[English] 日本語
Yorodumi
- PDB-7l4d: The internal aldimine form of the wild-type Salmonella typhimuriu... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7l4d
TitleThe internal aldimine form of the wild-type Salmonella typhimurium Tryptophan Synthase with cesium ion at the metal coordination site at 1.60 Angstrom resolution
Components(Tryptophan synthase ...) x 2
KeywordsLYASE / internal aldimine / wild-type
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 / 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. / Pyridoxal-phosphate dependent enzyme / Pyridoxal-phosphate dependent enzyme / Tryptophan synthase beta subunit-like PLP-dependent enzyme / Ribulose-phosphate binding barrel / Aldolase-type TIM barrel
Similarity search - Domain/homology
: / DI(HYDROXYETHYL)ETHER / PYRIDOXAL-5'-PHOSPHATE / 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 / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.6 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)2R01GM097569-06A1 United States
CitationJournal: To be Published
Title: The internal aldimine form of the wild-type Salmonella typhimurium Tryptophan Synthase with cesium ion at the metal coordination site at 1.60 Angstrom resolution
Authors: Hilario, E. / Dunn, M.F. / Mueller, L.J.
History
DepositionDec 18, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 29, 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)75,39051
Polymers71,6182
Non-polymers3,77249
Water13,331740
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)150,780102
Polymers143,2354
Non-polymers7,54598
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area26690 Å2
ΔGint-246 kcal/mol
Surface area44360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)182.549, 59.188, 67.073
Angle α, β, γ (deg.)90.000, 94.480, 90.000
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
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): CB149 / References: UniProt: P00929, 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 / Plasmid: pEBA-10 / Production host: Escherichia coli (E. coli) / Strain (production host): CB149 / References: UniProt: P0A2K1, tryptophan synthase

-
Non-polymers , 8 types, 789 molecules

#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical...
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 25 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cl
#7: Chemical ChemComp-CS / CESIUM ION


Mass: 132.905 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cs / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10NO6P / Feature type: SUBJECT OF INVESTIGATION
#9: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 740 / 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: 2.58 Å3/Da / Density % sol: 52.27 % / 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, 2 mM Spermine, pH 7.8
PH range: 7.8 / Temp details: constant

-
Data collection

DiffractionMean temperature: 100 K / Ambient temp details: constant / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Mar 23, 2020 / Details: VariMax HighFlux
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.598→90.995 Å / Num. obs: 86510 / % possible obs: 92 % / Redundancy: 2.6 % / Rmerge(I) obs: 0.03 / Rpim(I) all: 0.032 / Rrim(I) all: 0.053 / Rsym value: 0.03 / Net I/av σ(I): 7.3 / Net I/σ(I): 13.4
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
1.6-1.692.50.1295.426522104010.1030.170.1296.576.2
1.69-1.792.70.16.231460118030.0820.1360.18.391.3
1.79-1.912.70.0686.330008112320.0620.1020.06810.492.2
1.91-2.072.70.0523.728251105760.0490.0810.0521393.6
2.07-2.262.70.048.22636698710.040.0660.0415.194.6
2.26-2.532.70.03482418990730.0370.060.03416.595.8
2.53-2.922.70.02918.92152980650.0330.0540.02917.896.6
2.92-3.582.70.02511.21851769570.0270.0450.0251998
3.58-5.062.60.02117.61442654560.0230.0380.02119.998.9
5.06-39.0632.60.0218.8789030760.0290.0470.02119.499.2

-
Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.429
Highest resolutionLowest resolution
Rotation39.06 Å1.78 Å
Phasing dmMethod: Solvent flattening and Histogram matching / Reflection: 86422
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
8.67-10036.60.895625
6.13-8.6743.10.8891124
5.01-6.1339.80.8871420
4.34-5.0128.40.9241672
3.88-4.3426.40.9291860
3.54-3.8826.70.9242086
3.28-3.5426.40.9172220
3.07-3.2827.20.9112398
2.89-3.0727.50.9072514
2.74-2.8927.40.9072667
2.61-2.7424.90.9092762
2.5-2.6124.10.9142918
2.41-2.523.10.9192991
2.32-2.4122.10.923112
2.24-2.32220.9243198
2.17-2.2421.40.9283310
2.1-2.1721.60.9243394
2.04-2.121.70.9223454
1.99-2.0421.30.9193555
1.94-1.9921.40.9173652
1.89-1.9421.20.9193705
1.85-1.8921.90.9153751
1.81-1.8521.40.9153871
1.77-1.8122.30.9073948
1.73-1.7722.60.9133953
1.7-1.73220.9164066
1.67-1.724.80.9064104
1.64-1.6727.50.8793962
1.6-1.6432.70.8694130

-
Processing

Software
NameVersionClassification
xia20.5.902data reduction
SCALA3.3.22data scaling
MOLREP11.7.02phasing
DM7.0.078phasing
REFMAC5.8.0258refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7K0B

