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- PDB-6wdu: The external aldimine form of the Salmonella thypi wild-type tryp... -

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Basic information

Entry
Database: PDB / ID: 6wdu
TitleThe external aldimine form of the Salmonella thypi wild-type tryptophan synthase in open conformation showing multiple side chain conformations for the residue beta Q114 and sodium ion at the metal coordination site. One of the beta-Q114 rotamer conformations 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 / protein complex / LYASE / LYASE-LYASE INHIBITOR complex
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. / 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-KOU / DI(HYDROXYETHYL)ETHER / Tryptophan synthase alpha chain / Tryptophan synthase beta chain
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.4 Å
AuthorsHilario, E. / Fan, L. / Dunn, M.F. / Mueller, L.J.
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: The external aldimine form of the Salmonella thypi wild-type tryptophan synthase in open conformation showing multiple side chain conformations for the residue beta Q114 and sodium ion at the ...Title: The external aldimine form of the Salmonella thypi wild-type tryptophan synthase in open conformation showing multiple side chain conformations for the residue beta Q114 and sodium ion at the metal coordination site. One of the beta-Q114 rotamer conformations allows a hydrogen bond to form with the PLP oxygen at the position 3 in the ring.
Authors: Hilario, E. / Fan, L. / Dunn, M.F. / Mueller, L.J.
History
DepositionApr 1, 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)73,80129
Polymers71,6182
Non-polymers2,18327
Water13,565753
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, Protein is a dimer of dimer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7450 Å2
ΔGint16 kcal/mol
Surface area23790 Å2
Unit cell
Length a, b, c (Å)182.655, 59.415, 67.345
Angle α, β, γ (deg.)90.000, 94.890, 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: 42918.879 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: 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 , 6 types, 780 molecules

#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#7: 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
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 753 / 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: 2.34 Å3/Da / Density % sol: 47.5 % / Description: Large plate-like crystal (200 x 200 x 100)
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.8
Details: 50 mM Bicine-NaOH, 10% PEG 8,000, 2 mM Spermine, pH 7.8, 50mM NaCl
PH range: 7.60-8.00 / Temp details: near 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: Apr 18, 2019
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.398→90.995 Å / Num. all: 141196 / Num. obs: 141196 / % possible obs: 99.6 % / Redundancy: 5.6 % / Rpim(I) all: 0.042 / Rrim(I) all: 0.102 / Rsym value: 0.093 / Net I/av σ(I): 5.5 / Net I/σ(I): 9 / Num. measured all: 793906
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
1.4-1.485.30.920.8107971202970.4181.0140.921.598.4
1.48-1.575.40.5971.3105249194640.2740.6590.5972.499.6
1.57-1.675.60.3931.9101747182810.180.4340.3933.799.9
1.67-1.815.70.253397441170770.1150.2790.2535.699.9
1.81-1.985.80.1574.790776157510.0710.1720.1578.7100
1.98-2.215.80.1036.782795142420.0470.1130.10312.8100
2.21-2.565.70.0788.471336126060.0360.0870.07815.9100
2.56-3.135.40.0767.957348106690.0360.0840.07618.6100
3.13-4.436.30.055115183882810.0240.060.05523.6100
4.43-36.886.10.04214.22740545280.0180.0460.04223.797.5

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation6.46 Å36.88 Å
Translation6.46 Å36.88 Å
Phasing dmMethod: Solvent flattening and Histogram matching / Reflection: 141195
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
7.58-10037.70.903834
5.36-7.5836.70.8971686
4.37-5.3626.20.9332166
3.79-4.3723.90.9452524
3.39-3.7921.80.9382881
3.09-3.39240.923155
2.86-3.0924.20.9133456
2.68-2.8624.70.9143666
2.53-2.6823.70.9163925
2.4-2.5323.20.9174107
2.28-2.4210.9274369
2.19-2.2821.90.9254538
2.1-2.1920.60.9364724
2.03-2.121.90.9254914
1.96-2.0322.90.9125100
1.89-1.9622.60.9165264
1.84-1.8923.60.9045447
1.79-1.8424.70.8995541
1.74-1.7925.60.8955736
1.69-1.7427.30.8935863
1.65-1.6928.80.8926028
1.62-1.6530.70.8726203
1.58-1.6231.60.8736328
1.55-1.5832.60.8676454
1.52-1.55350.8566563
1.49-1.5237.60.846665
1.46-1.4938.80.8366819
1.43-1.4641.10.816845
1.4-1.43460.7599394

