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- PDB-6v82: Crystal structure of tryptophan synthase from Chlamydia trachomat... -

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Basic information

Entry
Database: PDB / ID: 6v82
TitleCrystal structure of tryptophan synthase from Chlamydia trachomatis D/UW-3/CX
Components
  • Tryptophan synthase alpha chain
  • Tryptophan synthase beta chain
KeywordsLYASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


tryptophan synthase / tryptophan synthase activity / tryptophan biosynthetic process / 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
sucrose / Tryptophan synthase beta chain / Tryptophan synthase alpha chain
Similarity search - Component
Biological speciesChlamydia trachomatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.424 Å
AuthorsMichalska, K. / Maltseva, N. / Jedrzejczak, R. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201700060C United States
CitationJournal: Protein Sci. / Year: 2021
Title: Catalytically impaired TrpA subunit of tryptophan synthase from Chlamydia trachomatis is an allosteric regulator of TrpB.
Authors: Michalska, K. / Wellington, S. / Maltseva, N. / Jedrzejczak, R. / Selem-Mojica, N. / Rosas-Becerra, L.R. / Barona-Gomez, F. / Hung, D.T. / Joachimiak, A.
History
DepositionDec 10, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 16, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 30, 2021Group: 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Sep 1, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 11, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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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)71,8616
Polymers70,9852
Non-polymers8774
Water3,999222
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)143,72312
Polymers141,9704
Non-polymers1,7538
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area10840 Å2
ΔGint-81 kcal/mol
Surface area45460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.923, 133.901, 128.428
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-548-

HOH

21B-665-

HOH

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Components

#1: Protein Tryptophan synthase alpha chain


Mass: 28083.996 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlamydia trachomatis (strain D/UW-3/Cx) (bacteria)
Strain: D/UW-3/Cx / Gene: trpA, CT_171 / Plasmid: pMCSG91 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Gold / References: UniProt: O84173, tryptophan synthase
#2: Protein Tryptophan synthase beta chain


Mass: 42900.777 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlamydia trachomatis (strain D/UW-3/Cx) (bacteria)
Strain: D/UW-3/Cx / Gene: trpB, CT_170 / Plasmid: pMCSG91 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Gold / References: UniProt: O84172, tryptophan synthase
#3: Polysaccharide beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose / sucrose /


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with reducing-end-to-reducing-end glycosidic bond
References: sucrose
DescriptorTypeProgram
DFrufb2-1DGlcpaGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[ha122h-2b_2-5][a2122h-1a_1-5]/1-2/a2-b1WURCSPDB2Glycan 1.1.0
[][b-D-Fruf]{[(2+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 222 / Source method: isolated from a natural source / Formula: H2O
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: 3.48 Å3/Da / Density % sol: 64.66 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 1.0 M ammonium sulfate, 0.1 M HEPES pH 7.0, 0.5% PEG8000, 3% 1,5-diaminopentane dihydrochloride, cryo saturated sucrose

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Oct 6, 2017 / Details: mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.42→30 Å / Num. obs: 37871 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 11.4 % / Biso Wilson estimate: 27.25 Å2 / CC1/2: 0.653 / Rmerge(I) obs: 0.342 / Net I/σ(I): 9.9
Reflection shellResolution: 2.42→2.46 Å / Redundancy: 6.2 % / Rmerge(I) obs: 1.356 / Mean I/σ(I) obs: 1.55 / Num. unique obs: 1857 / CC1/2: 0.653 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(dev_2947: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5KZM

