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- PDB-5cgq: Crystal structure of Tryptophan Synthase from Salmonella typhimur... -

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Basic information

Entry
Database: PDB / ID: 5cgq
TitleCrystal structure of Tryptophan Synthase from Salmonella typhimurium in complex with F9 ligand in the alpha-site and the product L-Tryptophan in the beta-site.
Components(Tryptophan synthase ...) x 2
KeywordsLYASE/LYASE INHIBITOR / Lyase / carbon-oxygen lyase / tryptophan biosynthesis / Salmonella typhimurium / F6F / inhibitor / allosteric enzyme / aromatic amino acid biosynthesis / pyridoxal phosphate / TRANSFERASE / LYASE-LYASE INHIBITOR complex
Function / homology
Function and homology information


tryptophan synthase / tryptophan synthase activity / L-tryptophan biosynthetic process / identical protein binding / 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
: / Chem-F9F / PYRIDOXAL-5'-PHOSPHATE / TRYPTOPHAN / Tryptophan synthase alpha chain / Tryptophan synthase beta chain
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.18 Å
AuthorsHilario, E. / Caulkins, B.G. / Young, R.P. / Dunn, M.F. / Mueller, L.J. / Fan, L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM097569 United States
CitationJournal: To Be Published
Title: Crystal structure of Tryptophan Synthase from Salmonella typhimurium in complex with F9 ligand and the product L-Tryptophan in the beta-site.
Authors: Hilario, E. / Caulkins, B.G. / Young, R.P. / Dunn, M.F. / Mueller, L.J. / Fan, L.
History
DepositionJul 9, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 13, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Author supporting evidence / Derived calculations / Refinement description
Category: pdbx_audit_support / pdbx_struct_oper_list / software
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation / _software.version
Revision 1.2Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_conn_type.id

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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)73,05810
Polymers71,6182
Non-polymers1,4418
Water14,178787
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)146,11620
Polymers143,2354
Non-polymers2,88116
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area8780 Å2
ΔGint-31 kcal/mol
Surface area43350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)182.553, 59.300, 67.368
Angle α, β, γ (deg.)90.000, 94.820, 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 enterica subsp. enterica serovar Typhimurium (bacteria)
Gene: trpA / Plasmid: Derivative of Pbr322 / 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: Derivative of Pbr322 / Production host: Escherichia coli (E. coli) / Strain (production host): Cb149 / References: UniProt: P0A2K1, tryptophan synthase

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Non-polymers , 7 types, 795 molecules

#3: Chemical ChemComp-F9F / 2-({[4-(TRIFLUOROMETHOXY)PHENYL]SULFONYL}AMINO)ETHYL DIHYDROGEN PHOSPHATE / N-(4'-TRIFLUOROMETHOXYBENZENESULFONYL)-2-AMINO-1-ETHYLPHOSPHATE, F9


Mass: 365.220 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H11F3NO7PS
#4: Chemical ChemComp-CS / CESIUM ION


Mass: 132.905 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cs
#5: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10NO6P
#6: Chemical ChemComp-TRP / TRYPTOPHAN


Type: L-peptide linking / Mass: 204.225 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H12N2O2
#7: Chemical ChemComp-BCN / BICINE


Mass: 163.172 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4 / Comment: pH buffer*YM
#8: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 787 / 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: 2.54 Å3/Da / Density % sol: 51.55 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.6
Details: 50 mM Bicine-CsOH, pH 7.6, 10% PEG 8,000, 100 mM CsCl2, 1 mM spermine
PH range: 7.6 -7.8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 12.3.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 4, 2012
RadiationMonochromator: SIBYLS KOHZU DUAL DOUBLE SI(111) CRYSTAL MONOCHROMATOR (DDCM)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.18→40 Å / Num. all: 231646 / Num. obs: 231646 / % possible obs: 98.6 % / Redundancy: 9.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.081 / Rpim(I) all: 0.028 / Rrim(I) all: 0.086 / Rsym value: 0.081 / Net I/σ(I): 14.7 / Num. measured all: 2151280
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) allRsym value% possible all
1.18-1.247.90.8723252941321870.7780.0150.03794.2
3.73-408.50.03739.66433075270.9990.0160.04798.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0123refinement
MOSFLM7.2.0data reduction
SCALA3.3.22data scaling
MOLREP11.3.02phasing
DM6.5.013phasing
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4HT3

