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- PDB-1k3u: CRYSTAL STRUCTURE OF WILD-TYPE TRYPTOPHAN SYNTHASE COMPLEXED WITH... -

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Basic information

Entry
Database: PDB / ID: 1k3u
TitleCRYSTAL STRUCTURE OF WILD-TYPE TRYPTOPHAN SYNTHASE COMPLEXED WITH N-[1H-INDOL-3-YL-ACETYL]ASPARTIC ACID
Components(Tryptophan Synthase ...) x 2
KeywordsLYASE / CARBON-OXYGEN LYASE / TRYPTOPHAN 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
N-[1H-INDOL-3-YL-ACETYL]ASPARTIC ACID / PYRIDOXAL-5'-PHOSPHATE / Tryptophan synthase alpha chain / Tryptophan synthase beta chain
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsWeyand, M. / Schlichting, I. / Marabotti, A. / Mozzarelli, A.
CitationJournal: J.Biol.Chem. / Year: 2002
Title: Crystal structures of a new class of allosteric effectors complexed to tryptophan synthase.
Authors: Weyand, M. / Schlichting, I. / Marabotti, A. / Mozzarelli, A.
History
DepositionOct 4, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 3, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: diffrn_source / pdbx_struct_special_symmetry ...diffrn_source / pdbx_struct_special_symmetry / software / struct_conn
Item: _diffrn_source.pdbx_synchrotron_site / _software.name ..._diffrn_source.pdbx_synchrotron_site / _software.name / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Aug 16, 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_ref_seq_dif / 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.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.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_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _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)72,0475
Polymers71,4862
Non-polymers5603
Water12,827712
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)144,09410
Polymers142,9734
Non-polymers1,1216
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Unit cell
Length a, b, c (Å)182.409, 59.718, 67.177
Angle α, β, γ (deg.)90.00, 94.52, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-1250-

HOH

21B-1254-

HOH

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Components

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Tryptophan Synthase ... , 2 types, 2 molecules AB

#1: Protein Tryptophan Synthase Alpha Chain / E.C.4.2.1.20


Mass: 28698.797 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Gene: TRPA/TRPB / Plasmid: PSTB7 / Production host: Escherichia coli (E. coli) / Strain (production host): CB149 / References: UniProt: P00929, tryptophan synthase
#2: Protein Tryptophan Synthase Beta Chain / E.C.4.2.1.20


Mass: 42787.688 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Gene: TRPA/TRPB / Plasmid: PSTB7 / Production host: Escherichia coli (E. coli) / Strain (production host): CB149 / References: UniProt: P0A2K1, tryptophan synthase

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Non-polymers , 4 types, 715 molecules

#3: Chemical ChemComp-IAD / N-[1H-INDOL-3-YL-ACETYL]ASPARTIC ACID


Mass: 290.271 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H14N2O5
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: 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
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 712 / 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: 2.55 Å3/Da / Density % sol: 51.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: PEG 8000, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlprotein1drop
250 mMsodium bicine1droppH7.8
310 mMsodium-EDTA1drop
41 mMdithioerythritol1drop
50.020 mMpyridoxal phosphate1drop
69-12 %PEG80001reservoir
71.5 mMspermine1reservoir
81 mMEDTA1reservoir
950 mMsodium bicine1reservoirpH7.8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.842
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Aug 10, 2000 / Details: Premirror, Bent mirror
RadiationMonochromator: Triangular monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.842 Å / Relative weight: 1
ReflectionResolution: 1.7→31 Å / Num. obs: 77570 / % possible obs: 97.7 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 3.05 % / Rsym value: 0.048 / Net I/σ(I): 14.4
Reflection shellResolution: 1.7→1.8 Å / Mean I/σ(I) obs: 2.5 / Rsym value: 0.123 / % possible all: 94.2
Reflection
*PLUS
Lowest resolution: 31 Å / Num. measured all: 236589 / Rmerge(I) obs: 0.048
Reflection shell
*PLUS
% possible obs: 94.2 % / Rmerge(I) obs: 0.123 / Mean I/σ(I) obs: 2.5

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Processing

Software
NameVersionClassification
REFMAC5refinement
CNSrefinement
XDSdata reduction
XSCALEdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1QOP

1qop


Resolution: 1.7→20 Å / SU B: 1.91043 / SU ML: 0.06314 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.09026 / ESU R Free: 0.09174 / Stereochemistry target values: Engh & Huber
Details: GLU 11 B exists in two conformations, each with 50% occupancy. With conformation A, HOH 709 exists. With conformation B, HOH 710 exists.
RfactorNum. reflection% reflectionSelection details
Rfree0.18774 3938 5.1 %RANDOM
Rwork0.15295 ---
all0.1547 73596 --
obs0.1547 73596 97.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å
Displacement parametersBiso mean: 18.909 Å2
Baniso -1Baniso -2Baniso -3
1--0.73 Å20 Å20.05 Å2
2--1.21 Å20 Å2
3----0.47 Å2
Refinement stepCycle: LAST / Resolution: 1.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4994 0 37 712 5743
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONr_bond_refined_d0.0290.021
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.2931.974
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2923
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.51315
X-RAY DIFFRACTIONr_chiral_restr0.1790.2
X-RAY DIFFRACTIONr_gen_planes_refined0.010.02
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1470.5
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2350.3
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it1.3041.5
X-RAY DIFFRACTIONr_mcangle_it2.0792
X-RAY DIFFRACTIONr_scbond_it3.3693
X-RAY DIFFRACTIONr_scangle_it5.3364.5
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.8 Å / % reflection obs: 94.2 %
Refinement
*PLUS
Lowest resolution: 20 Å / % reflection Rfree: 5 % / Rfactor obs: 0.1547 / Rfactor Rfree: 0.188 / Rfactor Rwork: 0.153
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.029
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg2.293

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