5kzm


Resolution: 2.424→29.836 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 20.53 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.194 1876 4.96 %
Rwork0.1593 --
obs0.1611 37837 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.424→29.836 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4925 0 56 222 5203
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075095
X-RAY DIFFRACTIONf_angle_d0.9316921
X-RAY DIFFRACTIONf_dihedral_angle_d16.5193026
X-RAY DIFFRACTIONf_chiral_restr0.051785
X-RAY DIFFRACTIONf_plane_restr0.006890
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4239-2.48940.31551430.24982703X-RAY DIFFRACTION99
2.4894-2.56260.29121370.22382736X-RAY DIFFRACTION100
2.5626-2.64520.28781220.21682760X-RAY DIFFRACTION100
2.6452-2.73970.23371410.20372756X-RAY DIFFRACTION100
2.7397-2.84930.2241270.19932766X-RAY DIFFRACTION100
2.8493-2.97890.23291360.18362732X-RAY DIFFRACTION100
2.9789-3.13580.23851510.17922757X-RAY DIFFRACTION100
3.1358-3.3320.22161520.17372725X-RAY DIFFRACTION100
3.332-3.58890.19181490.1572776X-RAY DIFFRACTION100
3.5889-3.94930.16331520.12652766X-RAY DIFFRACTION100
3.9493-4.51910.15251470.10832775X-RAY DIFFRACTION100
4.5191-5.68720.13721540.1162803X-RAY DIFFRACTION100
5.6872-29.83850.14761650.14862906X-RAY DIFFRACTION100
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)
17.59320.2245-0.47855.00660.20264.18910.13810.0356-0.1654-0.037-0.14670.93140.1215-0.66410.04010.26540.06820.05420.2731-0.04360.369712.399332.425164.6367
23.9861-1.6223-0.44584.3390.32833.23350.0082-0.10350.1249-0.02030.0231-0.0524-0.1465-0.0156-0.04490.20260.02060.02720.2027-0.04340.171225.01332.926266.4828
34.7843-1.09030.08085.2972-1.42628.5787-0.01220.1361-1.554-0.19050.04530.35931.6147-0.37070.01460.5549-0.01670.03170.2941-0.00330.677423.13739.94362.8078
45.44010.40151.64924.2164-1.04747.92140.30070.0463-0.5925-0.0897-0.23410.21990.8251-0.0903-0.04140.32730.08630.04890.3014-0.02160.318919.007116.827966.1481
53.42081.04610.56182.810.33714.8190.3190.46-1.1178-0.9826-0.24440.29421.1776-0.452-0.06690.58780.0164-0.02860.4344-0.22450.721313.488914.812959.5332
62.95090.72770.09064.3579-0.78173.35320.13660.6712-1.0823-1.25830.02951.52181.3518-1.308-0.33150.7064-0.0432-0.14860.7459-0.31471.12243.150316.350954.595
74.02881.06570.16115.1801-0.73033.62440.08230.83320.2645-0.68070.01890.6517-0.329-0.3812-0.02690.40290.2094-0.03760.4969-0.03530.374412.303736.372954.0616
83.8576-0.8118-1.13945.69552.80016.51520.0365-0.1882-0.07810.2265-0.29670.41090.1959-0.68460.23760.1815-0.08060.09090.28080.0450.215430.57857.753453.8972
90.6276-0.1432-0.11040.38570.06261.20010.0376-0.02130.09310.0145-0.02610.0425-0.0729-0.1057-0.00380.1571-0.01110.00550.1582-0.01880.156148.745312.833846.5232
101.5873-0.06850.19261.8225-0.76482.1937-0.0036-0.03970.3160.1094-0.1339-0.1642-0.21370.16270.01830.21420.00780.01770.216-0.01380.186664.996617.240646.0617
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 24 )
2X-RAY DIFFRACTION2chain 'A' and (resid 25 through 122 )
3X-RAY DIFFRACTION3chain 'A' and (resid 123 through 135 )
4X-RAY DIFFRACTION4chain 'A' and (resid 136 through 157 )
5X-RAY DIFFRACTION5chain 'A' and (resid 158 through 185 )
6X-RAY DIFFRACTION6chain 'A' and (resid 186 through 198 )
7X-RAY DIFFRACTION7chain 'A' and (resid 199 through 253 )
8X-RAY DIFFRACTION8chain 'B' and (resid 2 through 33 )
9X-RAY DIFFRACTION9chain 'B' and (resid 34 through 361 )
10X-RAY DIFFRACTION10chain 'B' and (resid 362 through 392 )

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