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- PDB-7lx1: The internal aldimine form of the wild-type Salmonella Typhimuriu... -

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Entry
Database: PDB / ID: 7lx1
TitleThe internal aldimine form of the wild-type Salmonella Typhimurium Tryptophan Synthase in complex with cesium ion at the metal coordination site at 1.61 Angstrom resolution
Components(Tryptophan synthase ...) x 2
KeywordsLYASE / internal aldimine
Function / homology
Function and homology information


tryptophan synthase / tryptophan synthase activity / tryptophan biosynthetic process / identical protein binding / cytoplasm / cytosol
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)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.61 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 in complex with cesium ion at the metal coordination site at 1.61 Angstrom resolution
Authors: Hilario, E. / Dunn, M.F. / Mueller, L.J.
History
DepositionMar 2, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 2, 2022Provider: 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)74,34735
Polymers71,6182
Non-polymers2,72933
Water10,809600
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)148,69370
Polymers143,2354
Non-polymers5,45866
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area20070 Å2
ΔGint-389 kcal/mol
Surface area44790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)182.332, 58.379, 67.229
Angle α, β, γ (deg.)90.000, 94.770, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-421-

CS

21B-731-

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

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Non-polymers , 7 types, 633 molecules

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


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


Mass: 78.133 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#7: Chemical
ChemComp-CS / CESIUM ION


Mass: 132.905 Da / Num. of mol.: 5 / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 600 / 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: 2.56 Å3/Da / Density % sol: 51.99 % / Description: large plate-like crystal
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7.8
Details: 50 mM Bicine-CsOH, 10% PEG 8,000, 2 mM Spermine, pH 7.8
PH range: 7.60-8.00 / 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: Oct 16, 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: 1.61→90.851 Å / Num. obs: 89475 / % possible obs: 98 % / Redundancy: 2.9 % / Rmerge(I) obs: 0.102 / Rpim(I) all: 0.079 / Rrim(I) all: 0.139 / Rsym value: 0.102 / Net I/av σ(I): 5.2 / Net I/σ(I): 5.1
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
1.61-1.72.60.4221.732006122350.3220.5550.4221.492.7
1.7-1.82.90.3432.135411122420.2510.4450.343297.6
1.8-1.922.90.2472.833678116130.1810.3210.247398.1
1.92-2.082.90.1943.531738108600.1380.2450.1944.298.8
2.08-2.282.90.1514.429397100390.1060.1870.1515.799.3
2.28-2.5530.1195.42705391600.0830.1480.1196.899.5
2.55-2.9430.0946.82429080980.0690.1230.094899.7
2.94-3.630.0659.52086868570.0510.090.0659.499.7
3.6-5.093.10.05111.21644953710.040.0710.05110.299.9
5.09-39.13930.0496906330000.0430.0740.04910.199.4

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Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.426
Highest resolutionLowest resolution
Rotation39.14 Å1.71 Å
Phasing dmMethod: Solvent flattening and Histogram matching / Reflection: 89475
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
8.73-10031.50.909606
6.17-8.7336.90.8931086
5.04-6.1733.60.8831386
4.36-5.0426.40.9161641
3.9-4.3622.90.9351847
3.56-3.923.10.9352030
3.3-3.5623.10.9212210
3.09-3.322.70.9232354
2.91-3.09240.9162528
2.76-2.9124.30.8992644
2.63-2.7622.90.9142771
2.52-2.6322.90.9142925
2.42-2.5223.80.913032
2.33-2.4221.90.9153100
2.25-2.3320.90.9283279
2.18-2.2521.20.9243324
2.12-2.1820.70.9293479
2.06-2.1221.60.9283543
2-2.0623.10.9223648
1.95-221.90.9313720
1.9-1.9523.20.9243821
1.86-1.924.50.9243883
1.82-1.8625.70.9213950
1.78-1.8228.20.924044
1.75-1.78290.9144142
1.71-1.7530.50.9174184
1.68-1.7131.70.9164226
1.65-1.6836.60.8954382
1.61-1.6544.80.8475690

