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- PDB-2dh5: Crystal structure of E. coli Holo-TrpB -

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Basic information

Entry
Database: PDB / ID: 2dh5
TitleCrystal structure of E. coli Holo-TrpB
Componentstryptophan synthase beta subunit
KeywordsLYASE / Tryptophan synthase / beta-chain / PLP / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


tryptophan synthase / tryptophan synthase activity / tryptophan biosynthetic process / aromatic amino acid family biosynthetic process / pyridoxal phosphate binding / protein homodimerization activity / identical protein binding / cytoplasm / cytosol
Similarity search - Function
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 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PYRIDOXAL-5'-PHOSPHATE / Tryptophan synthase beta chain
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsNishio, K. / Morimoto, Y. / Ogasahara, K. / Yutani, K. / Tsukihara, T. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: Febs J. / Year: 2010
Title: Large conformational changes in the Escherichia coli tryptophan synthase beta(2) subunit upon pyridoxal 5'-phosphate binding
Authors: Nishio, K. / Ogasahara, K. / Morimoto, Y. / Tsukihara, T. / Lee, S.J. / Yutani, K.
History
DepositionMar 23, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 24, 2007Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2007Group: 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_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

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Assembly

Deposited unit
A: tryptophan synthase beta subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,5645
Polymers43,0331
Non-polymers5314
Water1629
1
A: tryptophan synthase beta subunit
hetero molecules

A: tryptophan synthase beta subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,12910
Polymers86,0662
Non-polymers1,0638
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_655-x+y+1,y,-z+1/21
Buried area3290 Å2
ΔGint-12 kcal/mol
Surface area27580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)172.516, 172.516, 82.587
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein tryptophan synthase beta subunit / Tryptophan synthase beta-chain


Mass: 43032.906 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: pSTecoTB / Production host: Escherichia coli (E. coli) / Strain (production host): CB149 / References: UniProt: P0A879, tryptophan synthase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10NO6P
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / 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: 4.12 Å3/Da / Density % sol: 70.15 %
Crystal growTemperature: 288 K / Method: micro batch using paraffin oil / pH: 8
Details: ammonium sulfate, pH 8.0, micro batch using paraffin oil, temperature 288K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: Bruker DIP-6040 / Detector: CCD / Date: Sep 26, 2003
RadiationMonochromator: Mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.9→74.4 Å / Num. obs: 15920 / % possible obs: 96.8 % / Observed criterion σ(I): 6.6 / Redundancy: 4.7 % / Biso Wilson estimate: 86.257 Å2 / Rmerge(I) obs: 0.076
Reflection shellResolution: 2.9→3.06 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.39 / Num. unique all: 2297 / % possible all: 97.4

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Processing

Software
NameVersionClassification
CNS1.1refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: CHAIN B of 1BKS

1bks


Resolution: 2.9→30.33 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 1609319.19 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.244 800 5 %RANDOM
Rwork0.196 ---
obs0.196 15901 96.2 %-
all-15920 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 54.6382 Å2 / ksol: 0.372837 e/Å3
Displacement parametersBiso mean: 60.3 Å2
Baniso -1Baniso -2Baniso -3
1-1.72 Å214.84 Å20 Å2
2--1.72 Å20 Å2
3----3.45 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.4 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.45 Å0.36 Å
Refinement stepCycle: LAST / Resolution: 2.9→30.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2988 0 31 9 3028
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
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_deg1.6
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.97
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.791.5
X-RAY DIFFRACTIONc_mcangle_it2.922
X-RAY DIFFRACTIONc_scbond_it2.92
X-RAY DIFFRACTIONc_scangle_it4.272.5
LS refinement shellResolution: 2.9→3.08 Å / Rfactor Rfree error: 0.029 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.33 133 5.1 %
Rwork0.285 2497 -
obs--97.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
X-RAY DIFFRACTION5new_plp.paramnew_plp.top

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