: 0.999 / Rmerge(I) obs: 0.132 / Rrim(I) all: 0.145 / Net I/σ(I): 8
Reflection shellResolution: 1.436→1.494 Å / Redundancy: 5.5 % / Rmerge(I) obs: 1.781 / Num. unique obs: 3768 / CC1/2: 0.33 / Rrim(I) all: 1.955 / % possible all: 47.3

-
Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHASERphasing
Coot0.9model building
PHENIX1.18.2_3874refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2TYS.pdb

2tys


Resolution: 1.44→45.85 Å / SU ML: 0.1316 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 25.9892
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.198 1999 2.65 %
Rwork0.1653 73307 -
obs0.1662 75306 58.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.56 Å2
Refinement stepCycle: LAST / Resolution: 1.44→45.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5010 0 98 726 5834
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00535709
X-RAY DIFFRACTIONf_angle_d0.7977778
X-RAY DIFFRACTIONf_chiral_restr0.0627846
X-RAY DIFFRACTIONf_plane_restr0.00641034
X-RAY DIFFRACTIONf_dihedral_angle_d19.662148
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.44-1.470.364620.317363X-RAY DIFFRACTION0.72
1.47-1.510.23890.3427346X-RAY DIFFRACTION3.89
1.51-1.560.2887290.33631049X-RAY DIFFRACTION11.79
1.56-1.610.3305570.29812112X-RAY DIFFRACTION23.58
1.61-1.660.3388870.29583184X-RAY DIFFRACTION35.63
1.66-1.730.2921170.27384267X-RAY DIFFRACTION47.99
1.73-1.810.27711470.25595410X-RAY DIFFRACTION60.34
1.81-1.910.25811730.22336314X-RAY DIFFRACTION70.84
1.91-2.030.20841960.20297206X-RAY DIFFRACTION80.42
2.03-2.180.21282140.17317824X-RAY DIFFRACTION87.32
2.18-2.40.21782320.16418547X-RAY DIFFRACTION94.83
2.4-2.750.18972420.15878868X-RAY DIFFRACTION98.9
2.75-3.460.1642440.14148951X-RAY DIFFRACTION99.24
3.46-45.850.17022500.13189166X-RAY DIFFRACTION99.49
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)
12.110850015040.601365460215-0.1400908585394.27327652312-0.3881201137331.858907460960.2857011416890.2742788145180.364274400594-0.169589184836-0.2265145280880.258244805989-0.391032754859-0.503190577735-0.009928372902190.260931220580.1667438953490.07676761475830.3145418737240.03022998794650.33938349540540.497995489534.165208584921.5897360033
21.33560461966-0.532532439796-0.07332177513011.728759721760.3589095851271.134442761820.1572762788580.0930816591020.330687962968-0.0601756700658-0.105210614319-0.0698250999932-0.280302472814-0.0698516190611-0.03234610671230.1412617327930.02198040998690.06376895398720.1320097398360.01263882090580.22156806198153.013036635928.151862168425.8535801469
32.38119844305-0.5446367471430.3381881366781.38657206395-0.4239079947914.803772401540.2099646926280.481818423563-0.341833182454-0.183343742349-0.2511540298530.2623195664650.17828963978-0.3780685245350.01695792506920.1278771865420.04746599127740.008560682667210.252487342911-0.0673626946910.23461501370446.463177072616.252322644518.0993479863
42.581906632550.34299690861-0.1615987091294.17025482375-0.644029042511.468137700550.1821509785980.9364105550420.241781962612-0.554775509525-0.1582676490330.306382113306-0.369008860039-0.5230580559120.005836914499170.3353341323920.2206182440110.001523480253550.5846997937710.06981809571740.31275526622341.442049470331.340007178810.1327598712
50.610313280268-0.445380107477-0.5216009860131.031763080640.5713724512471.921897208640.1147467189790.146470089926-0.230180930167-0.0782081230524-0.09082471355430.08960491436850.13551562333-0.630964462680.0239127497170.0647555973106-0.053841567962-0.02422815173570.116972848113-0.01749161921350.16980229241161.48809773644.8110109578413.4437568351
