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- PDB-6oso: The crystal structure of the isolate tryptophan synthase alpha-ch... -

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Basic information

Entry
Database: PDB / ID: 6oso
TitleThe crystal structure of the isolate tryptophan synthase alpha-chain from Salmonella enterica serovar typhimurium at 1.75 Angstrom resolution
ComponentsTryptophan synthase alpha chain
KeywordsLYASE / tryptophan synthase / alpha-chain / wild-type / recombinant protein
Function / homology
Function and homology information


tryptophan synthase / tryptophan synthase activity / L-tryptophan biosynthetic process / cytosol
Similarity search - Function
Tryptophan synthase, alpha chain / Tryptophan synthase, alpha chain, active site / Tryptophan synthase alpha chain / Tryptophan synthase alpha chain signature. / Ribulose-phosphate binding barrel / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Tryptophan synthase alpha chain
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.75 Å
AuthorsHilario, E. / Dunn, M.F. / Mueller, L. / Chang, C. / Fan, L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)MCB-1350401 United States
CitationJournal: J.Biomol.Nmr / Year: 2020
Title: Backbone assignments and conformational dynamics in the S. typhimurium tryptophan synthase alpha-subunit from solution-state NMR.
Authors: Sakhrani, V.V. / Hilario, E. / Caulkins, B.G. / Hatcher-Skeers, M.E. / Fan, L. / Dunn, M.F. / Mueller, L.J.
History
DepositionMay 1, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 6, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 11, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,75816
Polymers28,6991
Non-polymers1,05915
Water5,729318
1
A: Tryptophan synthase alpha chain
hetero molecules

A: Tryptophan synthase alpha chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,51632
Polymers57,3982
Non-polymers2,11930
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_564x,x-y+1,-z-1/61
Buried area7010 Å2
ΔGint-302 kcal/mol
Surface area20480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.940, 70.940, 203.401
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-623-

HOH

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Components

#1: Protein Tryptophan synthase alpha chain


Mass: 28698.797 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Plasmid pEBA-10
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria)
Gene: trpA, STM1727 / Variant: LT2 / SGSC1412 / ATCC 700720 / Plasmid: pETSUMO / Details (production host): kanamycin / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta(DE3)pLysS / References: UniProt: P00929, tryptophan synthase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


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


Mass: 18.015 Da / Num. of mol.: 318 / Source method: isolated from a natural source / Formula: H2O

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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: 2.57 Å3/Da / Density % sol: 52.22 % / Description: Large triangle-like crystal
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 1.5-2.0 M ammonium sulfate / PH range: 7.0-7.5 / Temp details: constant

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: Oxford Cryosystems / 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: Nov 28, 2018 / Details: Varimax Confocal Max-Flux
RadiationMonochromator: Osmic Varimax HF ArcSec / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.75→61.436 Å / Num. all: 31527 / Num. obs: 31527 / % possible obs: 99.9 % / Redundancy: 12.8 % / Rpim(I) all: 0.023 / Rrim(I) all: 0.083 / Rsym value: 0.078 / Net I/av σ(I): 6.6 / Net I/σ(I): 18.2 / Num. measured all: 404229
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
1.75-1.8412.70.4871.65685744720.1440.5250.4874.499.8
1.84-1.9612.80.3322.25462742640.0980.3570.3326.799.9
1.96-2.0912.90.2213.25177240190.0640.2360.22110.4100
2.09-2.26130.1674.14865637560.0490.1780.16714100
2.26-2.47130.1315.24530734930.0380.1390.13117.5100
2.47-2.77130.0986.64133231750.0290.1040.09822.1100
2.77-3.2130.0659.73684228350.0190.070.06529.3100
3.2-3.9112.90.0649.63142424440.0190.0690.06438.9100
3.91-5.5312.60.0414.72447619440.0120.0430.0441.9100
5.53-19.60411.50.03514.21293611250.0110.0390.03536.697.5

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Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.508
Highest resolutionLowest resolution
Rotation19.6 Å1.97 Å
Phasing dmMethod: Solvent flattening and Histogram matching / Reflection: 31455
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
7.33-10032.70.916502
5.77-7.33450.87504
4.93-5.7734.80.904575
4.37-4.9326.30.933648
3.97-4.3726.40.934705
3.66-3.9724.50.944778
3.42-3.6627.10.933810
3.21-3.4223.60.923869
3.04-3.2126.30.902924
2.9-3.0423.30.924971
2.77-2.925.30.917996
2.66-2.7725.10.9121036
2.56-2.6623.10.9241075
2.47-2.5622.30.9351112
2.39-2.4720.90.9231159
2.32-2.3920.30.9231184
2.25-2.3218.50.9281228
2.19-2.2519.40.9411239
2.14-2.1918.60.9311283
2.08-2.14200.9321291
2.04-2.0819.30.9381364
1.99-2.0418.60.9361368
1.95-1.99200.9231403
1.91-1.95180.931415
1.87-1.9119.50.921450
1.84-1.8719.40.9161493
1.8-1.8423.80.9081497
1.75-1.829.70.8582576

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Processing

Software
NameVersionClassification
MOSFLM7.2.2data reduction
SCALA3.3.22data scaling
MOLREP11.6.04phasing
DM7.0.066phasing
PHENIX1.15.1-3469refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4KKX

4kkx


Resolution: 1.75→19.604 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 18.37
RfactorNum. reflection% reflection
Rfree0.2044 1579 5.02 %
Rwork0.1706 --
obs0.1724 31455 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 96.75 Å2 / Biso mean: 27.3165 Å2 / Biso min: 11.02 Å2
Refinement stepCycle: final / Resolution: 1.75→19.604 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1931 0 50 333 2314
Biso mean--53.24 38.78 -
Num. residues----258
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.75-1.80650.26731120.22522672278499
1.8065-1.8710.23751370.19592645278299
1.871-1.94580.21411360.180726492785100
1.9458-2.03430.19951430.171426722815100
2.0343-2.14140.19051510.164826512802100
2.1414-2.27540.19061330.158526922825100
2.2754-2.45080.221400.170527142854100
2.4508-2.69680.19431600.171226832843100
2.6968-3.08580.20461510.170827552906100
3.0858-3.88280.20551660.15827542920100
3.8828-19.6050.19931500.174229893139100
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)
11.20950.1385-0.25331.20450.4141.2431-0.03980.151-0.035-0.24040.00090.07030.03810.01520.04050.1895-0.0129-0.01210.11890.02870.1382-29.197113.724-1.3392
21.329-0.58210.44032.70160.0361.06740.03190.14420.1743-0.1464-0.04220.1995-0.0671-0.1020.01020.15360.0161-0.00490.20670.02230.1918-41.577224.4377-4.068
32.5913-0.4218-0.09161.3808-0.18490.79390.02280.15690.3935-0.1368-0.0522-0.134-0.11420.00820.04010.1733-0.03-0.02590.21660.03190.1861-25.120529.0812-0.5208
43.4406-1.8579-0.72846.4521.97652.6194-0.0292-0.0442-0.0520.09220.0548-0.37870.06670.20250.02270.1402-0.0225-0.01240.18070.03890.1801-14.716218.50644.1169
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 110 )A1 - 110
2X-RAY DIFFRACTION2chain 'A' and (resid 111 through 192 )A111 - 192
3X-RAY DIFFRACTION3chain 'A' and (resid 193 through 247 )A193 - 247
4X-RAY DIFFRACTION4chain 'A' and (resid 248 through 268 )A248 - 268

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