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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: 4HT3

4ht3


Resolution: 1.61→39.14 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.927 / SU B: 4.844 / SU ML: 0.087 / SU R Cruickshank DPI: 0.0999 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.1 / ESU R Free: 0.1 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2342 4443 5 %RANDOM
Rwork0.1997 ---
obs0.2014 85032 97.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 114.75 Å2 / Biso mean: 20.354 Å2 / Biso min: 4.03 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å2-0 Å2-0.02 Å2
2---0 Å2-0 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 1.61→39.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4882 0 117 621 5620
Biso mean--36.77 29.57 -
Num. residues----648
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0125176
X-RAY DIFFRACTIONr_angle_refined_deg1.5111.6317002
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2565671
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.58122.411253
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.65815837
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.081532
X-RAY DIFFRACTIONr_chiral_restr0.1050.2670
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023977
LS refinement shellResolution: 1.61→1.652 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.328 292 -
Rwork0.328 5778 -
all-6070 -
obs--90.56 %
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)
10.3979-0.08370.0050.75220.14650.40590.0316-0.00940.01160.0789-0.00290.1208-0.14290.0249-0.02860.0986-0.00380.02480.0620.01030.104138.63317.79711.9732
20.76370.7731-0.20620.835-0.26010.40770.0277-0.0301-0.0209-0.0268-0.039-0.0024-0.02320.02690.01130.0732-0.0132-0.00080.1175-0.00330.084338.88652.93266.8196
30.5342-0.05470.11272.80540.8420.41610.2122-0.239-0.24380.012-0.0959-0.108-0.0553-0.1151-0.11640.1644-0.069-0.06630.15330.10270.137148.11694.750821.0831
46.4403-3.99512.91635.7404-2.35941.4333-0.1789-0.19770.3260.50210.0064-0.2083-0.2069-0.03040.17250.2156-0.0867-0.04460.1166-0.01150.028150.089823.980720.764
50.34940.01850.10780.00170.00150.4851-0.0137-0.0483-0.01010.00280.00330.00150.03360.02140.01040.05760.001-0.00250.11140.00540.076412.2773-13.817624.7184
62.3622-1.1574-0.72731.5192-0.27760.66750.2480.28890.32090.0136-0.1125-0.1176-0.1259-0.0895-0.13550.10480.02870.01770.16290.03570.095715.03513.540433.0421
70.30080.1795-0.02140.16540.1070.2819-0.0072-0.010.02930.01420.01190.02080.06250.0914-0.00470.05230.00560.00050.15050.00860.074816.1739-9.434223.8233
80.5556-0.1334-0.0690.03350.00530.1439-0.00210.01440.08470.0007-0.0113-0.0170.02230.04950.01340.0565-0.0166-0.00120.11750.00470.09339.479-3.91110.4525
90.9577-0.3131-0.32720.1160.180.67630.00260.0010.0424-0.02190.0077-0.0051-0.05810.0281-0.01020.0645-0.01210.00250.10040.00420.08152.4011-3.828912.4534
100.34310.17110.00890.1060.10450.64260.0375-0.01430.03120.00270.0071-0.0025-0.0602-0.0713-0.04450.07220.00610.01070.1303-0.00480.0728-6.6884-2.030516.3532
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A15 - 91
2X-RAY DIFFRACTION2A92 - 159
3X-RAY DIFFRACTION3A160 - 247
4X-RAY DIFFRACTION4A248 - 268
5X-RAY DIFFRACTION5B2 - 100
6X-RAY DIFFRACTION6B101 - 165
7X-RAY DIFFRACTION7B166 - 220
8X-RAY DIFFRACTION8B221 - 301
9X-RAY DIFFRACTION9B302 - 343
10X-RAY DIFFRACTION10B344 - 396

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