61.41087328849-0.06353500556120.03008342922650.639658760150.3255721018341.88744723505-0.01376704455630.285111255318-0.0302532178450.0532566057153-0.03982720700270.102198616580.2461777757620.298812688722-0.01507365837070.0668269061086-0.007313801205220.02519663668370.02458281049910.009138446376830.068108154574890.22591720010.8744885655167.16175513012
71.35108076269-0.6615373628020.2236931828150.436790228533-0.2721691714561.160326949620.0572562431810.111728758837-0.0713250515374-0.0392620122028-0.009689563853230.0541484709774-0.0430848367415-0.170023537301-0.03778864825110.0622411150474-0.00519501995959-0.00742511979330.0987830688342-0.008908088539540.058160552532878.83188251259.784438465483.14882925347
82.04458634046-0.690402269607-1.406986521911.560895522731.066909594034.040773302210.517938726249-0.2965366063480.6391101287030.0111324680644-0.00094603507924-0.190259350169-1.036403701170.22173013212-0.4035110864840.374176373326-0.04655624670970.1376617664860.21692212376-0.03261207196420.24536663229478.334267360125.17858387422.6239126563
91.210679038670.0512858091683-0.0002519298335450.3720313720410.1724538609771.636641623550.02653959140930.0262069058718-0.012119604174-0.0182885185253-0.0220531369560.02492886106680.0236768816138-0.146370702504-0.009015311927030.0380299783235-0.01432854434590.003922180959610.05807178900440.01072273083230.051899668992278.51445480967.724114064914.8521872043
102.244283823010.179026744649-0.1396737964180.03261096187180.1551931962620.8404733648970.129390487627-0.1118625901840.4554719499910.0369288921628-0.07594930555870.139173489418-0.179111026746-0.0618779094779-0.06049933973140.0898586988846-0.004073281234240.01659729240750.0862884619173-0.02699603719660.15911677549472.004868432320.529057510523.9421483184
111.668462489420.205495488774-0.5502046028160.342813241853-0.2044213762341.434261653480.0219094746486-0.04851898465970.02961949534390.00462115026536-0.0163524274486-0.026925038545-0.03819497075780.130291337786-0.006124930102670.0604246673081-0.00511729082192-0.002410174464650.0586002795671-0.01632718481060.062538345209889.760498925813.371570866720.6622279015
120.672460934561-0.2471089388950.5918005476840.984286039931-0.2810889006571.54435293132-0.06367424608170.1891433703440.1773822836370.03439969391940.0687761271395-0.0331511712357-0.5513652074360.4182501848750.05106432205030.208312467886-0.0903756200860.02234888609450.1578784936070.01448256819280.095057237436696.452856283817.34642806915.7990755923
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 2 through 42 )AA2 - 421 - 41
22chain 'A' and (resid 43 through 136 )AA43 - 13642 - 151
33chain 'A' and (resid 137 through 187 )AA137 - 187152 - 207
44chain 'A' and (resid 188 through 268 )AA188 - 268208 - 293
55chain 'B' and (resid 2 through 37 )BF2 - 371 - 36
66chain 'B' and (resid 38 through 70 )BF38 - 7037 - 78
77chain 'B' and (resid 71 through 126 )BF71 - 12679 - 148
88chain 'B' and (resid 127 through 167 )BF127 - 167149 - 215
99chain 'B' and (resid 168 through 269 )BF168 - 269216 - 331
1010chain 'B' and (resid 270 through 301 )BF270 - 301332 - 374
1111chain 'B' and (resid 302 through 364 )BF302 - 364375 - 446
1212chain 'B' and (resid 365 through 397 )BF365 - 397447 - 485

+
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://pdbjlc1.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