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- PDB-7jtt: The external aldimine crystal structure of Salmonella typhimurium... -

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Basic information

Entry
Database: PDB / ID: 7jtt
TitleThe external aldimine crystal structure of Salmonella typhimurium Tryptophan Synthase mutant beta-S377A in complex F9 inhibitor at the alpha-site and cesium ion at the metal coordination site. The single beta-Q114 rotamer conformation allows a hydrogen bond to form with the PLP oxygen at the position 3 in the ring
Components(Tryptophan synthase ...) x 2
KeywordsLYASE/LYASE INHIBITOR / LYASE / inhibitor complex / tryptophan synthase / LYASE-LYASE INHIBITOR complex
Function / homology
Function and homology information


tryptophan synthase / tryptophan synthase activity / L-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. / Pyridoxal-phosphate dependent enzyme / 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. / Pyridoxal-phosphate dependent enzyme / Pyridoxal-phosphate dependent enzyme / Tryptophan synthase beta subunit-like PLP-dependent enzyme / Ribulose-phosphate binding barrel / Aldolase-type TIM barrel
Similarity search - Domain/homology
: / Chem-F9F / Chem-KOU / DI(HYDROXYETHYL)ETHER / Tryptophan synthase alpha chain / Tryptophan synthase beta chain
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.64 Å
AuthorsHilario, E. / Dunn, M.F. / Mueller, L.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)GM097569 United States
CitationJournal: To be Published
Title: The external aldimine crystal structure of Salmonella typhimurium Tryptophan Synthase mutant beta-S377A in complex F9 inhibitor at the alpha-site and cesium ion at the metal coordination site. ...Title: The external aldimine crystal structure of Salmonella typhimurium Tryptophan Synthase mutant beta-S377A in complex F9 inhibitor at the alpha-site and cesium ion at the metal coordination site. The single beta-Q114 rotamer conformation allows a hydrogen bond to form with the PLP oxygen at the position 3 in the ring.
Authors: Hilario, E. / Dunn, M.F. / Mueller, L.J.
History
DepositionAug 18, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 25, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)75,12542
Polymers71,6022
Non-polymers3,52340
Water11,367631
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, Protein is a tetramer (alpha2-beta2) in solution and composed of two alpha-chains and two beta-chains.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11690 Å2
ΔGint-56 kcal/mol
Surface area22460 Å2
Unit cell
Length a, b, c (Å)180.749, 57.850, 67.110
Angle α, β, γ (deg.)90.000, 94.540, 90.000
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 (strain LT2 / SGSC1412 / ATCC 700720) (bacteria)
Strain: LT2 / SGSC1412 / ATCC 700720 / Gene: trpA, STM1727 / Plasmid: pEBA-10 / Production host: Escherichia coli (E. coli) / Strain (production host): CB149 / References: UniProt: P00929, tryptophan synthase
#2: Protein Tryptophan synthase beta chain


Mass: 42902.879 Da / Num. of mol.: 1 / Mutation: S377A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (bacteria)
Strain: LT2 / SGSC1412 / ATCC 700720 / Gene: trpB, STM1726 / 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, 671 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-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-KOU / (E)-N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)-L-serine


Mass: 334.219 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H15N2O8P / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#8: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#9: Chemical ChemComp-CS / CESIUM ION


Mass: 132.905 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cs / Feature type: SUBJECT OF INVESTIGATION
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 631 / 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: 2.45 Å3/Da / Density % sol: 49.9 % / 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, 4 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: Oxford Cobra System / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jan 11, 2020 / Details: Osmic Varimax HF ArcSec
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.64→90.091 Å / Num. all: 78381 / Num. obs: 78381 / % possible obs: 92.3 % / Redundancy: 3.4 % / Rpim(I) all: 0.053 / Rrim(I) all: 0.1 / Rsym value: 0.074 / Net I/av σ(I): 6.5 / Net I/σ(I): 7.3 / Num. measured all: 263605
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRpim(I) allRrim(I) allRsym value% possible all
1.64-1.733.30.3092.1107690.2330.440.30987.3
1.73-1.833.40.2173.199580.1610.3060.21785.3
1.83-1.963.40.163493420.1180.2270.16384.9
1.96-2.123.30.124.990460.0840.1610.1288.4
2.12-2.323.20.1045.690520.0720.1350.10496.1
2.32-2.593.30.0926.584840.0630.1170.092100
2.59-2.993.50.0827.375530.0560.1050.082100
2.99-3.673.50.0797.563920.0520.10.079100
3.67-5.193.60.04114.449920.030.0580.041100
5.19-38.823.50.04112.927930.0340.0640.04199.7

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Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.395
Highest resolutionLowest resolution
Rotation38.82 Å1.85 Å
Phasing dmMethod: Solvent flattening and Histogram matching / Reflection: 78047
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
8.89-10030.80.942571
6.29-8.8938.90.9191018
5.13-6.29370.8851291
4.44-5.1328.10.9241509
3.98-4.4422.40.9361735
3.63-3.9825.50.9341881
3.36-3.6322.70.9362059
3.14-3.3622.40.9262221
2.96-3.1422.50.9282308
2.81-2.9622.70.9252475
2.68-2.8121.80.9282571
2.57-2.6819.80.9322706
2.47-2.57200.9322813
2.38-2.4719.80.9262923
2.3-2.3819.10.9332997
2.22-2.319.60.9243047
2.16-2.2220.30.9173053
2.1-2.1619.60.9243106
2.04-2.121.80.9053044
1.99-2.0421.30.9053052
1.94-1.9921.70.9063068
1.9-1.9422.20.9033138
1.85-1.923.60.8953196
1.81-1.8523.80.9053247
1.78-1.8124.10.8963319
1.74-1.7825.60.8923439
1.71-1.7426.90.9033509
1.68-1.7129.80.8773582
1.64-1.6836.60.8165169

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Processing

Software
NameVersionClassification
MOSFLM7.3.0data reduction
SCALA3.3.22data scaling
MOLREP11.7.02phasing
DM7.1.002phasing
REFMAC5.8.0266refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6SXY

6sxy


Resolution: 1.64→38.82 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.943 / SU B: 2.313 / SU ML: 0.076 / SU R Cruickshank DPI: 0.1104 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.11 / ESU R Free: 0.106 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.218 3825 4.9 %RANDOM
Rwork0.1875 ---
obs0.1889 74222 92.01 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 95.88 Å2 / Biso mean: 21.678 Å2 / Biso min: 7.32 Å2
Baniso -1Baniso -2Baniso -3
1--0.86 Å2-0 Å2-0.17 Å2
2--0.61 Å20 Å2
3---0.27 Å2
Refinement stepCycle: final / Resolution: 1.64→38.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5017 0 183 657 5857
Biso mean--36.37 35.05 -
Num. residues----664
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0125358
X-RAY DIFFRACTIONr_angle_refined_deg1.2131.6347230
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1745683
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.36122.115260
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.34815867
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3991535
X-RAY DIFFRACTIONr_chiral_restr0.0860.2683
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024077
LS refinement shellResolution: 1.64→1.683 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.371 299 -
Rwork0.389 5142 -
all-5441 -
obs--87.86 %

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