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- PDB-3cep: Structure of a tryptophan synthase quinonoid intermediate -

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Basic information

Entry
Database: PDB / ID: 3cep
TitleStructure of a tryptophan synthase quinonoid intermediate
Components(Tryptophan synthase ...) x 2
KeywordsLYASE / CARBON-OXYGEN LYASE / TRYPTOPHAN BIOSYNTHESIS / Allosteric enzyme / Amino-acid biosynthesis / Aromatic amino acid biosynthesis / Pyridoxal phosphate
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
: / SN-GLYCEROL-3-PHOSPHATE / INDOLINE / 3-hydroxy-2-iminopropanoic acid / PYRIDOXAL-5'-PHOSPHATE / Tryptophan synthase alpha chain / Tryptophan synthase beta chain
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.1 Å
AuthorsBarends, T.R.M. / Domratcheva, T. / Kulik, V. / Blumenstein, L. / Dunn, M.F. / Schlichting, I.
CitationJournal: Chembiochem / Year: 2008
Title: Structure and mechanistic implications of a tryptophan synthase quinonoid intermediate.
Authors: Barends, T.R. / Domratcheva, T. / Kulik, V. / Blumenstein, L. / Niks, D. / Dunn, M.F. / Schlichting, I.
History
DepositionFeb 29, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 1, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Dec 17, 2014Group: Experimental preparation
Revision 1.3Nov 1, 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_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_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_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_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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

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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)72,64610
Polymers71,4862
Non-polymers1,1598
Water5,008278
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)145,29220
Polymers142,9734
Non-polymers2,31916
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area13670 Å2
ΔGint-289.3 kcal/mol
Surface area40770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)184.024, 58.908, 67.086
Angle α, β, γ (deg.)90.00, 95.19, 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
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Gene: trpA / Plasmid: pSTB7 / Production host: Escherichia coli (E. coli) / Strain (production host): CB149 / References: UniProt: P00929, tryptophan synthase
#2: Protein Tryptophan synthase beta chain


Mass: 42787.688 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Gene: trpB / Plasmid: pSTB7 / Production host: Escherichia coli (E. coli) / Strain (production host): CB149 / References: UniProt: P0A2K1, tryptophan synthase

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Non-polymers , 6 types, 286 molecules

#3: Chemical ChemComp-G3P / SN-GLYCEROL-3-PHOSPHATE / Glycerol 3-phosphate


Mass: 172.074 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H9O6P
#4: Chemical ChemComp-IDM / INDOLINE / Indoline


Mass: 119.164 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H9N
#5: Chemical ChemComp-CS / CESIUM ION


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


Mass: 247.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10NO6P
#7: Chemical ChemComp-MH6 / 3-hydroxy-2-iminopropanoic acid


Type: peptide linking / Mass: 103.077 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5NO3
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 278 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsTHIS IS AN INADVERTENT MUTATION.

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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: 2.53 Å3/Da / Density % sol: 51.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: 50mM bicine (pH 7.8), 1mM EDTA, 5mM dithioerythritol, 0.02mM pyridoxal phosphate solution, 2mM spermine, and 10% PEG 8000, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Feb 25, 2001
Details: double-crystal monochromator Si(111), beam focused by a toroidal mirror
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.1→24 Å / Num. all: 41128 / Num. obs: 41128 / % possible obs: 97.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 2.5 % / Rmerge(I) obs: 0.119 / Net I/σ(I): 6.7
Reflection shellResolution: 2.1→2.2 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.348 / Mean I/σ(I) obs: 3.1 / Num. unique all: 5293 / % possible all: 98

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
ADSCQuantumdata collection
XDSdata reduction
XSCALEdata scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 1QOP

1qop


Resolution: 2.1→23.7 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.904 / SU B: 5.466 / SU ML: 0.143 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.228 / ESU R Free: 0.187 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.23843 2017 4.9 %RANDOM
Rwork0.19798 ---
all0.19997 39110 --
obs0.19997 39110 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 21.75 Å2
Baniso -1Baniso -2Baniso -3
1--2.21 Å20 Å2-0.02 Å2
2--3.09 Å20 Å2
3----0.88 Å2
Refinement stepCycle: LAST / Resolution: 2.1→23.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4936 0 52 278 5266
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0225086
X-RAY DIFFRACTIONr_angle_refined_deg1.1581.9816900
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5265657
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.18524.206214
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.36815814
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8041531
X-RAY DIFFRACTIONr_chiral_restr0.0680.2769
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.023884
X-RAY DIFFRACTIONr_nbd_refined0.1930.22700
X-RAY DIFFRACTIONr_nbtor_refined0.2990.23532
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1280.2387
X-RAY DIFFRACTIONr_metal_ion_refined0.2220.27
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1690.249
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1450.210
X-RAY DIFFRACTIONr_mcbond_it0.3851.53274
X-RAY DIFFRACTIONr_mcangle_it0.73425212
X-RAY DIFFRACTIONr_scbond_it1.18931812
X-RAY DIFFRACTIONr_scangle_it2.0144.51688
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.319 138 -
Rwork0.26 2833 -
obs--100 %

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