[English] 日本語
Yorodumi
- PDB-7k5a: The external aldimine form of Salmonella typhimurium Tryptophan S... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7k5a
TitleThe external aldimine form of Salmonella typhimurium Tryptophan Synthase mutant beta-Q114A in complex with cesium ion at the metal coordination site.
Components(Tryptophan synthase ...) x 2
KeywordsLYASE / tryptophan synthase
Function / homology
Function and homology information


tryptophan synthase / tryptophan synthase activity / tryptophan biosynthetic process / identical protein binding / cytoplasm / cytosol
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
: / Chem-KOU / DI(HYDROXYETHYL)ETHER / SERINE / Tryptophan synthase alpha chain / Tryptophan synthase beta chain
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.5 Å
AuthorsHilario, E. / Dunn, M.F. / Mueller, L.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)GM097569 United States
CitationJournal: To be Published
Title: The external aldimine form of Salmonella typhimurium Tryptophan Synthase mutant beta-Q114A in complex with cesium ion at the metal coordination site.
Authors: Hilario, E. / Dunn, M.F. / Mueller, L.J.
History
DepositionSep 16, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 22, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_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)73,18520
Polymers71,5612
Non-polymers1,62418
Water11,638646
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Tryptophan Synthase complex (alpha2-beta2) Protein is a tetramer in solution and composed of two alpha-chains and two beta-chains.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5210 Å2
ΔGint-102 kcal/mol
Surface area23890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)182.827, 59.527, 67.478
Angle α, β, γ (deg.)90.000, 94.880, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-845-

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 (strain LT2 / SGSC1412 / ATCC 700720) (bacteria)
Strain: LT2 / SGSC1412 / ATCC 700720 / Gene: trpA, STM1727 / Plasmid: pEBA-10 / Production host: Escherichia coli (E. coli) / Strain (production host): strain CB149 / References: UniProt: P00929, tryptophan synthase
#2: Protein Tryptophan synthase beta chain


Mass: 42861.828 Da / Num. of mol.: 1 / Mutation: Q114A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (bacteria)
Strain: LT2 / SGSC1412 / ATCC 700720 / Gene: trpB, STM1726 / Plasmid: pEBA-10 / Details (production host): beta-Q114A / Production host: Escherichia coli (E. coli) / Strain (production host): CB149 / References: UniProt: P0A2K1, tryptophan synthase

-
Non-polymers , 8 types, 664 molecules

#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-SER / SERINE


Type: L-peptide linking / Mass: 105.093 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7NO3
#5: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#6: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#7: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#8: Chemical ChemComp-KOU / (E)-N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)-L-serine


Mass: 334.219 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H15N2O8P / Feature type: SUBJECT OF INVESTIGATION
#9: Chemical ChemComp-CS / CESIUM ION


Mass: 132.905 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cs / Feature type: SUBJECT OF INVESTIGATION
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 646 / 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: 2.61 Å3/Da / Density % sol: 52.99 % / Description: large plate-like crystal
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.8
Details: 50 mM Bicine-CsOH, 9% PEG 8,000, 3 mM Spermine, pH 7.8
PH range: 7.6-8.0 / Temp details: constant

-
Data collection

DiffractionMean temperature: 100 K / Ambient temp details: constant / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.972 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 15, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.972 Å / Relative weight: 1
ReflectionResolution: 1.5→91.082 Å / Num. obs: 113436 / % possible obs: 98.2 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.082 / Rpim(I) all: 0.037 / Rrim(I) all: 0.095 / Rsym value: 0.082 / Net I/av σ(I): 4.2 / Net I/σ(I): 9.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
1.5-1.586.60.7151109606166410.3240.8350.715299.3
1.58-1.686.30.4831.599246157640.2240.5670.4832.899.1
1.68-1.796.70.2982.499150148670.1330.3460.2984.399.4
1.79-1.946.60.2113.391299137670.0940.2430.2116.298.9
1.94-2.126.20.1364.978035125640.0630.1580.1368.998
2.12-2.376.30.0996.271742113300.0450.1140.09912.597.3
2.37-2.746.30.0777.86294599330.0350.090.07715.596.7
2.74-3.3560.0678.54974582980.030.0770.0671995.4
3.35-4.746.50.0599.34289865640.0260.0680.05925.197.1
4.74-39.296.40.0618.12356537080.0270.070.06124.797.9

