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- PDB-6wx3: High resolution Tryptophan Synthase crystal structure from Salmon... -

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Basic information

Entry
Database: PDB / ID: 6wx3
TitleHigh resolution Tryptophan Synthase crystal structure from Salmonella typhimurium in complex with F9 inhibitor in the alpha-site, Cesium ion at the metal coordination site and internal aldimine form.
Components(Tryptophan synthase ...) x 2
KeywordsLYASE/LYASE INHIBITOR / lyase-inhibitor / protein complex / LYASE / 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 / Tryptophan synthase beta subunit-like PLP-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 / Tryptophan synthase beta subunit-like PLP-dependent enzyme / Pyridoxal-phosphate dependent enzyme / Ribulose-phosphate binding barrel / Aldolase-type TIM barrel
Similarity search - Domain/homology
: / Chem-F9F / PYRIDOXAL-5'-PHOSPHATE / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.2 Å
AuthorsHilario, E. / Dunn, M.F. / Mueller, L.J. / Fan, L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)2R01GM097569-06A1 United States
CitationJournal: To be Published
Title: High resolution Tryptophan Synthase crystal structure from Salmonella typhimurium in complex with F9 inhibitor in the alpha-site, Cesium ion at the metal coordination site and internal aldimine form.
Authors: Hilario, E. / Fan, L. / Dunn, M.F. / Mueller, L.J.
History
DepositionMay 9, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 10, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)73,38614
Polymers71,6182
Non-polymers1,76912
Water14,898827
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)146,77328
Polymers143,2354
Non-polymers3,53724
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area14420 Å2
ΔGint-217 kcal/mol
Surface area44070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)182.118, 59.060, 67.405
Angle α, β, γ (deg.)90.000, 94.840, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-1508-

HOH

21B-1883-

HOH

31B-1973-

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 / Plasmid: pEBA-10 / Production host: Escherichia coli (E. coli) / Strain (production host): CB149 / 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 / Plasmid: pEBA-10 / Production host: Escherichia coli (E. coli) / Strain (production host): CB149 / References: UniProt: P0A2K1, tryptophan synthase

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Non-polymers , 8 types, 839 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 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#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 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-CS / CESIUM ION


Mass: 132.905 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cs / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical
ChemComp-BCN / BICINE / Bicine


Mass: 163.172 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H13NO4 / Comment: pH buffer*YM
#8: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#9: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#10: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 827 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.54 Å3/Da / Density % sol: 51.22 % / Description: Large plate-like crystal
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.8
Details: 50 mM Bicine-CsOH, 10% PEG 8,000, 2 mM Spermine, pH 7.8
PH range: 7.6-8.0 / Temp details: constant

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: constant / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 12.3.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 4, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.2→90.735 Å / Num. all: 212937 / Num. obs: 212937 / % possible obs: 96.3 % / Redundancy: 6.6 % / Rpim(I) all: 0.047 / Rrim(I) all: 0.12 / Rsym value: 0.103 / Net I/av σ(I): 4.7 / Net I/σ(I): 9.1 / Num. measured all: 1401307
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
1.2-1.263.90.9750.6117005303870.5991.1850.9751.394.4
1.26-1.347.20.5571.1208653290870.2340.6330.5573.595.5
1.34-1.437.20.3431.9198859275230.1460.3950.343596.2
1.43-1.557.20.2143.1185842258750.0920.2490.214796.9
1.55-1.77.10.1394.9170825239140.0590.1590.1399.397.5
1.7-1.97.10.0996.5154363218480.0430.1140.09912.298.2
1.9-2.196.80.0867.1133142194510.0380.10.08615.898.8
2.19-2.686.50.0827.5107262164930.0370.0950.08217.999.3
2.68-3.796.90.0649.887916126910.0270.0720.06420.798.2
3.79-36.2046.60.063103744056680.0270.0710.06320.978.5

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Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.542
Highest resolutionLowest resolution
Rotation36.21 Å1.4 Å
Phasing dmMethod: Solvent flattening and Histogram matching / Reflection: 212882
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
6.51-10047.80.809841
4.6-6.5142.60.8752193
3.76-4.635.80.9162845
3.25-3.7627.30.9273791
2.91-3.2525.20.9224454
2.66-2.9125.20.9144892
2.46-2.6624.20.9195313
2.3-2.4622.60.935707
2.17-2.322.40.9296008
2.06-2.1722.50.9336416
1.96-2.06230.9256688
1.88-1.9623.90.9196989
1.8-1.8824.90.9127245
1.74-1.825.30.927485
1.68-1.7425.30.9247759
1.63-1.68270.9198036
1.58-1.6327.20.9168254
1.53-1.5827.20.9178471
1.49-1.5328.20.9158666
1.45-1.49290.9148931
1.42-1.4529.60.9169081
1.39-1.4230.80.9099254
1.36-1.3930.50.9079500
1.33-1.3631.70.9099652
1.3-1.3332.70.9019838
1.28-1.334.60.8859976
1.25-1.2840.90.81910145
1.23-1.2545.40.82110261
1.2-1.2356.10.73914191

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALA3.3.22data scaling
MOLREP11.7.02phasing
REFMAC5.8.0258refinement
DM7.0.078phasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4HT3

4ht3


Resolution: 1.2→36.23 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.961 / SU B: 1.49 / SU ML: 0.029 / SU R Cruickshank DPI: 0.0398 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.04 / ESU R Free: 0.039 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1813 10452 4.9 %RANDOM
Rwork0.1551 ---
obs0.1564 202430 95.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 243.66 Å2 / Biso mean: 17.604 Å2 / Biso min: 5.82 Å2
Baniso -1Baniso -2Baniso -3
1-0.9 Å20 Å20.28 Å2
2---1.67 Å2-0 Å2
3---0.71 Å2
Refinement stepCycle: final / Resolution: 1.2→36.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4963 0 97 850 5910
Biso mean--24.67 35.28 -
Num. residues----657
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0125562
X-RAY DIFFRACTIONr_angle_refined_deg1.3521.6367584
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2215754
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.15122.166277
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.29915936
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1681537
X-RAY DIFFRACTIONr_chiral_restr0.0970.2719
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024343
X-RAY DIFFRACTIONr_rigid_bond_restr6.12935562
LS refinement shellResolution: 1.2→1.232 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.304 727 -
Rwork0.299 14368 -
all-15095 -
obs--92.28 %

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