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- PDB-4hpx: Crystal structure of Tryptophan Synthase at 1.65 A resolution in ... -

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Basic information

Entry
Database: PDB / ID: 4hpx
TitleCrystal structure of Tryptophan Synthase at 1.65 A resolution in complex with alpha aminoacrylate E(A-A) and benzimidazole 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 / benzimidazole / 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 / 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-0JO / BENZIMIDAZOLE / : / 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 / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.65 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 24, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 18, 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_conn_angle ...database_2 / 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.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.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.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_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)73,93917
Polymers71,6182
Non-polymers2,32215
Water13,007722
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7020 Å2
ΔGint-67 kcal/mol
Surface area23250 Å2
MethodPISA
2
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)147,87934
Polymers143,2354
Non-polymers4,64430
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area17940 Å2
ΔGint-144 kcal/mol
Surface area42610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)183.960, 60.960, 67.410
Angle α, β, γ (deg.)90.000, 94.580, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-954-

HOH

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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, 737 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-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-BZI / BENZIMIDAZOLE


Mass: 118.136 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C7H6N2
#6: Chemical ChemComp-0JO / 2-{[(E)-{3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene]amino}prop-2-enoic acid


Mass: 316.204 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H13N2O7P
#7: Chemical ChemComp-BCN / BICINE


Mass: 163.172 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H13NO4 / Comment: pH buffer*YM
#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


Mass: 18.015 Da / Num. of mol.: 722 / 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: 2.63 Å3/Da / Density % sol: 53.24 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: 50 mM Bicine-CsOH, 10% PEG 8000, 2 mM Spermine, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Dec 31, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.65→91.686 Å / Num. all: 87817 / Num. obs: 87817 / % possible obs: 98.3 % / Observed criterion σ(F): -3 / Redundancy: 3.6 % / Rsym value: 0.061 / Net I/σ(I): 10.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.65-1.743.60.332.344289124650.3396.2
1.74-1.843.60.2243.442397118810.22496.9
1.84-1.973.60.1614.640255112980.16197.6
1.97-2.133.60.1136.537601105390.11398.2
2.13-2.333.60.0848.33504198180.08498.8
2.33-2.613.60.0699.83197689280.06999.4
2.61-3.013.60.05911.42867279340.05999.8
3.01-3.693.70.05311.72467367540.053100
3.69-5.223.70.034181935052520.034100
5.22-29.3763.60.034181067429480.03499.5

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 48.68 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å29.38 Å
Translation2.5 Å29.38 Å
Phasing dmMethod: Solvent flattening and Histogram matching / Reflection: 87788
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
8.94-10022.20.876599
6.32-8.9426.70.8551068
5.16-6.3225.80.8441356
4.47-5.1619.20.8931610
4-4.4719.30.8941815
3.65-419.90.8822008
3.38-3.6519.80.8882157
3.16-3.3821.50.8662335
2.98-3.1621.70.8522477
2.83-2.9823.10.8392582
2.7-2.83240.8372720
2.58-2.723.80.8462867
2.48-2.58240.8432969
2.39-2.4824.10.8373064
2.31-2.3923.60.8483170
2.24-2.3122.80.8553262
2.17-2.24240.8463368
2.11-2.1722.60.8453419
2.05-2.1124.20.8453591
2-2.0523.60.8453639
1.95-225.20.8413737
1.91-1.9524.90.8463752
1.86-1.9125.20.8453897
1.83-1.86260.843942
1.79-1.8326.40.8534023
1.75-1.7927.20.8464076
1.72-1.7528.30.8294147
1.69-1.7228.60.8394243
1.65-1.6938.90.765895

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.3.16data scaling
PHASER2.1.4phasing
DM6.1phasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
CrystalCleardata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1TJP

