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- PDB-5kin: Crystal structure of tryptophan synthase alpha beta complex from ... -

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Basic information

Entry
Database: PDB / ID: 5kin
TitleCrystal structure of tryptophan synthase alpha beta complex from Streptococcus pneumoniae
Components
  • Tryptophan synthase alpha chain
  • Tryptophan synthase beta chain
KeywordsLYASE / Structural Genomics / CSGID / tryptophan synthase A / tryptophan synthase B / Center for Structural Genomics of Infectious Diseases
Function / homology
Function and homology information


L-tryptophan metabolic process / tryptophan synthase / tryptophan synthase activity / 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. / Rossmann fold - #1100 / Pyridoxal-phosphate 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. / Rossmann fold - #1100 / Pyridoxal-phosphate dependent enzyme / Pyridoxal-phosphate dependent enzyme / Tryptophan synthase beta subunit-like PLP-dependent enzyme / Ribulose-phosphate binding barrel / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Tryptophan synthase beta chain / Tryptophan synthase alpha chain
Similarity search - Component
Biological speciesStreptococcus pneumoniae serotype 4 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsChang, C. / Michalska, K. / Bigelow, L. / Jedrzejczak, R. / ANDERSON, W.F. / JOACHIMIAK, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: Iucrj / Year: 2019
Title: Conservation of the structure and function of bacterial tryptophan synthases.
Authors: Michalska, K. / Gale, J. / Joachimiak, G. / Chang, C. / Hatzos-Skintges, C. / Nocek, B. / Johnston, S.E. / Bigelow, L. / Bajrami, B. / Jedrzejczak, R.P. / Wellington, S. / Hung, D.T. / Nag, ...Authors: Michalska, K. / Gale, J. / Joachimiak, G. / Chang, C. / Hatzos-Skintges, C. / Nocek, B. / Johnston, S.E. / Bigelow, L. / Bajrami, B. / Jedrzejczak, R.P. / Wellington, S. / Hung, D.T. / Nag, P.P. / Fisher, S.L. / Endres, M. / Joachimiak, A.
History
DepositionJun 16, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 6, 2016Provider: repository / Type: Initial release
Revision 2.0May 9, 2018Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / entity / entity_poly / entity_poly_seq / entity_src_gen / pdbx_poly_seq_scheme / pdbx_prerelease_seq / pdbx_struct_mod_residue / pdbx_struct_oper_list / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / struct_conf / struct_conn / struct_mon_prot_cis / struct_ref / struct_ref_seq / struct_ref_seq_dif / struct_sheet_range / struct_site_gen
Item: _atom_site.label_seq_id / _atom_site_anisotrop.pdbx_label_seq_id ..._atom_site.label_seq_id / _atom_site_anisotrop.pdbx_label_seq_id / _entity.formula_weight / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _pdbx_struct_mod_residue.label_seq_id / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _pdbx_unobs_or_zero_occ_atoms.label_seq_id / _struct_conf.beg_label_seq_id / _struct_conf.end_label_seq_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_label_seq_id / _struct_mon_prot_cis.label_seq_id / _struct_mon_prot_cis.pdbx_label_seq_id_2 / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq.seq_align_beg / _struct_ref_seq.seq_align_end / _struct_sheet_range.beg_label_seq_id / _struct_sheet_range.end_label_seq_id / _struct_site_gen.label_seq_id
Revision 3.0Sep 18, 2019Group: Data collection / Database references / Polymer sequence
Category: citation / citation_author ...citation / citation_author / entity_poly / pdbx_database_related
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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 / _entity_poly.pdbx_target_identifier
Revision 3.1Sep 27, 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
Revision 3.2Nov 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
C: Tryptophan synthase alpha chain
D: Tryptophan synthase beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,7467
Polymers144,4694
Non-polymers2763
Water1,964109
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9360 Å2
ΔGint-38 kcal/mol
Surface area47710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.697, 71.160, 138.682
Angle α, β, γ (deg.)90.000, 101.690, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Tryptophan synthase alpha chain


Mass: 27765.680 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4) (bacteria)
Strain: ATCC BAA-334 / TIGR4 / Gene: trpA, SP_1811 / Plasmid: pMCSG68 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q97P33, tryptophan synthase
#2: Protein Tryptophan synthase beta chain