4ht3


Resolution: 1.18→39.21 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.971 / WRfactor Rfree: 0.1629 / WRfactor Rwork: 0.1413 / FOM work R set: 0.8915 / SU B: 1.035 / SU ML: 0.021 / SU R Cruickshank DPI: 0.033 / SU Rfree: 0.0326 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.033 / ESU R Free: 0.033 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1605 11610 5 %RANDOM
Rwork0.1404 ---
obs0.1414 219965 98.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 74.37 Å2 / Biso mean: 17.768 Å2 / Biso min: 7.53 Å2
Baniso -1Baniso -2Baniso -3
1-0.08 Å2-0 Å20.44 Å2
2---0.29 Å2-0 Å2
3---0.13 Å2
Refinement stepCycle: final / Resolution: 1.18→39.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4971 0 70 825 5866
Biso mean--16.81 27.97 -
Num. residues----658
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0195555
X-RAY DIFFRACTIONr_angle_refined_deg1.4061.9787552
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.815742
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.2723.957235
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.60715924
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1871538
X-RAY DIFFRACTIONr_chiral_restr0.0920.2822
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0214317
X-RAY DIFFRACTIONr_mcbond_it1.1861.7762851
X-RAY DIFFRACTIONr_mcangle_it1.4373.0123632
X-RAY DIFFRACTIONr_scbond_it1.7842.1892704
X-RAY DIFFRACTIONr_rigid_bond_restr10.7335555
X-RAY DIFFRACTIONr_sphericity_free18.5355164
X-RAY DIFFRACTIONr_sphericity_bonded10.79656058
LS refinement shellResolution: 1.18→1.211 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.227 777 -
Rwork0.224 15296 -
all-16073 -
obs--92.83 %
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)
10.1656-0.0982-0.00970.07440.01640.05360.0007-0.00350.0035-00.0014-0.00620.00110.005-0.00210.0085-0.001-0.00760.01510.00030.007851.773312.171412.0277
20.0066-0.0013-0.00010.01980.00650.0022-0.0005-0.00060.0003-0.00030.00030.0002-0.0001-0.00030.00020.00920.0002-0.00780.0170.00010.00737.823410.04118.8811
30.16510.0087-0.12190.0663-0.01280.23660.0019-0.00790.004-0.00220.0027-0.0018-0.00240.0024-0.00450.0083-0.0006-0.00780.01630.00060.007943.81-1.060219.5649
40.7396-0.965-1.06151.58551.44431.7342-0.0919-0.0968-0.01390.1540.0835-0.02740.13040.13780.00830.02440.005-0.00950.03020.00560.012452.3529-2.323825.7029
50.0712-0.1446-0.01880.2970.04060.0068-0.0021-0.0033-0.010.00760.00070.01770.0021-0.00450.00140.0095-0.0005-0.00690.01850.00060.006946.805512.300923.0406
60.6447-0.41520.14370.3854-0.09640.1317-0.00920.00270.04310.0129-0.0004-0.0338-0.005800.00950.0089-0.0011-0.00720.0153-00.00849.305324.492321.1462
70.02050.0152-0.00760.0119-0.00960.03230.0001-0.0017-0.0006-0-0.0012-0.00060.00030.00090.00120.0090.0003-0.00750.0164-0.00010.007327.6367-12.951819.4993
80.0407-0.01190.00490.0078-0.00870.01760.0001-0.0024-0.00480.00020.00080.00110.0008-0.0007-0.00090.0091-0.0001-0.00760.0156-0.00020.00751.1782-17.630927.8217
90.00050.00040.00080.00210.0030.0044-0.0005-0.00080.001-0.00040.0003-0-0.0004-0.00010.00020.00960.0001-0.00770.01680.00010.007610.3106-8.564230.2993
100.0410.0138-0.02740.0057-0.01080.02980.00460.00220.0058-0.00030.00080.0032-0.0043-0.001-0.00540.01030-0.00730.0171-0.00030.008813.93347.189432.1506
110.01520.01030.00370.00730.00210.00160.0001-0.0008-0.0008-0.0002-0.0004-0.00060-0.00010.00040.00930.0001-0.00770.0168-0.00010.007512.6782-11.270921.1792
120.0022-0.00130.00070.0011-0.00090.0015-0.0006-0.0001-00.00050.0003-0.0003-0.0003-0.00010.00030.00930.0002-0.00780.016800.007411.81130.17678.899
130.0134-0.0052-0.00960.00270.00210.01070.00040.00040.001-0.00020.0001-0.0005-0.0004-0.0003-0.00060.0094-0.0001-0.00770.0166-0.00010.00762.3492-4.082612.5204
140.00810.010.01050.01890.02060.0951-0.0007-0.00090.0009-0.001-0.00020.0011-0.0082-0.00280.0010.00940.0006-0.00760.01650.00010.0075-6.2635-3.893516.4177
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 29
2X-RAY DIFFRACTION2A30 - 159
3X-RAY DIFFRACTION3A160 - 187
4X-RAY DIFFRACTION4A188 - 202
5X-RAY DIFFRACTION5A203 - 247
6X-RAY DIFFRACTION6A248 - 268
7X-RAY DIFFRACTION7B2 - 37
8X-RAY DIFFRACTION8B38 - 70
9X-RAY DIFFRACTION9B71 - 126
10X-RAY DIFFRACTION10B127 - 165
11X-RAY DIFFRACTION11B166 - 244
12X-RAY DIFFRACTION12B245 - 301
13X-RAY DIFFRACTION13B302 - 343
14X-RAY DIFFRACTION14B344 - 391

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