[English] 日本語
Yorodumi
- PDB-6c73: Tryptophan synthase Q114A mutant (internal aldimine state) in com... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6c73
TitleTryptophan synthase Q114A mutant (internal aldimine state) in complex with N-(4'-trifluoromethoxybenzenesulfonyl)-2-amino-1-ethylphosphate (F9F) with cesium ion bound in the metal coordination site
Components(Tryptophan synthase ...) x 2
KeywordsLYASE / F9F ligand / cesium ion / mutant beta-Q114A
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
: / Chem-F9F / DI(HYDROXYETHYL)ETHER / PYRIDOXAL-5'-PHOSPHATE / Tryptophan synthase alpha chain / Tryptophan synthase beta chain
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.65 Å
AuthorsHilario, E. / Dunn, M.F. / Mueller, L.J. / Fan, L.
CitationJournal: To be Published
Title: Tryptophan synthase Q114A mutant (internal aldimine state) in complex with N-(4'-trifluoromethoxybenzenesulfonyl)-2-amino-1-ethylphosphate (F9F) with cesium ion bound in the metal coordination site.
Authors: Hilario, E. / Dunn, M.F. / Mueller, L.J. / Fan, L.
History
DepositionJan 19, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 23, 2019Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support
Revision 1.3Sep 29, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.oper_expression / _pdbx_struct_assembly_prop.value / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn_type.id
Revision 1.4Oct 4, 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)74,47535
Polymers71,3162
Non-polymers3,15933
Water15,547863
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)148,95070
Polymers142,6334
Non-polymers6,31766
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area8570 Å2
ΔGint-32 kcal/mol
Surface area44630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)181.609, 58.980, 67.150
Angle α, β, γ (deg.)90.000, 94.400, 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 enterica subsp. enterica serovar Typhimurium (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: 42617.480 Da / Num. of mol.: 1 / Mutation: Q114A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Gene: trpB, STM1726 / Plasmid: PEBA-10 / Details (production host): mutant Q114A / Production host: Escherichia coli (E. coli) / Strain (production host): CB149 / References: UniProt: P0A2K1, tryptophan synthase

-
Non-polymers , 8 types, 896 molecules

#3: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical ChemComp-F9F / 2-({[4-(TRIFLUOROMETHOXY)PHENYL]SULFONYL}AMINO)ETHYL DIHYDROGEN PHOSPHATE / N-(4'-TRIFLUOROMETHOXYBENZENESULFONYL)-2-AMINO-1-ETHYLPHOSPHATE, F9


Mass: 365.220 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H11F3NO7PS
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical
ChemComp-CS / CESIUM ION


Mass: 132.905 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cs
#8: 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
#9: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#10: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 863 / 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: 2.51 Å3/Da / Density % sol: 51.07 % / Description: large plate-like crystal
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.8
Details: 100 mM Bicine-CsOH, pH 7.8, 5-10% PEG8000, 1 mM DTT, 1 mM EDTA, 2 mM F9F
PH range: 7.6-8.0

-
Data collection

DiffractionMean temperature: 100 K / Ambient temp details: nitrogen flow
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Nov 7, 2017 / Details: VariMax
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.65→20 Å / Num. obs: 85206 / % possible obs: 99.9 % / Redundancy: 3.5 % / Biso Wilson estimate: 11.917 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.041 / Rpim(I) all: 0.032 / Rrim(I) all: 0.062 / Rsym value: 0.041 / Net I/av σ(I): 12.9 / Net I/σ(I): 15.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allRsym value% possible all
1.65-1.743.40.183.9123230.9610.1350.2530.1899.6
1.74-1.843.40.1265.6117360.0940.1770.12699.9
1.84-1.973.40.097.7110270.0670.1260.09100
1.97-2.133.50.06510.7102850.0490.0930.065100
2.13-2.333.60.04913.894770.0380.0720.049100
2.33-2.613.60.04116.285640.0320.0620.041100
2.61-3.013.70.03916.475800.030.0580.039100
3.01-3.693.70.03617.564610.0260.0510.036100
3.69-5.223.70.02449970.020.0380.024100
5.22-19.813.60.02227560.0230.0440.02298.2

-
Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.382
Highest resolutionLowest resolution
Rotation19.82 Å1.8 Å

-
Processing

Software
NameVersionClassification
SCALA3.3.22data scaling
MOLREP11.6.02phasing
REFMAC5.8.0135refinement
PDB_EXTRACT3.24data extraction
iMOSFLM7.2.1data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4HT3