Mass: 44469.051 Da / Num. of mol.: 2 / Fragment: UNP residues 4-402
Source method: isolated from a genetically manipulated source
Details: modified residue 91 LLP
Source: (gene. exp.) Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4) (bacteria)
Strain: ATCC BAA-334 / TIGR4 / Gene: trpB, SP_1812 / Plasmid: pMCSG68 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q97P32, tryptophan synthase
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 109 / 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: 2.29 Å3/Da / Density % sol: 46.29 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.2 M Ammonium Acetate, 0.1 M Tris-Cl, 25% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9793373 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 16, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793373 Å / Relative weight: 1
ReflectionResolution: 2.45→50 Å / Num. obs: 48447 / % possible obs: 99.7 % / Redundancy: 3.6 % / Biso Wilson estimate: 38.88 Å2 / Rmerge(I) obs: 0.141 / Rpim(I) all: 0.088 / Rrim(I) all: 0.166 / Χ2: 1.69 / Net I/av σ(I): 14.277 / Net I/σ(I): 7.4 / Num. measured all: 174816
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.45-2.493.30.7423860.6830.4720.880.84199.8
2.49-2.543.50.72124120.7090.4510.8520.851100
2.54-2.593.70.70424040.7080.4360.8310.85199.9
2.59-2.643.70.66124130.760.4030.7760.846100
2.64-2.73.70.5923860.7970.3620.6931.014100
2.7-2.763.70.48424410.8570.2960.5690.995100
2.76-2.833.70.45324130.8540.2750.531.06100
2.83-2.93.70.39524210.9050.2420.4641.084100
2.9-2.993.70.3324290.9060.20.3871.122100
2.99-3.093.70.27324220.9260.1670.3211.248100
3.09-3.23.70.22323910.9490.1360.2621.42799.9
3.2-3.323.70.18624240.9490.1150.2191.592100
3.32-3.483.70.15724110.9480.0970.1861.78399.9
3.48-3.663.60.12424390.9810.0760.1462.00999.8
3.66-3.893.60.11124260.9810.070.1322.41399.8
3.89-4.193.60.09824400.9790.0620.1172.79399.6
4.19-4.613.50.08224110.9860.0520.0983.00399.3
4.61-5.283.40.07424440.9870.0480.0892.93299.3
5.28-6.653.40.07824520.9880.050.0932.78499.5
6.65-503.30.05724820.9910.0370.0683.64297.8

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Processing

Software
NameVersionClassification
PHENIXdev_2386refinement
SCALEPACKdata scaling
PDB_EXTRACT3.2data extraction
HKL-3000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4NEG

4neg


Resolution: 2.45→49.126 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2275 2264 4.76 %
Rwork0.1805 45342 -
obs0.1828 47606 99.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 135.16 Å2 / Biso mean: 49.1718 Å2 / Biso min: 12.06 Å2
Refinement stepCycle: final / Resolution: 2.45→49.126 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9877 0 18 109 10004
Biso mean--63.01 40.13 -
Num. residues----1297
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00210113
X-RAY DIFFRACTIONf_angle_d0.50813715
X-RAY DIFFRACTIONf_chiral_restr0.041552
X-RAY DIFFRACTIONf_plane_restr0.0031797
X-RAY DIFFRACTIONf_dihedral_angle_d12.4946033
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 16

