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- PDB-4hpj: Crystal structure of Tryptophan Synthase at 1.45 A resolution in ... -

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Basic information

Entry
Database: PDB / ID: 4hpj
TitleCrystal structure of Tryptophan Synthase at 1.45 A resolution in complex with 2-aminophenol quinonoid in the beta site and the F9 inhibitor in the alpha site
Components(Tryptophan synthase ...) x 2
KeywordsLYASE/LYASE INHIBITOR / Lyase / carbon-oxygen lyase / tryptophan biosynthesis / Salmonella / F9F / Allosteric enzyme / Amino-acid biosynthesis / Aromatic amino acid biosynthesis / Pyridoxal phosphate / alpha amino acrylate / LYASE-LYASE INHIBITOR complex
Function / homology
Function and homology information


tryptophan synthase / tryptophan synthase activity / 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 / 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
Chem-1D0 / : / Chem-F9F / DI(HYDROXYETHYL)ETHER / 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 / molecular replacement / Resolution: 1.45 Å
AuthorsHilario, E. / Niks, D. / Dunn, M.F. / Mueller, L.J. / Fan, L.
CitationJournal: Biochemistry / Year: 2013
Title: Allostery and substrate channeling in the tryptophan synthase bienzyme complex: evidence for two subunit conformations and four quaternary states.
Authors: Niks, D. / Hilario, E. / Dierkers, A. / Ngo, H. / Borchardt, D. / Neubauer, T.J. / Fan, L. / Mueller, L.J. / Dunn, M.F.
History
DepositionOct 23, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 25, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2014Group: Database references
Revision 1.2Sep 29, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_conn_angle / struct_conn / struct_site
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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_alt_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Sep 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)73,51018
Polymers71,6182
Non-polymers1,89216
Water11,602644
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)147,02036
Polymers143,2354
Non-polymers3,78432
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area8590 Å2
ΔGint-34 kcal/mol
Surface area42810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)184.329, 59.716, 67.527
Angle α, β, γ (deg.)90.00, 94.68, 90.00
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
Details: Yang et al (1996) Protein Expression and Purification, 8:126-136.
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Gene: STM1727, trpA / 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
Details: Yang et al (1996) Protein Expression and Purification, 8:126-136.
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Gene: STM1726, trpB / Production host: Escherichia coli (E. coli) / Strain (production host): CB149 / References: UniProt: P0A2K1, tryptophan synthase

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Non-polymers , 7 types, 660 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-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-1D0 / (2E)-2-[({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)imino]-3-[(2-hydroxyphenyl)amino]propanoic acid


Mass: 425.330 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H20N3O8P
#6: Chemical ChemComp-BCN / BICINE / Bicine


Mass: 163.172 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4 / Comment: pH buffer*YM
#7: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#8: Chemical ChemComp-CS / CESIUM ION


Mass: 132.905 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cs
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 644 / 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: 2.59 Å3/Da / Density % sol: 52.44 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: 50 mM Bicine-CsOH, 10% PEG 8,000, 2 mM Spermine, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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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 11, 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: 1.449→91.858 Å / Num. all: 109585 / Num. obs: 109585 / % possible obs: 84.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.7 % / Rsym value: 0.095 / Net I/σ(I): 13.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.45-1.532.60.4471.630907118720.44762.9
1.53-1.624.40.4461.553827123150.44669.3
1.62-1.737.70.3532108764140600.35384
1.73-1.878.10.2323.1112800138800.23289.2
1.87-2.058.30.164.2111040134030.1693.3
2.05-2.298.70.1195.5107342123130.11995.3
2.29-2.658.90.104697694109830.10495.9
2.65-3.249.90.0877.19315993790.08796.4
3.24-4.5911.50.0699.18433573230.06997
4.59-19.78910.90.069.94417340570.0696.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.3.20data scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1TJP

1tjp


Resolution: 1.45→19.67 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.957 / WRfactor Rfree: 0.1893 / WRfactor Rwork: 0.1466 / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.8972 / SU B: 2.298 / SU ML: 0.039 / SU R Cruickshank DPI: 0.0773 / SU Rfree: 0.0701 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.077 / ESU R Free: 0.07 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1893 5519 5 %RANDOM
Rwork0.1466 ---
all0.1488 117892 --
obs0.1488 109556 84.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 82.48 Å2 / Biso mean: 19.7331 Å2 / Biso min: 5.12 Å2
Baniso -1Baniso -2Baniso -3
1--0.08 Å20 Å20.07 Å2
2--0.13 Å20 Å2
3----0.05 Å2
Refinement stepCycle: LAST / Resolution: 1.45→19.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5009 0 99 644 5752
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0195315
X-RAY DIFFRACTIONr_angle_refined_deg1.4531.9877216
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6485703
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.53824.148229
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.47415884
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7581535
X-RAY DIFFRACTIONr_chiral_restr0.0970.2797
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0214058
X-RAY DIFFRACTIONr_rigid_bond_restr2.80535315
X-RAY DIFFRACTIONr_sphericity_free26.6665191
X-RAY DIFFRACTIONr_sphericity_bonded11.52855665
LS refinement shellResolution: 1.45→1.487 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.262 277 -
Rwork0.218 5448 -
all-5725 -
obs--61.33 %
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)
10.183-0.0557-0.02250.02870.03690.1185-0.021-0.0005-0.00830.00870.0105-0.0064-0.01920.01860.01060.02940.006-0.02150.02040.00330.060153.92542.7329-21.2739
20.0563-0.0059-0.01750.20250.04580.07040.0007-0.00260.00310.0054-0.0008-0.01120-0.003600.045-0.0007-0.00470.0360.00250.049840.290339.9264-25.3345
30.2402-0.0761-0.13210.30530.0780.0981-0.0047-0.0216-0.01620.03090.0049-0.03390.01350.0055-0.00020.04880-0.0120.03090.00540.05348.718429.721-11.1582
40.1516-0.09460.00560.28980.0310.00590.002300.010.0117-0.0025-0.029-0.00180.00030.00020.045-0.0003-0.00740.0310.00240.054548.164343.4521-10.7828
50.0484-0.01980.01080.3516-0.08120.02090.0537-0.02220.00930.0697-0.06410.0336-0.01160.01260.01050.0785-0.03160.00690.041-0.01210.074350.698554.9673-12.9702
60.05170.04070.02290.0508-0.04110.19980.00130.0162-0.01060.00150.0009-0.01010.01070.0432-0.00220.052-0.0011-0.00230.01920.0050.048130.445716.924-13.9286
70.02690.01690.00410.0162-0.00760.0536-0.0002-0.0020.00130.0018-0.00140.0021-0.002-0.00080.00160.04870.0005-0.00350.0366-0.00030.046411.006123.6902-12.7904
80.02410.02640.0830.16260.13580.3243-0.0088-0.0153-0.0008-0.00760.0051-0.0004-0.0295-0.02690.00370.04810.0025-0.0010.03-0.00240.0454-4.116629.021-15.3373
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 29
2X-RAY DIFFRACTION2A30 - 159
3X-RAY DIFFRACTION3A160 - 202
4X-RAY DIFFRACTION4A203 - 247
5X-RAY DIFFRACTION5A248 - 268
6X-RAY DIFFRACTION6B2 - 37
7X-RAY DIFFRACTION7B38 - 364
8X-RAY DIFFRACTION8B365 - 396

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