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- PDB-1wdw: Structural basis of mutual activation of the tryptophan synthase ... -

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Basic information

Entry
Database: PDB / ID: 1wdw
TitleStructural basis of mutual activation of the tryptophan synthase a2b2 complex from a hyperthermophile, Pyrococcus furiosus
Components
  • Tryptophan synthase alpha chain
  • Tryptophan synthase beta chain 1
KeywordsLYASE / alpha/beta / alpha+beta / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Structural Genomics
Function / homology
Function and homology information


tryptophan synthase / tryptophan synthase activity
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
PYRIDOXAL-5'-PHOSPHATE / Tryptophan synthase beta chain 1 / Tryptophan synthase alpha chain
Similarity search - Component
Biological speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsLee, S.J. / Ogasahara, K. / Ma, J. / Nishio, K. / Ishida, M. / Yamagata, Y. / Tsukihara, T. / Yutani, K. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: Biochemistry / Year: 2005
Title: Conformational Changes in the Tryptophan Synthase from a Hyperthermophile upon alpha(2)beta(2) Complex Formation: Crystal Structure of the Complex
Authors: Lee, S.J. / Ogasahara, K. / Ma, J. / Nishio, K. / Ishida, M. / Yamagata, Y. / Tsukihara, T. / Yutani, K.
History
DepositionMay 19, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 12, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 25, 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 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_conn.ptnr2_label_seq_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 1
C: Tryptophan synthase alpha chain
D: Tryptophan synthase beta chain 1
E: Tryptophan synthase alpha chain
F: Tryptophan synthase beta chain 1
G: Tryptophan synthase alpha chain
H: Tryptophan synthase beta chain 1
I: Tryptophan synthase alpha chain
J: Tryptophan synthase beta chain 1
K: Tryptophan synthase alpha chain
L: Tryptophan synthase beta chain 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)420,59118
Polymers419,10812
Non-polymers1,4836
Water3,981221
1
A: Tryptophan synthase alpha chain
B: Tryptophan synthase beta chain 1
C: Tryptophan synthase alpha chain
D: Tryptophan synthase beta chain 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)140,1976
Polymers139,7034
Non-polymers4942
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10820 Å2
ΔGint-38 kcal/mol
Surface area43550 Å2
MethodPISA
2
E: Tryptophan synthase alpha chain
F: Tryptophan synthase beta chain 1
G: Tryptophan synthase alpha chain
H: Tryptophan synthase beta chain 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)140,1976
Polymers139,7034
Non-polymers4942
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10750 Å2
ΔGint-36 kcal/mol
Surface area43860 Å2
MethodPISA
3
I: Tryptophan synthase alpha chain
J: Tryptophan synthase beta chain 1
K: Tryptophan synthase alpha chain
L: Tryptophan synthase beta chain 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)140,1976
Polymers139,7034
Non-polymers4942
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10580 Å2
ΔGint-35 kcal/mol
Surface area43490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.056, 220.257, 292.560
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Tryptophan synthase alpha chain / tryptophan synthase alpha subunit


Mass: 27535.844 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Gene: TRPA / Plasmid: pTV119Nde / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: Q8U094, tryptophan synthase
#2: Protein
Tryptophan synthase beta chain 1 / tryptophan synthase beta subunit


Mass: 42315.504 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Gene: TRPB / Plasmid: pTV119Nde / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: Q8U093, tryptophan synthase
#3: Chemical
ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C8H10NO6P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 221 / 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: 2.9 Å3/Da / Density % sol: 58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: sodium citrate, PEG 8000, potassium acetate, ethylene glycol, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: OXFORD PX210 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 3→89.17 Å / Num. all: 115486 / Num. obs: 115486 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.8 % / Rmerge(I) obs: 0.091
Reflection shellHighest resolution: 3 Å / Rmerge(I) obs: 0.367 / % possible all: 99.8

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Processing

Software
NameVersionClassification
CNS1.1refinement
d*TREKdata scaling
EPMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1V8Z, 1GEQ

1v8z

1geq


Resolution: 3→89.17 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 1632427.86 / Data cutoff low absF: 0 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.231 5718 5 %RANDOM
Rwork0.196 ---
obs0.196 113449 97.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 70.8967 Å2 / ksol: 0.356564 e/Å3
Displacement parametersBiso mean: 72 Å2
Baniso -1Baniso -2Baniso -3
1-7.75 Å20 Å20 Å2
2---10.45 Å20 Å2
3---2.7 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.43 Å0.35 Å
Luzzati d res low-5 Å
Luzzati sigma a0.63 Å0.49 Å
Refinement stepCycle: LAST / Resolution: 3→89.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms29252 0 90 221 29563
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.77
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 3→3.19 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.411 920 5 %
Rwork0.353 17402 -
obs--95.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2PLP_PAR.TXTWATER.TOP
X-RAY DIFFRACTION3PARAM.PLP_LYSPLP_TOP.TXT
X-RAY DIFFRACTION4WATER_REP.PARAM
X-RAY DIFFRACTION5ION.PARAM

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