7k0b


Resolution: 1.6→39.06 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.953 / SU B: 2.719 / SU ML: 0.051 / SU R Cruickshank DPI: 0.0904 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.09 / ESU R Free: 0.088 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1947 4190 4.8 %RANDOM
Rwork0.168 ---
obs0.1693 82231 91.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 73.77 Å2 / Biso mean: 20.893 Å2 / Biso min: 3.61 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å2-0 Å2-0.01 Å2
2--0.01 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 1.6→39.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4921 0 187 774 5882
Biso mean--38.22 34.27 -
Num. residues----652
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0125274
X-RAY DIFFRACTIONr_angle_refined_deg1.5161.6337110
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3295675
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.61722.374257
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.98615851
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7231533
X-RAY DIFFRACTIONr_chiral_restr0.0980.2674
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.024015
LS refinement shellResolution: 1.6→1.641 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.221 235 -
Rwork0.205 4203 -
all-4438 -
obs--64.48 %
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)
11.7064-0.67190.48080.47750.00640.6717-0.02760.01640.03560.07380.00990.0139-0.13820.05940.01770.1191-0.01720.01050.0060.00220.050645.344320.543613.3096
20.78590.06980.26140.06650.16070.58450.0037-0.03330.05160.0401-0.03590.008-0.0003-0.08810.03210.0817-0.01660.02250.01860.00130.06832.898114.979715.5933
30.8650.8430.10331.1631-0.09990.19940.0230.05820.02230.0260.00010.0628-0.04940.0093-0.02310.06380.01320.01760.03530.00340.055438.079713.24774.4073
40.48140.4969-0.05130.6263-0.33190.7290.0173-0.0326-0.0394-0.0027-0.0353-0.0440.0017-0.00290.0180.06410.00490.00110.0232-0.00180.054239.6930.76346.9959
51.66960.6547-0.18881.525-0.31232.24580.1732-0.1984-0.1488-0.0741-0.0602-0.06540.06420.0469-0.1130.05-0.0257-0.04630.02520.02350.075346.8749-4.348717.2164
60.6962-0.50010.21993.79881.38830.7653-0.0238-0.0478-0.09340.32240.1243-0.07810.12710.0275-0.10050.08530.0122-0.00940.019-0.00480.057352.0502-0.210221.996
71.7288-1.40280.85421.9291-0.32280.61790.0371-0.1587-0.03640.04220.0136-0.02650.0024-0.1239-0.05070.1049-0.02960.01060.0483-0.00510.022946.14916.733924.1194
84.0621-3.64311.38564.3603-1.11230.6773-0.1079-0.08610.25070.22080.0053-0.1798-0.15710.04740.10260.1317-0.0533-0.02860.055-0.01710.037449.970424.321220.7805
90.5848-0.0122-0.30670.0152-0.0430.33340.006-0.0085-0.0538-0.0172-0.02980.00110.03950.11790.02370.05450.0138-0.01260.07910.00070.04127.9611-12.734319.4075
100.2991-0.15490.06480.1529-0.18430.3524-0.0183-0.0599-0.0242-0.01440.03750.00950.0653-0.0581-0.01920.0579-0.0088-0.010.04920.00840.04561.2984-17.313727.7447
110.25820.0320.30270.19660.1050.3819-0.0141-0.03720.01570.01840.0064-0.00850.004-0.03950.00770.05940.0011-0.00660.05440.00630.03356.0847-11.65727.6675
120.1069-0.1444-0.03590.9422-0.26570.82490.08850.01460.05140.04210.0027-0.0026-0.07140.006-0.09120.10110.00890.04660.0260.01960.051115.1953.411332.8719
130.180.08580.0170.08910.07210.11990.0078-0.01050.0006-0.0062-0.0053-0.00420.02590.0201-0.00250.06470.0022-0.0010.04230.00290.047111.1909-9.663918.3687
141.6825-0.1556-0.01240.1266-0.12230.13620.0199-0.02640.2053-0.0246-0.0129-0.01160.02840.0175-0.0070.042-0.01490.00520.025200.089716.6853.56349.5015
150.4632-0.0968-0.09120.0239-0.00960.34510.0086-0.0130.0258-0.00610.0089-0.0061-0.0191-0.0104-0.01750.0615-0.00310.00260.0321-0.00090.049-0.2168-4.066313.0099
160.52550.1385-0.07190.19320.20380.62760.0461-0.04870.03840.00220.04440.0166-0.0593-0.0001-0.09050.0580.00350.02290.05340.02050.0424-6.9967-0.791517.7749
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A14 - 43
2X-RAY DIFFRACTION2A44 - 77
3X-RAY DIFFRACTION3A78 - 110
4X-RAY DIFFRACTION4A111 - 159
5X-RAY DIFFRACTION5A160 - 192
6X-RAY DIFFRACTION6A193 - 216
7X-RAY DIFFRACTION7A217 - 247
8X-RAY DIFFRACTION8A248 - 268
9X-RAY DIFFRACTION9B2 - 37
10X-RAY DIFFRACTION10B38 - 70
11X-RAY DIFFRACTION11B71 - 100
12X-RAY DIFFRACTION12B101 - 165
13X-RAY DIFFRACTION13B166 - 269
14X-RAY DIFFRACTION14B270 - 301
15X-RAY DIFFRACTION15B302 - 364
16X-RAY DIFFRACTION16B365 - 396

+
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