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Processing

Software
NameVersionClassification
SCALA3.3.22data scaling
PHASER2.8.3phasing
DM7.0.078phasing
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4HN4

4hn4


Resolution: 1.4→36.91 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.96 / SU B: 3.027 / SU ML: 0.051 / SU R Cruickshank DPI: 0.0638 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.064 / ESU R Free: 0.059 / Details: U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1949 6919 4.9 %RANDOM
Rwork0.1618 ---
obs0.1634 134277 99.38 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 58.62 Å2 / Biso mean: 22.033 Å2 / Biso min: 9.56 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å2-0 Å20.01 Å2
2---0.05 Å2-0 Å2
3---0.02 Å2
Refinement stepCycle: final / Resolution: 1.4→36.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4906 0 126 790 5822
Biso mean--32.18 33.22 -
Num. residues----650
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0125402
X-RAY DIFFRACTIONr_angle_refined_deg1.5261.6387316
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2425706
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.46622.481266
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.38515891
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7071534
X-RAY DIFFRACTIONr_chiral_restr0.1010.2693
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.024173
X-RAY DIFFRACTIONr_rigid_bond_restr7.31135402
LS refinement shellResolution: 1.4→1.434 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.323 501 -
Rwork0.293 9495 -
obs--95.6 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
17.21071.9121.44092.55121.64395.95750.0957-0.1149-0.16020.2458-0.0810.23440.3009-0.5161-0.01470.11910.01070.0270.2469-0.0080.2688-59.822-21.6825.761
21.196-0.6601-0.02191.9983-0.25640.7440.09070.05250.1237-0.0844-0.0768-0.0075-0.0969-0.0208-0.01390.04370.0120.01880.2099-0.01160.1409-41.58-19.06824.02
31.40040.07440.38595.3355-0.95541.98650.02250.2447-0.2395-0.56780.03370.01720.3442-0.1574-0.05620.14380.0077-0.04010.2916-0.0370.2431-52.252-32.43413.59
43.26221.84051.15022.78530.64331.3010.07730.06320.2306-0.238-0.08290.0653-0.1873-0.05930.00560.15830.0425-0.02550.26480.02270.1963-50.223-9.83510.945
51.83-0.0308-1.00040.64940.99942.1216-0.0380.0684-0.24350.0338-0.16460.11440.1159-0.36970.20260.0349-0.0272-0.05010.26060.0210.1659-30.614-42.75713.98
61.33720.09690.10380.62930.10471.4721-0.00910.1952-0.11060.00370.01940.02380.11730.143-0.01040.0230.0125-0.00550.1294-0.00470.0532-4.019-47.1945.67
71.6549-0.37630.71410.4752-0.24771.11270.02960.1318-0.0093-0.0429-0.01810.03060.0192-0.0189-0.01150.0093-0.0024-0.01490.1801-0.01510.033-8.798-41.5855.787
81.0273-0.034-0.06872.16080.43561.90520.10160.06370.1831-0.12640.01210.0276-0.3602-0.1251-0.11370.1130.03050.01250.24520.01780.106-17.486-26.7010.806
91.15610.1754-0.07450.34270.15221.01390.01440.01220.0928-0.0023-0.01280.0333-0.0365-0.0614-0.00150.0057-0.0034-0.01060.15630.00310.0417-11.047-35.65418.446
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 13
2X-RAY DIFFRACTION2A14 - 159
3X-RAY DIFFRACTION3A160 - 216
4X-RAY DIFFRACTION4A217 - 267
5X-RAY DIFFRACTION5B2 - 37
6X-RAY DIFFRACTION6B38 - 70
7X-RAY DIFFRACTION7B71 - 100
8X-RAY DIFFRACTION8B101 - 165
9X-RAY DIFFRACTION9B166 - 365

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