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- PDB-1a5s: CRYSTAL STRUCTURE OF WILD-TYPE TRYPTOPHAN SYNTHASE COMPLEXED WITH... -

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Database: PDB / ID: 1a5s
TitleCRYSTAL STRUCTURE OF WILD-TYPE TRYPTOPHAN SYNTHASE COMPLEXED WITH 5-FLUOROINDOLE PROPANOL PHOSPHATE AND L-SER BOUND AS AMINO ACRYLATE TO THE BETA SITE
Components(TRYPTOPHAN SYNTHASE ...) x 2
KeywordsCOMPLEX (LYASE/INHIBITOR) / LYASE / CARBON-OXYGEN LYASE / TRYPTOPHAN BIOSYNTHESIS / PYRIDOXAL PHOSPHATE / COMPLEX (LYASE-INHIBITOR) / COMPLEX (LYASE-INHIBITOR) complex
Function / homologyAldolase-type TIM barrel / Tryptophan synthase beta chain/beta chain-like / Tryptophan synthase beta chain pyridoxal-phosphate attachment site. / Tryptophan synthase alpha chain signature. / Pyridoxal-phosphate dependent enzyme / Tryptophan synthase alpha chain / Pyridoxal-phosphate dependent enzyme / Tryptophan synthase, alpha chain / Tryptophan synthase, beta chain, conserved site / Tryptophan synthase, beta chain ...Aldolase-type TIM barrel / Tryptophan synthase beta chain/beta chain-like / Tryptophan synthase beta chain pyridoxal-phosphate attachment site. / Tryptophan synthase alpha chain signature. / Pyridoxal-phosphate dependent enzyme / Tryptophan synthase alpha chain / Pyridoxal-phosphate dependent enzyme / Tryptophan synthase, alpha chain / Tryptophan synthase, beta chain, conserved site / Tryptophan synthase, beta chain / Ribulose-phosphate binding barrel / Tryptophan synthase beta subunit-like PLP-dependent enzyme / Tryptophan synthase, alpha chain, active site / tryptophan synthase / tryptophan synthase activity / tryptophan biosynthetic process / chloroplast / identical protein binding / cytoplasm / Tryptophan synthase alpha chain / Tryptophan synthase beta chain / Tryptophan synthase beta chain
Function and homology information
Specimen sourceSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / ISOMORPHOUS WITH PDB ENTRY 1WSY. / 2.3 Å resolution
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
DateDeposition: Feb 17, 1998 / Release: Mar 30, 1999
RevisionDateData content typeGroupProviderType
1.0Mar 30, 1999Structure modelrepositoryInitial release
1.1Mar 24, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelNon-polymer description / Version format compliance

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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)72,3366
Polyers71,6882
Non-polymers6484
Water2,090116
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)144,67212
Polyers143,3764
Non-polymers1,2978
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, 60.800, 67.500
Angle α, β, γ (deg.)90.00, 94.60, 90.00
Int Tables number5
Space group name H-MC 1 2 1

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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 / Source: (gene. exp.) Salmonella typhimurium (bacteria) / Genus: Salmonella / Cell line: CB149 / Gene: TRPA/TRPB / Plasmid name: PSTB7 / Genus (production host): Escherichia / Production host: Escherichia coli (E. coli) / References: UniProt: P00929, tryptophan synthase
#2: Protein/peptide TRYPTOPHAN SYNTHASE (BETA CHAIN)


Mass: 42988.996 Da / Num. of mol.: 1 / Source: (gene. exp.) Salmonella typhimurium (bacteria) / Genus: Salmonella / Cell line: CB149 / Gene: TRPA/TRPB / Plasmid name: PSTB7 / Genus (production host): Escherichia / Production host: Escherichia coli (E. coli)
References: UniProt: P00933, UniProt: P0A2K1*PLUS, tryptophan synthase

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Non-polymers , 5 types, 120 molecules

