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- PDB-7l5h: The external aldimine form of the wild-type Salmonella typhimuriu... -

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Basic information

Entry
Database: PDB / ID: 7l5h
TitleThe external aldimine form of the wild-type Salmonella typhimurium Tryptophan Synthase at 1.80 Angstrom resolution with cesium ion at the metal coordination site
Components(Tryptophan synthase ...) x 2
KeywordsLYASE / external 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
: / Chem-KOU / 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: 1.8 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 external aldimine form of the wild-type Salmonella typhimurium Tryptophan Synthase at 1.80 Angstrom resolution with cesium ion at the metal coordination site.
Authors: Hilario, E. / Dunn, M.F. / Mueller, L.J.
History
DepositionDec 22, 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)72,3589
Polymers71,6182
Non-polymers7407
Water6,900383
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)144,71618
Polymers143,2354
Non-polymers1,48114
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area9740 Å2
ΔGint-136 kcal/mol
Surface area41690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)182.620, 58.160, 67.170
Angle α, β, γ (deg.)90.000, 95.310, 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 , 6 types, 390 molecules

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


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-CS / CESIUM ION


Mass: 132.905 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cs / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / 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-DMS / DIMETHYL SULFOXIDE


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


Mass: 18.015 Da / Num. of mol.: 383 / 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: 2.55 Å3/Da / Density % sol: 51.87 % / 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
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: May 15, 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: 1.8→90.918 Å / Num. obs: 49845 / % possible obs: 76.6 % / Redundancy: 2.4 % / Rmerge(I) obs: 0.062 / Rpim(I) all: 0.054 / Rrim(I) all: 0.091 / Rsym value: 0.062 / Net I/av σ(I): 8.4 / Net I/σ(I): 6.7
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
1.8-1.92.50.4671.61709769580.410.6890.4671.273.7
1.9-2.012.40.3082.41591065080.2760.4650.3082.172.6
2.01-2.152.40.1834.11483961160.1640.2760.1833.672.6
2.15-2.322.40.135.61363656780.1160.1960.134.972.2
2.32-2.552.40.0917.71248551760.080.1360.0916.271.8
2.55-2.852.30.0768.91122747980.0640.1090.0767.773.5
2.85-3.292.20.0718.41036246620.060.10.0711080.1
3.29-4.022.30.04911.71016343850.0420.0690.0491490
4.02-5.692.50.0320.2893235740.0270.0460.0315.793.9
5.69-29.082.50.02917.8497219900.0250.0430.0291693.2

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Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.469
Highest resolutionLowest resolution
Rotation29.08 Å2.04 Å
Phasing dmMethod: Solvent flattening and Histogram matching / Reflection: 49733
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
8.89-10037.70.867519
6.57-8.8937.50.86766
5.45-6.57350.885983
4.76-5.4529.10.9021122
4.28-4.7623.20.9291266
3.92-4.28230.9171373
3.63-3.9221.10.9171461
3.41-3.6321.30.9241510
3.22-3.4122.70.8981577
3.05-3.2223.30.8981564
2.91-3.0522.80.8691561
2.79-2.9122.80.8831575
2.68-2.7923.10.8711600
2.59-2.6825.20.8691633
2.5-2.5923.50.8751701
2.42-2.523.40.8761745
2.35-2.4224.20.8581749
2.29-2.3524.40.8751863
2.23-2.2923.20.8831910
2.17-2.2322.50.8961935
2.12-2.1723.90.8882057
2.07-2.12230.8932050
2.03-2.0724.90.8752102
1.98-2.0326.40.8562166
1.94-1.9828.20.8522200
1.91-1.9428.20.8472227
1.87-1.9132.90.8122335
1.84-1.8734.30.8052336
1.8-1.8439.60.752847

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Processing

Software
NameVersionClassification
iMOSFLM7.2.2data reduction
SCALA3.3.22data scaling
MOLREP11.7.02phasing
DM7.0.078phasing
PHENIX1.7.1-3660refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6DUC

6duc


Resolution: 1.8→29.08 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 28.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2502 2511 5.05 %
Rwork0.2012 47222 -
obs0.2038 49733 76.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 126.22 Å2 / Biso mean: 42.3781 Å2 / Biso min: 11.76 Å2
Refinement stepCycle: final / Resolution: 1.8→29.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4791 0 38 390 5219
Biso mean--41.09 41.19 -
Num. residues----646
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 18

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8-1.830.35151130.3192553266674
1.83-1.870.39551350.3192499263473
1.87-1.910.33481200.30372502262273
1.91-1.960.32261340.26752480261473
1.96-2.010.2831170.2572481259872
2.01-2.060.32591440.23662446259072
2.06-2.120.27521340.23652504263873
2.12-2.190.29381350.22562474260973
2.19-2.270.24111360.22682459259572
2.27-2.360.25061390.22182474261372
2.36-2.470.30381190.21492453257271
2.47-2.60.28581410.20432459260072
2.6-2.760.27561410.21152485262673
2.76-2.970.2208970.22662595269274
2.97-3.270.25121470.20982804295181
3.27-3.740.26691790.17963062324188
3.74-4.710.19161860.1553192337892
4.71-29.080.21421940.173300349493
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)
11.00210.0261-0.31760.5299-0.28871.22940.3675-0.34810.11820.7099-0.37-0.07-0.43540.55010.15020.6366-0.32960.18490.4561-0.03980.719641.018915.967812.8562
21.30750.7396-0.43061.78790.5440.70620.2735-0.3033-0.03320.1259-0.3248-0.5802-0.11110.43710.08750.2229-0.07690.00210.37790.08520.394141.04752.81789.1497
31.1175-0.4152-0.10110.79310.00490.75010.3897-0.93550.1960.5566-0.3179-0.0855-0.47490.3487-0.06240.9324-0.5353-0.03940.9810.01460.769946.145818.260222.2857
41.03180.2595-0.43670.3177-0.00331.2190.0176-0.1758-0.06670.0763-0.0531-0.08530.0450.23160.03280.17590.0283-0.03830.18790.03360.174413.0822-12.861925.8174
50.720.2926-0.7241.0961-0.47072.07060.3804-0.11620.4002-0.1870.1080.1488-1.24790.3144-0.27910.6022-0.08760.11940.2919-0.05320.309114.04624.247730.5304
60.9825-0.1801-0.34570.4586-0.08811.16980.04170.02660.10070.0159-0.0165-0.0643-0.01370.0992-0.02810.14030.0051-0.01590.1515-0.00320.13676.8635-6.636514.1144
70.84560.16550.49290.6466-0.05431.87360.0467-0.01250.20010.12370.0120.1472-0.3248-0.3022-0.0470.2190.06310.03250.23530.03540.2115-7.3175-1.776817.2602
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 77 )A1 - 77
2X-RAY DIFFRACTION2chain 'A' and (resid 78 through 203 )A78 - 203
3X-RAY DIFFRACTION3chain 'A' and (resid 204 through 267 )A204 - 267
4X-RAY DIFFRACTION4chain 'B' and (resid 2 through 113 )B2 - 113
5X-RAY DIFFRACTION5chain 'B' and (resid 114 through 180 )B114 - 180
6X-RAY DIFFRACTION6chain 'B' and (resid 181 through 364 )B181 - 364
7X-RAY DIFFRACTION7chain 'B' and (resid 365 through 396 )B365 - 396

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