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- PDB-7l4d: The internal aldimine form of the wild-type Salmonella typhimuriu... -

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Basic information

Entry
Database: PDB / ID: 7l4d
TitleThe internal aldimine form of the wild-type Salmonella typhimurium Tryptophan Synthase with cesium ion at the metal coordination site at 1.60 Angstrom resolution
Components(Tryptophan synthase ...) x 2
KeywordsLYASE / internal aldimine / wild-type
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
: / DI(HYDROXYETHYL)ETHER / 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 / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.6 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)2R01GM097569-06A1 United States
CitationJournal: To be Published
Title: The internal aldimine form of the wild-type Salmonella typhimurium Tryptophan Synthase with cesium ion at the metal coordination site at 1.60 Angstrom resolution
Authors: Hilario, E. / Dunn, M.F. / Mueller, L.J.
History
DepositionDec 18, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 29, 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)75,39051
Polymers71,6182
Non-polymers3,77249
Water13,331740
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)150,780102
Polymers143,2354
Non-polymers7,54598
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area26690 Å2
ΔGint-246 kcal/mol
Surface area44360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)182.549, 59.188, 67.073
Angle α, β, γ (deg.)90.000, 94.480, 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 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, 789 molecules

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


Mass: 62.068 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical...
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 25 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cl
#7: Chemical ChemComp-CS / CESIUM ION


Mass: 132.905 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cs / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10NO6P / Feature type: SUBJECT OF INVESTIGATION
#9: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 740 / 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: 2.58 Å3/Da / Density % sol: 52.27 % / Description: Large plate-like crystal
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.8
Details: 50 mM Bicine-CsOH, 9% PEG 8,000, 2 mM Spermine, pH 7.8
PH range: 7.8 / Temp details: constant

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: constant / 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: Mar 23, 2020 / Details: VariMax HighFlux
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.598→90.995 Å / Num. obs: 86510 / % possible obs: 92 % / Redundancy: 2.6 % / Rmerge(I) obs: 0.03 / Rpim(I) all: 0.032 / Rrim(I) all: 0.053 / Rsym value: 0.03 / Net I/av σ(I): 7.3 / Net I/σ(I): 13.4
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
1.6-1.692.50.1295.426522104010.1030.170.1296.576.2
1.69-1.792.70.16.231460118030.0820.1360.18.391.3
1.79-1.912.70.0686.330008112320.0620.1020.06810.492.2
1.91-2.072.70.0523.728251105760.0490.0810.0521393.6
2.07-2.262.70.048.22636698710.040.0660.0415.194.6
2.26-2.532.70.03482418990730.0370.060.03416.595.8
2.53-2.922.70.02918.92152980650.0330.0540.02917.896.6
2.92-3.582.70.02511.21851769570.0270.0450.0251998
3.58-5.062.60.02117.61442654560.0230.0380.02119.998.9
5.06-39.0632.60.0218.8789030760.0290.0470.02119.499.2

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Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.429
Highest resolutionLowest resolution
Rotation39.06 Å1.78 Å
Phasing dmMethod: Solvent flattening and Histogram matching / Reflection: 86422
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
8.67-10036.60.895625
6.13-8.6743.10.8891124
5.01-6.1339.80.8871420
4.34-5.0128.40.9241672
3.88-4.3426.40.9291860
3.54-3.8826.70.9242086
3.28-3.5426.40.9172220
3.07-3.2827.20.9112398
2.89-3.0727.50.9072514
2.74-2.8927.40.9072667
2.61-2.7424.90.9092762
2.5-2.6124.10.9142918
2.41-2.523.10.9192991
2.32-2.4122.10.923112
2.24-2.32220.9243198
2.17-2.2421.40.9283310
2.1-2.1721.60.9243394
2.04-2.121.70.9223454
1.99-2.0421.30.9193555
1.94-1.9921.40.9173652
1.89-1.9421.20.9193705
1.85-1.8921.90.9153751
1.81-1.8521.40.9153871
1.77-1.8122.30.9073948
1.73-1.7722.60.9133953
1.7-1.73220.9164066
1.67-1.724.80.9064104
1.64-1.6727.50.8793962
1.6-1.6432.70.8694130

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Processing

Software
NameVersionClassification
xia20.5.902data reduction
SCALA3.3.22data scaling
MOLREP11.7.02phasing
DM7.0.078phasing
REFMAC5.8.0258refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7K0B

