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- PDB-2rhg: Tryptophan synthase complexed with IGP, pH 7.0, internal aldimine -

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Basic information

Entry
Database: PDB / ID: 2rhg
TitleTryptophan synthase complexed with IGP, pH 7.0, internal aldimine
Components(Tryptophan synthase ...) x 2
KeywordsLYASE / AROMATIC AMINO ACID BIOSYNTHESIS / TRYPTOPHAN BIOSYNTHESIS / CARBON-OXYGEN LYASE / AMINOACID BIOSYNTHESIS / ALLOSTERIC ENZYME / PYRIDOXAL PHOSPHATE / Amino-acid biosynthesis
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
INDOLE-3-GLYCEROL PHOSPHATE / PYRIDOXAL-5'-PHOSPHATE / Tryptophan synthase alpha chain / Tryptophan synthase beta chain
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2 Å
AuthorsKulik, V. / Barends, T. / Schlichting, I.
CitationJournal: To be Published
Title: Tryptophan synthase complexed with IGP, pH 7.0, internal aldimine
Authors: Kulik, V. / Barends, T. / Schlichting, I.
History
DepositionOct 9, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 20, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / 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)72,1755
Polymers71,6182
Non-polymers5573
Water4,918273
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)144,35010
Polymers143,2354
Non-polymers1,1156
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area9840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)183.654, 59.573, 67.547
Angle α, β, γ (deg.)90.00, 94.71, 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) / Gene: trpA / Plasmid: pSTB7 / 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 typhimurium (bacteria) / Gene: trpB / 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, 276 molecules

#3: Chemical ChemComp-IGP / INDOLE-3-GLYCEROL PHOSPHATE


Mass: 287.206 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H14NO6P
#4: Chemical ChemComp-NA / SODIUM ION


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.: 273 / 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: 2.57 Å3/Da / Density % sol: 52.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Protein: 50 mM Bicine pH 7.8, 10 mM Na-EDTA, 1 mM DTE, 20 uM PLP. Reservoir: 50 mM Bicine pH 7.8, 5 mM DTE, 5 mM Na-EDTA, 0.1 M PLP, 2 mM spermine, 2 mM NaN3, 8-12% PEG8000. Crystal soaked ...Details: Protein: 50 mM Bicine pH 7.8, 10 mM Na-EDTA, 1 mM DTE, 20 uM PLP. Reservoir: 50 mM Bicine pH 7.8, 5 mM DTE, 5 mM Na-EDTA, 0.1 M PLP, 2 mM spermine, 2 mM NaN3, 8-12% PEG8000. Crystal soaked in 15% PEG8000, 20% glycerol, 23 mM IGP, pH controlled at pH 9.0 before flash-cooling, VAPOR DIFFUSION, HANGING DROP, temperature 293K, pH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, Hamburg / Beamline: BW7B / Wavelength: 0.84
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Dec 14, 1999
RadiationMonochromator: Si [111], horizontally focussing / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.84 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 76750 / Num. obs: 76750 / % possible obs: 69.8 % / Observed criterion σ(I): -3 / Redundancy: 2 % / Biso Wilson estimate: 15.2 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 10.8
Reflection shellResolution: 1.9→1.95 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.175 / Mean I/σ(I) obs: 4.5 / Num. unique all: 3174 / % possible all: 74.3

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Processing

Software
NameVersionClassification
CNS1refinement
MAR345dtbdata collection
XDSdata reduction
XSCALEdata scaling
CNS1phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2→19.99 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 4243541.31 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.239 1693 5 %RANDOM
Rwork0.212 ---
obs0.212 40137 68.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 53.8044 Å2 / ksol: 0.38885 e/Å3
Displacement parametersBiso mean: 26.5 Å2
Baniso -1Baniso -2Baniso -3
1--5.63 Å20 Å2-1.49 Å2
2--11.06 Å20 Å2
3----5.43 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.3 Å0.22 Å
Refinement stepCycle: LAST / Resolution: 2→19.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4593 0 35 273 4901
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d22
X-RAY DIFFRACTIONc_improper_angle_d0.81
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.331 342 5 %
Rwork0.267 6488 -
obs--84.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2TRPS_lig.parTRPS_lig.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top

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