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- PDB-1a50: CRYSTAL STRUCTURE OF WILD-TYPE TRYPTOPHAN SYNTHASE COMPLEXED WITH... -

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Entry
Database: PDB / ID: 1a50
TitleCRYSTAL STRUCTURE OF WILD-TYPE TRYPTOPHAN SYNTHASE COMPLEXED WITH 5-FLUOROINDOLE PROPANOL PHOSPHATE
Components(TRYPTOPHAN SYNTHASE ...) x 2
KeywordsLYASE / CARBON-OXYGEN LYASE / TRYPTOPHAN BIOSYNTHESIS / PYRIDOXAL PHOSPHATE
Function / homology
Function and homology information


tryptophan synthase / tryptophan synthase activity / tryptophan biosynthetic process / chloroplast / identical protein binding / cytoplasm
Tryptophan synthase beta chain/beta chain-like / Aldolase-type TIM barrel / Pyridoxal-phosphate dependent enzyme / Tryptophan synthase alpha chain / Tryptophan synthase beta subunit-like PLP-dependent enzyme / Tryptophan synthase, alpha chain, active site / Pyridoxal-phosphate dependent enzyme / Tryptophan synthase, alpha chain / Tryptophan synthase, beta chain, conserved site / Tryptophan synthase, beta chain ...Tryptophan synthase beta chain/beta chain-like / Aldolase-type TIM barrel / Pyridoxal-phosphate dependent enzyme / Tryptophan synthase alpha chain / Tryptophan synthase beta subunit-like PLP-dependent enzyme / Tryptophan synthase, alpha chain, active site / Pyridoxal-phosphate dependent enzyme / Tryptophan synthase, alpha chain / Tryptophan synthase, beta chain, conserved site / Tryptophan synthase, beta chain / Ribulose-phosphate binding barrel / Rossmann fold - #1100 / Aldolase class I / TIM Barrel / Alpha-Beta Barrel / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Tryptophan synthase alpha chain / Tryptophan synthase beta chain
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / ISOMORPHOUS WITH PDB ENTRY 1WSY. / Resolution: 2.3 Å
AuthorsSchneider, T.R. / Gerhardt, E. / Lee, M. / Liang, P.-H. / Anderson, K.S. / Schlichting, I.
CitationJournal: Biochemistry / Year: 1998
Title: Loop closure and intersubunit communication in tryptophan synthase.
Authors: Schneider, T.R. / Gerhardt, E. / Lee, M. / Liang, P.H. / Anderson, K.S. / Schlichting, I.
Validation Report
SummaryFull reportAbout validation report
History
DepositionFeb 18, 1998-
Revision 1.0Mar 30, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic 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)72,1005
Polymers71,5572
Non-polymers5433
Water4,288238
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)144,20010
Polymers143,1134
Non-polymers1,0876
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Unit cell
γ
α
β
Length a, b, c (Å)182.700, 60.700, 67.500
Angle α, β, γ (deg.)90.00, 94.50, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-1369-

HOH

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Components

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TRYPTOPHAN SYNTHASE ... , 2 types, 2 molecules AB

#1: Protein/peptide TRYPTOPHAN SYNTHASE (ALPHA CHAIN)


Mass: 28698.797 Da / Num. of mol.: 1
Details: INHIBITOR 5-FLUOROINDOLE PROPANOL PHOSPHATE BOUND TO THE ALPHA SITE
Source method: isolated from a natural source / Source: (natural) Salmonella typhimurium (bacteria) / Cell line: CB149 / Plasmid: PSTB7 / References: UniProt: P00929, tryptophan synthase
#2: Protein/peptide TRYPTOPHAN SYNTHASE (BETA CHAIN)


Mass: 42857.805 Da / Num. of mol.: 1
Details: INHIBITOR 5-FLUOROINDOLE PROPANOL PHOSPHATE BOUND TO THE ALPHA SITE
Source method: isolated from a natural source / Source: (natural) Salmonella typhimurium (bacteria) / Cell line: CB149 / Plasmid: PSTB7 / References: UniProt: P0A2K1, tryptophan synthase

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Non-polymers , 4 types, 241 molecules

#3: Chemical ChemComp-FIP / 5-FLUOROINDOLE PROPANOL PHOSPHATE


Mass: 273.197 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H13FNO4P
#4: Chemical ChemComp-NA / SODIUM ION / Sodium


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: 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
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 238 / Source method: isolated from a natural source / Formula: H2O

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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: 2.61 Å3/Da / Density % sol: 48 %
Crystal growpH: 7.8 / Details: pH 7.8
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS

Crystal-ID: 1

IDConc.Common nameSol-ID
110 mg/mlenzymedrop
250 mMBicinedrop
30.02 Mpyridoxal phosphatedrop
450 mMbicinereservoir
51-2 mMsperminereservoir
610 %PEG8000reservoir

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1.15
DetectorType: MARRESEARCH / Detector: IMAGE PLATE AREA DETECTOR / Date: Nov 1, 1995 / Details: SYNCHROTRON
RadiationMonochromator: SYNCHROTRON / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.15 Å / Relative weight: 1
ReflectionResolution: 2.29→26.9 Å / Num. obs: 31823 / % possible obs: 95.6 % / Observed criterion σ(I): -3 / Redundancy: 2.2 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 13.4
Reflection shellResolution: 2.29→2.34 Å / Rmerge(I) obs: 0.21 / Mean I/σ(I) obs: 6.4 / % possible all: 91.6
Reflection
*PLUS
Highest resolution: 2.29 Å / Lowest resolution: 26.9 Å / Num. measured all: 66781
Reflection shell
*PLUS
% possible obs: 91.6 %

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: ISOMORPHOUS WITH PDB ENTRY 1WSY.
Starting model: 1WSY

1wsy
PDB Unreleased entry


Resolution: 2.3→10 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.247 3126 10 %RANDOM
Rwork0.177 ---
Obs0.177 30327 93.8 %-
Displacement parametersBiso mean: 17.5 Å2
Refine analyzeLuzzati d res low obs: 10 Å / Luzzati sigma a obs: 0.21 Å
Refinement stepCycle: LAST / Resolution: 2.3→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4919 0 34 238 5191
Refine LS restraints

Refinement-ID: X-RAY DIFFRACTION

TypeDev idealDev ideal target
x_bond_d0.006
x_bond_d_na
x_bond_d_prot
x_angle_d
x_angle_d_na
x_angle_d_prot
x_angle_deg1.3
x_angle_deg_na
x_angle_deg_prot
x_dihedral_angle_d
x_dihedral_angle_d_na
x_dihedral_angle_d_prot
x_improper_angle_d
x_improper_angle_d_na
x_improper_angle_d_prot
x_mcbond_it1.53.3
x_mcangle_it24.1
x_scbond_it25.3
x_scangle_it2.56.9
LS refinement shellResolution: 2.3→2.34 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2893 164 -
Rwork0.2219 1337 -
Obs--91.61 %
Xplor file

Refinement-ID: X-RAY DIFFRACTION

Serial noParam fileTopol file
1PARAM19X.PROTOPH19X.PRO
2PARAM.IPP.NEWTOP.IPP.NEW
3PARAM.PLP.NEWTOP.PLP.NEW
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.3 Å / Num. reflection obs: 31627 / Rfactor obs: 0.164 / Rfactor Rfree: 0.221 / Rfactor Rwork: 0.162

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