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


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


Mass: 22.990 Da / Num. of mol.: 1 / Formula: Na / Sodium
#5: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 1 / Formula: C8H10NO6P / Pyridoxal phosphate
#6: Chemical ChemComp-SER / SERINE


Mass: 105.093 Da / Num. of mol.: 1 / Formula: C3H7NO3 / Serine
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 116 / Formula: H2O / Water

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Details

Compound detailsRESIDUE 902 C SER IS NOT REALLY SERINE BUT AN AMINOACRYLATE COVALENTLY BOUND TO THE PYRIDOXAL PHOSPHATE (PLP).

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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 / Density percent sol: 48 %
Crystal growpH: 7.8 / Details: pH 7.8
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Details: drop consists of equal volume of enzyme and reservoir solutions
components of the solutions
*PLUS
IDConcCommon nameCrystal IDSol ID
110 mg/mlenzyme1drop
250 mMbicine1drop
30.02 Mpyridoxal phosphate1drop
450 mMbicine1reservoir
51-2 mMspermine1reservoir
610 %PEG80001reservoir

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Data collection

DiffractionMean temperature: 277 kelvins
SourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1.15
DetectorType: MARRESEARCH / Details: SYNCHROTRON / Detector: IMAGE PLATE AREA DETECTOR / Collection date: Nov 1, 1995
RadiationMonochromator: SYNCHROTRON / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.15 Å / Relative weight: 1
ReflectionD resolution high: 2.3 Å / D resolution low: 3 Å / Number obs: 31198 / Observed criterion sigma I: -3 / Rmerge I obs: 0.067 / NetI over sigmaI: 13.5 / Redundancy: 2.2 % / Percent possible obs: 93.8
Reflection shellRmerge I obs: 0.21 / Highest resolution: 2.3 Å / Lowest resolution: 2.4 Å / MeanI over sigI obs: 4.2 / Redundancy: 2.4 % / Percent possible all: 89.8
Reflection
*PLUS
Number measured all: 68449
Reflection shell
*PLUS
Percent possible obs: 89.8

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefineMethod to determine structure: ISOMORPHOUS WITH PDB ENTRY 1WSY.
Starting model: 1WSY
R Free selection details: RANDOM / Data cutoff high absF: 1 / Data cutoff low absF: 0.1 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / Sigma F: 2
Displacement parametersB iso mean: 25.6 Å2
Least-squares processR factor R free: 0.247 / R factor R work: 0.177 / R factor obs: 0.177 / Highest resolution: 2.3 Å / Lowest resolution: 1 Å / Number reflection R free: 3126 / Number reflection obs: 30327 / Percent reflection R free: 1 / Percent reflection obs: 93.8
Refine analyzeLuzzati d res low obs: 1 Å / Luzzati sigma a obs: 0.27 Å
Refine hist #LASTHighest resolution: 2.3 Å / Lowest resolution: 1 Å
Number of atoms included #LASTProtein: 4876 / Nucleic acid: 0 / Ligand: 40 / Solvent: 116 / Total: 5032
Refine LS restraints
Refine IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.006
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.3
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.53.6
X-RAY DIFFRACTIONx_mcangle_it2.04.7
X-RAY DIFFRACTIONx_scbond_it2.05.5
X-RAY DIFFRACTIONx_scangle_it2.57.2
Refine LS shellHighest resolution: 2.3 Å / R factor R free: 0.3223 / R factor R work: 0.2596 / Lowest resolution: 2.34 Å / Number reflection R free: 160 / Number reflection R work: 1290 / Total number of bins used: 20 / Percent reflection obs: 89.8
Xplor file
Refine IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARAM19X.PROTOPH19X.PRO
X-RAY DIFFRACTION2PARAM.IPP.NEWTOP.IPP.NEW
X-RAY DIFFRACTION3PARAM.PLP.NEWTOP.PLP.NEW

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