1tjp


Resolution: 1.65→28.19 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.96 / WRfactor Rfree: 0.1874 / WRfactor Rwork: 0.1415 / Occupancy max: 1 / Occupancy min: 0.08 / FOM work R set: 0.8794 / SU B: 3.776 / SU ML: 0.056 / SU R Cruickshank DPI: 0.1118 / SU Rfree: 0.0871 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.112 / ESU R Free: 0.087 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1901 4390 5 %RANDOM
Rwork0.1421 ---
all0.1445 87867 --
obs0.1445 87784 97.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 87.34 Å2 / Biso mean: 23.318 Å2 / Biso min: 8.59 Å2
Baniso -1Baniso -2Baniso -3
1--0.08 Å20 Å20.12 Å2
2--0.22 Å20 Å2
3----0.12 Å2
Refinement stepCycle: LAST / Resolution: 1.65→28.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5008 0 140 722 5870
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0195542
X-RAY DIFFRACTIONr_angle_refined_deg1.4271.9977550
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8085755
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.17724.139244
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.31815940
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3571539
X-RAY DIFFRACTIONr_chiral_restr0.0950.2831
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214258
X-RAY DIFFRACTIONr_rigid_bond_restr2.62835540
X-RAY DIFFRACTIONr_sphericity_free28.9065164
X-RAY DIFFRACTIONr_sphericity_bonded11.41455961
LS refinement shellResolution: 1.65→1.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.401 285 -
Rwork0.321 5824 -
all-6109 -
obs--95.63 %
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)
10.21770.0826-0.13430.0802-0.04830.11440.00050.04550.0169-0.00650.00570.0158-0.0019-0.0186-0.00610.01130.0014-0.01150.0158-0.00090.0436-53.6722-2.375421.4103
20.1063-0.10210.00890.14310.06280.1150.0014-0.0020.011-0.00320.0024-0.00950.0006-0.0006-0.00370.0250.0012-0.0080.0058-0.00150.0422-38.56663.211523.8852
30.18-0.128-0.0630.24120.02370.02530.0131-0.00080.0075-0.0007-0.01190.0074-0.00630.0013-0.00130.02920.0008-0.0070.0152-0.00280.0357-40.1167-9.912928.3448
40.34820.2045-0.13260.3641-0.21210.1244-0.00810.0327-0.0206-0.02980.00940.00410.017-0.0078-0.00130.02610.0049-0.00940.0115-0.00350.0328-45.2036-16.309418.4609
51.28710.8907-1.65581.8083-1.55422.2726-0.03690.2557-0.0628-0.0991-0.01390.06580.063-0.26580.05080.02810.0093-0.03420.0817-0.03510.051-53.6435-15.34516.9898
60.1253-0.01490.03890.0372-0.01250.019100.02020.0221-0.0174-0.0020.0295-0.00490.00020.0020.02740.0093-0.01390.01030.00060.0407-48.0561-1.529610.9864
72.101820.43681.91820.46190.33820.0351-0.0140.12660.0234-0.02540.11410.0086-0.0137-0.00970.02510.0151-0.00690.0128-0.00010.0416-50.117910.386813.4969
80.0715-0.0306-0.05670.0251-0.01080.161-0.00650.0107-0.0130.00350.00470.00770.0171-0.04670.00180.0341-0.0052-0.010.0173-0.00350.0329-30.4258-27.967913.8662
90.0810.09780.07060.15230.13650.1492-0.00370.00080.00360.0124-0.00560.01110.0240.0070.00930.0313-0.0016-0.00620.0192-0.00250.0336-6.2987-33.14373.199
100.028-0.0028-0.00370.0008-0.00050.03470.00160.00250.0008-0.0014-0.002600.0003-0.00480.0010.0340.0004-0.00810.0134-0.00020.033-14.0212-20.44712.8119
110.0392-0.00460.00120.00840.01630.0419-0.0029-0.00430.0042-0.00120.00250.0047-0.00420.01180.00040.0326-0.001-0.00850.0165-0.00040.03253.4491-18.129519.3155
120.106-0.14540.23550.2223-0.35040.5778-0.01730.01750.01030.0356-0.0128-0.0258-0.06120.03420.03020.0374-0.0057-0.00580.01410.00030.03274.2832-16.365715.4909
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 29
2X-RAY DIFFRACTION2A30 - 91
3X-RAY DIFFRACTION3A92 - 136
4X-RAY DIFFRACTION4A137 - 187
5X-RAY DIFFRACTION5A188 - 202
6X-RAY DIFFRACTION6A203 - 247
7X-RAY DIFFRACTION7A248 - 268
8X-RAY DIFFRACTION8B2 - 37
9X-RAY DIFFRACTION9B38 - 66
10X-RAY DIFFRACTION10B67 - 322
11X-RAY DIFFRACTION11B323 - 364
12X-RAY DIFFRACTION12B365 - 396

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