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- PDB-2dzp: Structure of mutant tryptophan synthase alpha-subunit (D17N) from... -

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Basic information

Entry
Database: PDB / ID: 2dzp
TitleStructure of mutant tryptophan synthase alpha-subunit (D17N) from a hyperthermophile, Pyrococcus furiosus
ComponentsTryptophan synthase alpha chain
KeywordsLYASE / tryptophan synthase alpha-subunit / hyperthermophile / pyrococcus furiosus / x-ray analysis / stability / calorimetry / 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 / cytosol
Similarity search - Function
Tryptophan synthase, alpha chain / Tryptophan synthase, alpha chain, active site / Tryptophan synthase alpha chain / Tryptophan synthase alpha chain signature. / Ribulose-phosphate binding barrel / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Tryptophan synthase alpha chain
Similarity search - Component
Biological speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.4 Å
AuthorsOgasahara, K. / Yamagata, Y. / Yutani, K. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
Citation
Journal: To be Published
Title: Structures of mutant tryptophan synthase alpha-subunits from a hyperthermophile, Pyrococcus furiosus
Authors: Ogasahara, K. / Yamagata, Y. / Yutani, K.
#1: Journal: J.Biol.Chem. / Year: 2001
Title: Entropic stabilization of the tryptophan synthase alpha-subunit from a hyperthermophile, Pyrococcus furiosus. X-ray analysis and calorimetry
Authors: Yamagata, Y. / Ogasahara, K. / Hioki, Y. / Lee, S.J. / Nakagawa, A. / Nakamura, H. / Ishida, M. / Kuramitsu, S. / Yutani, K.
History
DepositionSep 30, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 28, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 10, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3Oct 25, 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

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Assembly

Deposited unit
A: Tryptophan synthase alpha chain
B: Tryptophan synthase alpha chain


Theoretical massNumber of molelcules
Total (without water)55,0702
Polymers55,0702
Non-polymers00
Water6,485360
1
A: Tryptophan synthase alpha chain


Theoretical massNumber of molelcules
Total (without water)27,5351
Polymers27,5351
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Tryptophan synthase alpha chain


Theoretical massNumber of molelcules
Total (without water)27,5351
Polymers27,5351
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.268, 75.777, 165.869
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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


Mass: 27534.859 Da / Num. of mol.: 2 / Mutation: D17A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Gene: trpA / Plasmid: pa1974 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: Q8U094, tryptophan synthase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 360 / 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: 2.12 Å3/Da / Density % sol: 41.93 %
Crystal growTemperature: 283 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M MES-NAOH, 10-15% PEG 20000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 283K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL40B2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 15, 2001 / Details: mirror
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.21→20 Å / Num. all: 23451 / Num. obs: 23451 / % possible obs: 96.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Biso Wilson estimate: 32.8 Å2 / Rmerge(I) obs: 0.049 / Net I/σ(I): 36.7
Reflection shellResolution: 2.21→2.28 Å / Rmerge(I) obs: 0.126 / Mean I/σ(I) obs: 18.3 / Num. unique all: 2080 / % possible all: 87.2

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Processing

Software
NameVersionClassification
CNS1.1refinement
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 1GEQ

1geq


Resolution: 2.4→19.98 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 2421910.49 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.279 869 4.8 %RANDOM
Rwork0.218 ---
obs0.218 18134 97.2 %-
all-18134 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 43.7904 Å2 / ksol: 0.311861 e/Å3
Displacement parametersBiso mean: 31.4 Å2
Baniso -1Baniso -2Baniso -3
1--5.54 Å20 Å20 Å2
2--6.57 Å20 Å2
3----1.03 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.29 Å0.19 Å
Refinement stepCycle: LAST / Resolution: 2.4→19.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3837 0 0 360 4197
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
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_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.7
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.411.5
X-RAY DIFFRACTIONc_mcangle_it2.22
X-RAY DIFFRACTIONc_scbond_it1.942
X-RAY DIFFRACTIONc_scangle_it2.722.5
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.318 139 4.6 %
Rwork0.24 2886 -
obs--99.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top

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