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- PDB-2cll: Tryptophan Synthase (external aldimine state) in complex with N-(... -

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Basic information

Entry
Database: PDB / ID: 2cll
TitleTryptophan Synthase (external aldimine state) in complex with N-(4'- trifluoromethoxybenzenesulfonyl)-2-amino-1-ethylphosphate (F9)
Components(TRYPTOPHAN SYNTHASE ...) x 2
KeywordsLYASE / AROMATIC AMINO ACID BIOSYNTHESIS / CARBON-OXYGEN LYASE / AMINO-ACID BIOSYNTHESIS / TRYPTOPHAN BIOSYNTHESIS / ALLOSTERIC ENZYME / PYRIDOXAL PHOSPHATE
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 / Chem-PLS / Tryptophan synthase alpha chain / Tryptophan synthase beta chain
Similarity search - Component
Biological speciesSALMONELLA TYPHIMURIUM (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsNgo, H. / Kimmich, N. / Harris, R. / Niks, D. / Blumenstein, L. / Kulik, V. / Barends, T.R. / Schlichting, I. / Dunn, M.F.
CitationJournal: Biochemistry / Year: 2007
Title: Allosteric Regulation of Substrate Channeling in Tryptophan Synthase: Modulation of the L-Serine Reaction in Stage I of the Beta-Reaction by Alpha-Site Ligands.
Authors: Ngo, H. / Kimmich, N. / Harris, R. / Niks, D. / Blumenstein, L. / Kulik, V. / Barends, T.R. / Schlichting, I. / Dunn, M.F.
History
DepositionApr 28, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 12, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)72,2115
Polymers71,4862
Non-polymers7243
Water9,422523
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)144,42210
Polymers142,9734
Non-polymers1,4496
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area9640 Å2
ΔGint-54.8 kcal/mol
Surface area51800 Å2
MethodPQS
Unit cell
Length a, b, c (Å)182.530, 59.770, 67.340
Angle α, β, γ (deg.)90.00, 94.66, 90.00
Int Tables number5
Space group name H-MC121

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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) / Plasmid: PSTB7 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): CB149 / References: UniProt: P00929, tryptophan synthase
#2: Protein TRYPTOPHAN SYNTHASE BETA CHAIN


Mass: 42787.688 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SALMONELLA TYPHIMURIUM (bacteria) / Plasmid: PSTB7 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): CB149 / References: UniProt: P0A2K1, tryptophan synthase

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Non-polymers , 4 types, 526 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-PLS / [3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHYL]-SERINE / PYRIDOXYL-SERINE-5-MONOPHOSPHATE


Mass: 336.235 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H17N2O8P
#5: Chemical ChemComp-NA / SODIUM ION


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


Mass: 18.015 Da / Num. of mol.: 523 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsTHE ALPHA SUBUNIT IS RESPONSIBLE FOR THE ALDOL CLEAVAGE OF INDOLEGLYCEROL PHOSPHATE TO INDOLE AND ...THE ALPHA SUBUNIT IS RESPONSIBLE FOR THE ALDOL CLEAVAGE OF INDOLEGLYCEROL PHOSPHATE TO INDOLE AND GLYCERALDEHYDE 3-PHOSPHATE. THE BETA SUBUNIT IS RESPONSIBLE FOR THE SYNTHESIS OF L-TRYPTOPHAN FROM INDOLE AND L-SERINE.

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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: 2.41 Å3/Da / Density % sol: 48.57 %
Crystal growpH: 7.8 / Details: pH 7.80

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.931
DetectorType: ADSC CCD / Detector: CCD / Date: Apr 1, 2003 / Details: SAGITALLY FOCUSING GE 220 AND A MULTILAYER
RadiationMonochromator: DIAMOND 111, GE 220 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.931 Å / Relative weight: 1
ReflectionResolution: 1.5→19.36 Å / Num. obs: 116340 / % possible obs: 81.8 % / Observed criterion σ(I): 0 / Redundancy: 2 % / Biso Wilson estimate: 18.3 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 17.3
Reflection shellResolution: 1.6→1.7 Å / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 3.7 / % possible all: 90.2

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Processing

Software
NameVersionClassification
CNS1refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→19.36 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 3449164.27 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.245 4568 5 %RANDOM
Rwork0.217 ---
obs0.217 91369 95.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 53.6027 Å2 / ksol: 0.390331 e/Å3
Displacement parametersBiso mean: 22 Å2
Baniso -1Baniso -2Baniso -3
1--2.73 Å20 Å20.72 Å2
2--7 Å20 Å2
3----4.27 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.22 Å0.21 Å
Refinement stepCycle: LAST / Resolution: 1.6→19.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4857 0 45 523 5425
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.015
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.09
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 1.6→1.7 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.326 740 5 %
Rwork0.3 14112 -
obs--94 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2TRPS_LIG.PARAMTRPS_LIG.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP

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