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- PDB-5kzm: Crystal structure of Tryptophan synthase alpha-beta chain complex... -

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Basic information

Entry
Database: PDB / ID: 5kzm
TitleCrystal structure of Tryptophan synthase alpha-beta chain complex from Francisella tularensis
Components
  • Tryptophan synthase alpha chain
  • Tryptophan synthase beta chain
KeywordsLYASE / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


tryptophan synthase / tryptophan synthase activity
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 / Tryptophan synthase beta subunit-like PLP-dependent enzyme / Pyridoxal-phosphate 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
ACETATE ION / Tryptophan synthase beta chain / Tryptophan synthase alpha chain
Similarity search - Component
Biological speciesFrancisella tularensis subsp. tularensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.804 Å
AuthorsChang, C. / Michalska, K. / Joachimiak, G. / 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
DepositionJul 25, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 10, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 7, 2016Group: Database references / Structure summary
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 / atom_type / entity / entity_poly / entity_poly_seq / entity_src_gen / pdbx_poly_seq_scheme / pdbx_struct_conn_angle / 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_gene_src_scientific_name / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_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_align_begin / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.pdbx_auth_seq_align_beg / _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 2.1Sep 18, 2019Group: Data collection / Database references
Category: citation / citation_author / 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

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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)73,5325
Polymers73,3932
Non-polymers1393
Water18010
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)147,06410
Polymers146,7854
Non-polymers2786
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556x,-y,-z+11
Buried area9980 Å2
ΔGint-67 kcal/mol
Surface area46330 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3100 Å2
ΔGint-27 kcal/mol
Surface area25060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.176, 171.986, 76.109
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-508-

HOH

DetailsUnknown

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Components

#1: Protein Tryptophan synthase alpha chain


Mass: 29556.131 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Francisella tularensis subsp. tularensis (bacteria)
Strain: SCHU S4 / Schu 4 / Gene: trpA, FTT_1772c / Plasmid: pMCSG68 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q5NE80, tryptophan synthase
#2: Protein Tryptophan synthase beta chain


Mass: 43836.512 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Francisella tularensis subsp. tularensis (strain SCHU S4 / Schu 4) (bacteria)
Strain: SCHU S4 / Schu 4 / Gene: trpB, FTT_1773c / Plasmid: pMCSG68 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q5NE79, tryptophan synthase
#3: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 10 / 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: 2.52 Å3/Da / Density % sol: 51.16 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / Details: 0.2M calcium acetate, 0.1M imidazole, 10% PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97934 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 16, 2015
RadiationMonochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.8→30 Å / Num. obs: 18264 / % possible obs: 100 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.132 / Rpim(I) all: 0.067 / Rrim(I) all: 0.143 / Χ2: 1.277 / Net I/av σ(I): 12.868 / Net I/σ(I): 5.8 / Num. measured all: 87874
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allΧ2% possible allRrim(I) all
2.8-2.854.90.9819020.5660.4910.858100
2.85-2.94.90.8718940.660.4380.8231000.977
2.9-2.964.90.7348950.7240.3720.8331000.825
2.96-3.024.90.6748980.7920.3380.8641000.756
3.02-3.084.90.4718940.8740.2370.8551000.528
3.08-3.154.90.429010.8830.2110.8561000.472
3.15-3.234.90.3738970.9190.1890.8921000.42
3.23-3.324.90.2979090.9420.1490.9061000.333
3.32-3.424.90.2389180.960.120.9081000.267
3.42-3.534.80.1968990.970.0991.0331000.22
3.53-3.654.90.1629050.9750.0810.9971000.182
3.65-3.84.90.1289000.9850.0641.07499.90.143
3.8-3.974.80.1139280.9880.0571.1371000.127
3.97-4.184.90.18870.9890.051.3031000.112
4.18-4.444.80.0819250.9930.0411.52799.90.091
4.44-4.784.70.0779160.9950.0391.6951000.086
4.78-5.264.70.0749210.9940.0381.5841000.083
5.26-6.024.60.0849310.9920.0431.7031000.094
6.02-7.564.70.0779520.9930.0392.2391000.086
7.56-304.40.0579920.9950.033.60599.80.064