4ht3


Resolution: 1.65→19.82 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.952 / SU B: 3.314 / SU ML: 0.051 / SU R Cruickshank DPI: 0.1211 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.121 / ESU R Free: 0.086 / Details: U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1829 4306 5.1 %RANDOM
Rwork0.1383 ---
obs0.1406 80889 99.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 89.32 Å2 / Biso mean: 18.708 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å2-0.02 Å2
2--0.02 Å20 Å2
3----0 Å2
Refinement stepCycle: final / Resolution: 1.65→19.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5005 0 150 917 6072
Biso mean--27.89 32.15 -
Num. residues----663
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0195567
X-RAY DIFFRACTIONr_angle_refined_deg1.5351.9897552
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.755734
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.5824.163233
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.47515921
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4091536
X-RAY DIFFRACTIONr_chiral_restr0.1020.2838
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0214257
X-RAY DIFFRACTIONr_rigid_bond_restr2.37335567
X-RAY DIFFRACTIONr_sphericity_free27.9375227
X-RAY DIFFRACTIONr_sphericity_bonded9.06456153
LS refinement shellResolution: 1.65→1.693 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.291 320 -
Rwork0.225 5862 -
all-6182 -
obs--99.53 %
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)
10.12910.04270.0770.33870.03490.17360.01870.01170.0091-0.008-0.01490.0156-0.00510.0018-0.00370.0408-0.00520.0160.02410.0070.044337.860410.02268.8869
20.5457-0.19960.0380.60010.35070.30090.0228-0.1119-0.08290.03640.04640.01660.07670.001-0.06910.0595-0.0025-0.04930.02330.01310.070547.1109-1.597921.7771
30.1731-0.01840.24260.71170.43750.66150.0436-0.02560.01750.0404-0.003-0.08470.0757-0.025-0.04060.04-0.0144-0.01140.04-0.00770.04351.3526.699322.9123
41.892-1.41170.26296.9934-0.69150.07830.0633-0.12810.04960.1986-0.0814-0.1069-0.0139-0.00490.01810.06610.00490.0030.0236-0.01250.037437.417924.479523.1137
53.0183-2.49770.70372.9359-0.13560.4022-0.0906-0.04450.20330.06530.0601-0.1786-0.04650.01050.03050.069-0.02490.00040.0115-0.00650.05749.284624.400321.1961
60.3923-0.0194-0.42770.00150.02020.5001-0.0239-0.0409-0.0397-0.00330.00110.00290.03780.08240.02280.03860.0046-0.01550.06190.00120.040827.836-13.150619.3565
70.0309-0.0416-0.01410.2036-0.13590.1847-0.0241-0.0069-0.00190.00470.0222-0.00930.042-0.04160.00190.0388-0.0055-0.00420.06270.00980.02481.354-17.638127.8067
80.01260.04310.01650.16550.06540.02720.01160.0051-0.00070.0251-0.0069-0.01160.0119-0.0112-0.00460.04540.0055-0.00860.06120.01190.022610.558-8.700630.2135
90.12090.22330.20260.46220.21190.87720.01650.02250.00190.06690.05680.0276-0.13510.0139-0.07320.05640.00870.03820.02790.02050.045914.30877.163232.2552
100.07280.0431-0.02520.11540.1130.196-0.0098-0.0128-0.0177-0.0068-0.0006-0.00770.01430.02040.01040.0429-0.0009-0.00890.04930.00740.032712.8717-11.430421.1607
110.05070.02550.07850.6693-0.19260.2194-0.01130.03250.0128-0.0232-0.01290.01170.00070.04550.02420.04570.00120.00150.04620.00490.03455.9126-4.21097.5083
120.75420.0603-0.17930.8729-0.52790.35250.0523-0.01060.1418-0.0287-0.02260.030.01840.0231-0.02980.0382-0.00450.01010.03270.01820.073820.82483.04098.9535
130.5483-0.3421-0.15360.26250.2020.27850.015-0.01910.0504-0.00650.0283-0.04630.00890.024-0.04330.036-0.00860.00210.05690.00340.027611.2068-4.276711.6063
140.27260.0571-0.00390.0426-0.08650.2465-0.0080.0080.0140.00490.01430.003-0.0329-0.0309-0.00630.04720.002-0.00080.04880.00440.0279-6.387-2.977613.8906
150.13420.19280.13660.29490.18620.53640.014-0.00920.02550.02970.01140.0501-0.0533-0.0567-0.02550.04730.01480.01390.06160.00770.0269-6.9634-0.38418.472
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A30 - 159
2X-RAY DIFFRACTION2A160 - 202
3X-RAY DIFFRACTION3A203 - 234
4X-RAY DIFFRACTION4A235 - 247
5X-RAY DIFFRACTION5A248 - 268
6X-RAY DIFFRACTION6B2 - 37
7X-RAY DIFFRACTION7B38 - 70
8X-RAY DIFFRACTION8B71 - 126
9X-RAY DIFFRACTION9B127 - 165
10X-RAY DIFFRACTION10B166 - 244
11X-RAY DIFFRACTION11B245 - 273
12X-RAY DIFFRACTION12B274 - 295
13X-RAY DIFFRACTION13B296 - 322
14X-RAY DIFFRACTION14B323 - 365
15X-RAY DIFFRACTION15B366 - 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