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- PDB-7mt6: Crystal structure of tryptophan synthase in complex with F9, Cs+,... -

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Basic information

Entry
Database: PDB / ID: 7mt6
TitleCrystal structure of tryptophan synthase in complex with F9, Cs+, benzimidazole, pH7.8 - alpha aminoacrylate form - E(A-A)(BZI)
Components(Tryptophan synthase ...) x 2
KeywordsLYASE/INHIBITOR / PLP-dependent enzyme Tryptophan synthase / LYASE / LYASE-INHIBITOR complex
Function / homology
Function and homology information


tryptophan synthase / tryptophan synthase activity / tryptophan biosynthetic process / identical protein binding / 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
Chem-0JO / BENZIMIDAZOLE / : / Chem-F9F / 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 / Resolution: 1.7 Å
AuthorsDrago, V. / Hilario, E. / Dunn, M.F. / Mueser, T.C. / Mueller, L.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM137008 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2022
Title: Imaging active site chemistry and protonation states: NMR crystallography of the tryptophan synthase alpha-aminoacrylate intermediate.
Authors: Holmes, J.B. / Liu, V. / Caulkins, B.G. / Hilario, E. / Ghosh, R.K. / Drago, V.N. / Young, R.P. / Romero, J.A. / Gill, A.D. / Bogie, P.M. / Paulino, J. / Wang, X. / Riviere, G. / Bosken, Y.K. ...Authors: Holmes, J.B. / Liu, V. / Caulkins, B.G. / Hilario, E. / Ghosh, R.K. / Drago, V.N. / Young, R.P. / Romero, J.A. / Gill, A.D. / Bogie, P.M. / Paulino, J. / Wang, X. / Riviere, G. / Bosken, Y.K. / Struppe, J. / Hassan, A. / Guidoulianov, J. / Perrone, B. / Mentink-Vigier, F. / Chang, C.A. / Long, J.R. / Hooley, R.J. / Mueser, T.C. / Dunn, M.F. / Mueller, L.J.
History
DepositionMay 12, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 29, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 19, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 26, 2022Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.3Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tryptophan synthase alpha chain
B: Tryptophan synthase beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,8018
Polymers71,6182
Non-polymers1,1846
Water12,791710
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)145,60216
Polymers143,2354
Non-polymers2,36712
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area11770 Å2
ΔGint-177 kcal/mol
Surface area42370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)183.96, 60.96, 67.4101
Angle α, β, γ (deg.)90.0, 94.58, 90.0
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-723-

HOH

21B-799-

HOH

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Components

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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, 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

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Non-polymers , 5 types, 716 molecules

#3: 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
#4: Chemical ChemComp-0JO / 2-{[(E)-{3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene]amino}prop-2-enoic acid


Mass: 316.204 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H13N2O7P
#5: Chemical ChemComp-CS / CESIUM ION


Mass: 132.905 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cs
#6: Chemical ChemComp-BZI / BENZIMIDAZOLE


Mass: 118.136 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H6N2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 710 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.63 Å3/Da / Density % sol: 53.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 50 mM Bicine-CsOH pH 7.8, 10% PEG 8000, 2 mM spermine

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5419 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Dec 31, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5419 Å / Relative weight: 1
ReflectionResolution: 1.7→39.23 Å / Num. obs: 89264 / % possible obs: 98.5 % / Redundancy: 3.6 % / Biso Wilson estimate: 19.8 Å2 / CC1/2: 0.998 / Net I/σ(I): 13.5
Reflection shellResolution: 1.7→1.79 Å / Num. unique obs: 11881 / CC1/2: 0.975

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Processing

Software
NameVersionClassification
PHENIX1.9-1692refinement
SCALAdata scaling
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1tjp

1tjp


Resolution: 1.7→39.23 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflection
Rfree0.1926 --
Rwork0.1602 132257 -
obs-80523 86.7 %
Solvent computationSolvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.47 Å2
Refinement stepCycle: LAST / Resolution: 1.7→39.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5009 0 63 710 5782
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007212204176355220
X-RAY DIFFRACTIONf_angle_d1.137875738777079
X-RAY DIFFRACTIONf_chiral_restr0.0437088532553778
X-RAY DIFFRACTIONf_plane_restr0.00557075434192936
X-RAY DIFFRACTIONf_dihedral_angle_d13.0024660771932

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