-
Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation6.45 Å39.29 Å
Phasing dmMethod: Solvent flattening and Histogram matching / Reflection: 113150
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
8.13-10033.50.915770
5.75-8.1339.50.8971355
4.69-5.7531.20.9021702
4.07-4.6922.60.9442031
3.64-4.0722.30.9272265
3.32-3.6422.30.9242470
3.07-3.3223.30.9132682
2.87-3.0724.70.9132829
2.71-2.8723.90.9123030
2.57-2.7123.10.9133252
2.45-2.5723.90.9083397
2.35-2.4523.40.9123587
2.26-2.3522.20.9133763
2.17-2.2621.40.9133844
2.1-2.1722.50.9124014
2.03-2.124.20.9024219
1.97-2.0324.30.94339
1.92-1.9724.70.8864401
1.87-1.9224.90.8844610
1.82-1.8726.10.8934717
1.77-1.8226.70.8934878
1.73-1.7727.80.8844993
1.7-1.73280.895078
1.66-1.7320.8635199
1.63-1.6633.30.8585313
1.59-1.6333.50.8695386
1.56-1.5935.30.8625475
1.54-1.5638.10.8565644
1.5-1.5443.80.8087907

-
Processing

Software
NameVersionClassification
XDSVERSION Jun 1, 2017 BUILT=20170923)data reduction
SCALA3.3.22data scaling
PHASER2.8.3phasing
DM7.1.003phasing
REFMAC5.8.0267refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7k0b

7k0b


Resolution: 1.5→39.29 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.954 / SU B: 4.166 / SU ML: 0.066 / SU R Cruickshank DPI: 0.0832 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.083 / ESU R Free: 0.078 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.22 5713 5 %RANDOM
Rwork0.1683 ---
obs0.1709 107437 97.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 116.61 Å2 / Biso mean: 30.771 Å2 / Biso min: 12.52 Å2
Baniso -1Baniso -2Baniso -3
1--1.23 Å2-0 Å20.46 Å2
2--1.05 Å20 Å2
3---0.1 Å2
Refinement stepCycle: final / Resolution: 1.5→39.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4897 0 80 656 5633
Biso mean--43.12 41.73 -
Num. residues----650
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0125190
X-RAY DIFFRACTIONr_angle_refined_deg1.4291.6337033
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2235674
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.5322.283254
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.8215849
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9981533
X-RAY DIFFRACTIONr_chiral_restr0.1010.2675
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023978
X-RAY DIFFRACTIONr_rigid_bond_restr4.10835190
LS refinement shellResolution: 1.5→1.539 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.322 440 -
Rwork0.281 7936 -
all-8376 -
obs--99.01 %
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)
10.04870.002-0.0830.83340.81740.95130.1073-0.06510.07570.2142-0.07170.07620.03510.0429-0.03560.2599-0.16430.15250.1297-0.04770.226341.504717.83313.6003
20.96510.8821-0.24171.0077-0.24850.06670.1415-0.01890.07730.0356-0.11140.046-0.02930.0269-0.03020.0897-0.00160.04150.12320.00830.158437.31097.73777.5286
31.9032-0.91860.8220.7113-0.69341.98240.0693-0.2046-0.0955-0.002-0.0637-0.1604-0.00840.2078-0.00560.0171-0.0379-0.03590.20180.09320.213249.0536-4.880119.3915
40.5728-0.2330.17960.6452-0.40910.27820.0491-0.10820.03310.1629-0.05360.0338-0.10350.06020.00450.0755-0.0391-0.02010.1416-0.03630.144248.031716.453322.3273
50.64250.0485-0.59690.0072-0.05870.7166-0.0282-0.0467-0.1175-0.0113-0.0253-0.010.01230.18870.05350.06550.0047-0.00780.16850.01380.140927.6307-12.74719.7296
60.18690.001-0.20370.0739-0.11870.4254-0.0637-0.0444-0.0221-0.00590.0328-0.01840.0747-0.04920.03090.09560.00370.0010.130.01260.13221.1788-17.38527.8782
70.0414-0.0113-0.1410.00820.06490.6950.0364-0.0405-0.0227-0.0063-0.0062-0-0.08610.093-0.03010.1069-0.01620.00350.13920.00890.123212.8478-5.21227.9462
80.4526-0.27020.08860.1757-0.0770.0806-0.01160.07370.11090.0075-0.0303-0.05330.01950.01140.04180.0886-0.00270.01050.12010.02310.150811.88290.28958.7809
90.3509-0.1823-0.0720.15880.08570.359-0.00750.04580.02820.0160.0064-0.0139-0.0184-0.00760.00120.09810.00590.01030.11340.00750.12772.4114-3.92312.4364
100.1330.0728-0.03530.04160.00470.55450.04420.02210.00410.02430.01670.0039-0.0794-0.0703-0.06090.11090.01310.01840.14290.00330.1139-6.4431-2.478216.41
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A14 - 61
2X-RAY DIFFRACTION2A62 - 159
3X-RAY DIFFRACTION3A160 - 202
4X-RAY DIFFRACTION4A203 - 268
5X-RAY DIFFRACTION5B2 - 37
6X-RAY DIFFRACTION6B38 - 70
7X-RAY DIFFRACTION7B71 - 224
8X-RAY DIFFRACTION8B245 - 301
9X-RAY DIFFRACTION9B302 - 343
10X-RAY DIFFRACTION10B344 - 395

+
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