7k0b


Resolution: 1.6→39.06 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.953 / SU B: 2.719 / SU ML: 0.051 / SU R Cruickshank DPI: 0.0904 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.09 / ESU R Free: 0.088 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1947 4190 4.8 %RANDOM
Rwork0.168 ---
obs0.1693 82231 91.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 73.77 Å2 / Biso mean: 20.893 Å2 / Biso min: 3.61 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å2-0 Å2-0.01 Å2
2--0.01 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 1.6→39.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4921 0 187 774 5882
Biso mean--38.22 34.27 -
Num. residues----652
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0125274
X-RAY DIFFRACTIONr_angle_refined_deg1.5161.6337110
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3295675
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.61722.374257
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.98615851
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7231533
X-RAY DIFFRACTIONr_chiral_restr0.0980.2674
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.024015
LS refinement shellResolution: 1.6→1.641 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.221 235 -
Rwork0.205 4203 -
all-4438 -
obs--64.48 %
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)
11.7064-0.67190.48080.47750.00640.6717-0.02760.01640.03560.07380.00990.0139-0.13820.05940.01770.1191-0.01720.01050.0060.00220.050645.344320.543613.3096
20.78590.06980.26140.06650.16070.58450.0037-0.03330.05160.0401-0.03590.008-0.0003-0.08810.03210.0817-0.01660.02250.01860.00130.06832.898114.979715.5933
30.8650.8430.10331.1631-0.09990.19940.0230.05820.02230.0260.00010.0628-0.04940.0093-0.02310.06380.01320.01760.03530.00340.055438.079713.24774.4073
40.48140.4969-0.05130.6263-0.33190.7290.0173-0.0326-0.0394-0.0027-0.0353-0.0440.0017-0.00290.0180.06410.00490.00110.0232-0.00180.054239.6930.76346.9959
51.66960.6547-0.18881.525-0.31232.24580.1732-0.1984-0.1488-0.0741-0.0602-0.06540.06420.0469-0.1130.05-0.0257-0.04630.02520.02350.075346.8749-4.348717.2164
60.6962-0.50010.21993.79881.38830.7653-0.0238-0.0478-0.09340.32240.1243-0.07810.12710.0275-0.10050.08530.0122-0.00940.019-0.00480.057352.0502-0.210221.996
71.7288-1.40280.85421.9291-0.32280.61790.0371-0.1587-0.03640.04220.0136-0.02650.0024-0.1239-0.05070.1049-0.02960.01060.0483-0.00510.022946.14916.733924.1194
84.0621-3.64311.38564.3603-1.11230.6773-0.1079-0.08610.25070.22080.0053-0.1798-0.15710.04740.10260.1317-0.0533-0.02860.055-0.01710.037449.970424.321220.7805
90.5848-0.0122-0.30670.0152-0.0430.33340.006-0.0085-0.0538-0.0172-0.02980.00110.03950.11790.02370.05450.0138-0.01260.07910.00070.04127.9611-12.734319.4075
100.2991-0.15490.06480.1529-0.18430.3524-0.0183-0.0599-0.0242-0.01440.03750.00950.0653-0.0581-0.01920.0579-0.0088-0.010.04920.00840.04561.2984-17.313727.7447
110.25820.0320.30270.19660.1050.3819-0.0141-0.03720.01570.01840.0064-0.00850.004-0.03950.00770.05940.0011-0.00660.05440.00630.03356.0847-11.65727.6675
120.1069-0.1444-0.03590.9422-0.26570.82490.08850.01460.05140.04210.0027-0.0026-0.07140.006-0.09120.10110.00890.04660.0260.01960.051115.1953.411332.8719
130.180.08580.0170.08910.07210.11990.0078-0.01050.0006-0.0062-0.0053-0.00420.02590.0201-0.00250.06470.0022-0.0010.04230.00290.047111.1909-9.663918.3687
141.6825-0.1556-0.01240.1266-0.12230.13620.0199-0.02640.2053-0.0246-0.0129-0.01160.02840.0175-0.0070.042-0.01490.00520.025200.089716.6853.56349.5015
150.4632-0.0968-0.09120.0239-0.00960.34510.0086-0.0130.0258-0.00610.0089-0.0061-0.0191-0.0104-0.01750.0615-0.00310.00260.0321-0.00090.049-0.2168-4.066313.0099
160.52550.1385-0.07190.19320.20380.62760.0461-0.04870.03840.00220.04440.0166-0.0593-0.0001-0.09050.0580.00350.02290.05340.02050.0424-6.9967-0.791517.7749
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A14 - 43
2X-RAY DIFFRACTION2A44 - 77
3X-RAY DIFFRACTION3A78 - 110
4X-RAY DIFFRACTION4A111 - 159
5X-RAY DIFFRACTION5A160 - 192
6X-RAY DIFFRACTION6A193 - 216
7X-RAY DIFFRACTION7A217 - 247
8X-RAY DIFFRACTION8A248 - 268
9X-RAY DIFFRACTION9B2 - 37
10X-RAY DIFFRACTION10B38 - 70
11X-RAY DIFFRACTION11B71 - 100
12X-RAY DIFFRACTION12B101 - 165
13X-RAY DIFFRACTION13B166 - 269
14X-RAY DIFFRACTION14B270 - 301
15X-RAY DIFFRACTION15B302 - 364
16X-RAY DIFFRACTION16B365 - 396

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