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Processing

Software
NameVersionClassification
PHENIXdev_2386refinement
PDB_EXTRACT3.2data extraction
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 2.804→29.496 Å / SU ML: 0.47 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 25.68
RfactorNum. reflection% reflection
Rfree0.2347 1689 4.9 %
Rwork0.1832 --
obs0.1858 34456 99.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 174.36 Å2 / Biso mean: 56.0905 Å2 / Biso min: 27.67 Å2
Refinement stepCycle: final / Resolution: 2.804→29.496 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4962 0 6 10 4978
Biso mean--75.37 38.11 -
Num. residues----655
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035066
X-RAY DIFFRACTIONf_angle_d0.5746855
X-RAY DIFFRACTIONf_chiral_restr0.042776
X-RAY DIFFRACTIONf_plane_restr0.003895
X-RAY DIFFRACTIONf_dihedral_angle_d11.8013067
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.8044-2.88690.45991460.34542682282899
2.8869-2.980.34961390.288827572896100
2.98-3.08640.31151360.248727332869100
3.0864-3.20980.27261360.247227452881100
3.2098-3.35570.31161300.236327632893100
3.3557-3.53240.27111460.208327182864100
3.5324-3.75330.23771570.17727222879100
3.7533-4.04240.21261090.158927392848100
4.0424-4.44790.20371490.141727412890100
4.4479-5.08870.18211550.135927312886100
5.0887-6.40040.23041430.168127172860100
6.4004-29.49780.17571430.15527192862100
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)
11.1643-0.40370.55070.93440.29621.90140.06360.26090.1783-0.3474-0.1695-0.041-0.2525-0.02110.0510.55350.1208-0.01220.47360.05310.298846.205533.8192.5668
21.96020.0490.07860.94140.44871.34770.09490.3080.062-0.2462-0.19410.2037-0.2458-0.16180.06680.59270.1251-0.05230.45560.03740.412533.27235.33851.8347
32.0680.3310.08221.4917-0.38662.1416-0.02680.3424-0.3199-0.2875-0.0093-0.15840.58820.15890.07790.68580.1412-0.00390.6149-0.04010.391351.484125.3265-4.3257
41.070.6946-0.45471.40020.0031.82420.1950.1936-0.3077-0.332-0.13930.2905-0.4845-0.2559-0.01780.41040.1686-0.10680.4351-0.06540.441917.61821.740112.4769
51.0238-0.4444-0.39010.7378-0.24582.0420.02670.0712-0.01950.09130.06290.4332-0.0794-0.2125-0.0660.26720.02270.00550.3977-0.05960.563717.75687.467931.1201
61.54550.0470.27780.9933-0.93420.9431-0.0261-0.0570.11440.0530.09270.037-0.094-0.0056-0.03230.36430.0647-0.00280.4221-0.03160.42935.28964.460622.2425
70.77890.13040.12121.1583-0.07952.03750.07040.10390.02350.0462-0.0480.3904-0.3867-0.14020.01030.32680.11070.03810.3163-0.04790.47421.460320.180328.7093
80.8150.2136-0.0131.1036-0.69211.24240.26230.03130.02560.3089-0.14160.1738-0.657-0.0563-0.06880.50150.02840.05020.3583-0.08240.36228.43322.265239.0588
91.41060.08840.01771.30450.3941.8781-0.0826-0.2352-0.13080.1250.05550.1361-0.65470.09370.02230.46620.01530.05390.3878-0.08810.415529.121113.571546.2259
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 78 )A1 - 78
2X-RAY DIFFRACTION2chain 'A' and (resid 79 through 211 )A79 - 211
3X-RAY DIFFRACTION3chain 'A' and (resid 212 through 269 )A212 - 269
4X-RAY DIFFRACTION4chain 'B' and (resid 1 through 36 )B1 - 36
5X-RAY DIFFRACTION5chain 'B' and (resid 37 through 112 )B37 - 112
6X-RAY DIFFRACTION6chain 'B' and (resid 113 through 164 )B113 - 164
7X-RAY DIFFRACTION7chain 'B' and (resid 165 through 285 )B165 - 285
8X-RAY DIFFRACTION8chain 'B' and (resid 286 through 363 )B286 - 363
9X-RAY DIFFRACTION9chain 'B' and (resid 364 through 395 )B364 - 395

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