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.45-2.50330.3121430.26728112954100
2.5033-2.56160.33181450.253727982943100
2.5616-2.62560.3341580.259428162974100
2.6256-2.69660.31671560.2527852941100
2.6966-2.77590.33581570.243828172974100
2.7759-2.86550.31371320.237628412973100
2.8655-2.96790.27521300.229628402970100
2.9679-3.08670.28481340.2228673001100
3.0867-3.22720.28671270.215828352962100
3.2272-3.39730.23011300.206928522982100
3.3973-3.61010.25791150.182128482963100
3.6101-3.88870.20291320.167728222954100
3.8887-4.27990.18061420.143228552997100
4.2799-4.89870.17221630.13042823298699
4.8987-6.16990.18321630.14522834299799
6.1699-49.1360.16351370.1372898303598
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)
10.3107-0.11540.39871.6305-0.21591.1430.16070.1390.007-0.47060.2030.57820.0297-0.55520.14110.60090.0907-0.12630.71930.00580.322446.687742.8314-2.466
20.77350.15370.43660.4215-0.31670.63140.11940.2611-0.2334-0.1948-0.04690.030.1171-0.117100.60250.0877-0.07360.6952-0.13160.349756.602938.90844.266
30.34650.21370.02160.1622-0.01630.033-0.48730.30440.65620.01520.18960.0766-0.44440.0476-0.00670.76970.1941-0.11080.7507-0.03380.510951.338560.37611.2499
40.01660.01020.00760.00620.00930.01470.08980.0034-0.1698-0.14980.44320.0460.18620.29190.00020.90150.0846-0.07921.5426-0.19010.940836.571452.8825.2701
50.194-0.22880.03680.2701-0.02660.14140.01020.04140.0107-0.2776-0.24280.7075-0.0106-0.4748-0.00720.7040.0314-0.11840.8853-0.02120.478236.619443.43374.3333
60.677-0.39380.05110.84340.19810.99550.05110.2440.1385-0.1803-0.1978-0.1327-0.1903-0.1449-0.00310.21240.07690.03370.23340.04720.19275.779760.987631.2555
70.4102-0.3466-0.34180.89490.43661.47030.09360.2786-0.1419-0.0898-0.23230.00080.2151-0.7103-0.06240.27860.1485-0.04190.4895-0.1080.277858.009158.586931.8623
80.5551-0.2260.05110.1562-0.06040.62880.14820.15990.0347-0.0623-0.0724-0.0948-0.0538-0.02400.25760.04370.03970.2270.02720.261584.577756.658832.1698
90.3520.06910.3692-0.00030.06440.39390.24360.2287-0.1120.0482-0.20090.02350.249-0.0462-00.48230.0494-0.01230.4545-0.01220.337872.796841.384624.4873
100.2739-0.13530.27750.60930.4050.83640.18980.0132-0.04370.0991-0.0815-0.07020.1759-0.153800.23170.00980.01070.18910.02250.251478.953143.141244.61
111.3664-0.3952-0.02871.1122-0.08110.6285-0.0446-0.1816-0.01010.19270.0567-0.0678-0.1003-0.0100.2609-0.05790.02980.2481-0.04910.210564.681455.9423102.0392
120.4450.4164-0.42230.5665-0.57830.820.1068-0.3751-0.05610.1721-0.1735-0.26780.01810.5344-0.01290.3391-0.0089-0.03340.3675-0.00430.31283.206854.971498.9224
130.3656-0.0406-0.43810.23-0.0490.5708-0.1717-0.3706-0.210.2363-0.0359-0.10780.08620.13020.00010.3270.0103-0.0070.3160.03650.37373.088340.4871103.954
140.12040.05040.14390.2326-0.1150.2985-0.0121-0.22680.0920.15990.0149-0.2174-0.30190.1397-00.276-0.0339-0.03180.2378-0.02830.300882.008866.383181.1511
150.1972-0.06980.0790.0273-0.01150.26960.0856-0.02350.013-0.0577-0.1025-0.0388-0.237-0.19010.00430.15010.06160.03480.15380.02450.248574.881169.049753.8505
160.3887-0.0540.05260.57810.64531.29720.0275-0.0954-0.01930.0741-0.166-0.09350.1497-0.3562-0.05270.1238-0.06170.00940.11240.00170.217475.52951.001469.5772
170.4032-0.15290.21680.76360.52620.62040.0055-0.03080.0540.017-0.0447-0.0273-0.2521-0.1169-0.00140.18820.02950.04080.12140.00010.265872.976776.632162.5326
180.02930.0824-0.15770.1842-0.36050.67450.084-0.1463-0.120.1318-0.0468-0.0995-0.0547-0.3008-0.00020.26030.00540.01020.2818-0.040.298460.637168.03676.7422
190.57560.056-0.01660.20710.29310.4368-0.11930.20990.1307-0.0867-0.22560.1414-0.0849-0.1762-0.16390.17730.112-0.01830.2751-0.04890.323155.094469.334356.8988
200.53590.11750.58070.6381-0.20260.78640.11750.00120.07570.3752-0.08480.01990.0558-0.36880.00190.19390.04750.03730.3032-0.01080.227457.505167.986255.606
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 31 )A2 - 31
2X-RAY DIFFRACTION2chain 'A' and (resid 32 through 151 )A32 - 151
3X-RAY DIFFRACTION3chain 'A' and (resid 152 through 210 )A152 - 210
4X-RAY DIFFRACTION4chain 'A' and (resid 211 through 224 )A211 - 224
5X-RAY DIFFRACTION5chain 'A' and (resid 225 through 258 )A225 - 258
6X-RAY DIFFRACTION6chain 'B' and (resid 4 through 92 )B4 - 92
7X-RAY DIFFRACTION7chain 'B' and (resid 93 through 200 )B93 - 200
8X-RAY DIFFRACTION8chain 'B' and (resid 201 through 264 )B201 - 264
9X-RAY DIFFRACTION9chain 'B' and (resid 265 through 327 )B265 - 327
10X-RAY DIFFRACTION10chain 'B' and (resid 328 through 402 )B328 - 402
11X-RAY DIFFRACTION11chain 'C' and (resid 1 through 138 )C1 - 138
12X-RAY DIFFRACTION12chain 'C' and (resid 139 through 203 )C139 - 203
13X-RAY DIFFRACTION13chain 'C' and (resid 204 through 258 )C204 - 258
14X-RAY DIFFRACTION14chain 'D' and (resid 4 through 39 )D4 - 39
15X-RAY DIFFRACTION15chain 'D' and (resid 40 through 92 )D40 - 92
16X-RAY DIFFRACTION16chain 'D' and (resid 93 through 200 )D93 - 200
17X-RAY DIFFRACTION17chain 'D' and (resid 201 through 264 )D201 - 264
18X-RAY DIFFRACTION18chain 'D' and (resid 265 through 327 )D265 - 327
19X-RAY DIFFRACTION19chain 'D' and (resid 328 through 348 )D328 - 348
20X-RAY DIFFRACTION20chain 'D' and (resid 349 through 402 )D349 - 402

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