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- PDB-1pwe: Rat Liver L-Serine Dehydratase Apo Enzyme -

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Basic information

Entry
Database: PDB / ID: 1pwe
TitleRat Liver L-Serine Dehydratase Apo Enzyme
ComponentsL-serine dehydratase
KeywordsLYASE / RAT LIVER / L-SERINE DEHYDRATASE / APO ENZYME
Function / homology
Function and homology information


Threonine catabolism / threonine ammonia-lyase / threonine deaminase activity / L-serine ammonia-lyase / L-serine ammonia-lyase activity / threonine catabolic process / pyruvate biosynthetic process / L-serine catabolic process / isoleucine biosynthetic process / response to cobalamin ...Threonine catabolism / threonine ammonia-lyase / threonine deaminase activity / L-serine ammonia-lyase / L-serine ammonia-lyase activity / threonine catabolic process / pyruvate biosynthetic process / L-serine catabolic process / isoleucine biosynthetic process / response to cobalamin / response to amino acid / response to nutrient levels / gluconeogenesis / lipid metabolic process / pyridoxal phosphate binding / protein-containing complex assembly / protein homodimerization activity / cytoplasm
Similarity search - Function
: / Serine/threonine dehydratase, pyridoxal-phosphate-binding site / Serine/threonine dehydratases pyridoxal-phosphate attachment site. / Rossmann fold - #1100 / Pyridoxal-phosphate dependent enzyme / Pyridoxal-phosphate dependent enzyme / Tryptophan synthase beta subunit-like PLP-dependent enzyme / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
L-serine dehydratase/L-threonine deaminase
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SIR / Resolution: 2.8 Å
AuthorsYamada, T. / Komoto, J. / Takata, Y. / Ogawa, H. / Takusagawa, F.
CitationJournal: Biochemistry / Year: 2003
Title: Crystal structure of serine dehydratase from rat liver.
Authors: Yamada, T. / Komoto, J. / Takata, Y. / Ogawa, H. / Pitot, H.C. / Takusagawa, F.
History
DepositionJul 1, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 2, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 300BIOMOLECULE: 1, 2, 3, 4, 5, 6 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH ...BIOMOLECULE: 1, 2, 3, 4, 5, 6 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 6 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). THE AUTHORS STATE THAT CHAINS AB, CD, EF FORM HOMODIMERS IN TERMS OF STRUCTURE. HOWEVER, SINCE THE ACTIVE SITE IN ONE SUBUNIT IS INDEPENDENT FROM THE OTHER SUBUNIT, THE ENZYMATIC REACTION PROCEEDS MONOMERICALLY.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: L-serine dehydratase
B: L-serine dehydratase
C: L-serine dehydratase
D: L-serine dehydratase
E: L-serine dehydratase
F: L-serine dehydratase


Theoretical massNumber of molelcules
Total (without water)207,0376
Polymers207,0376
Non-polymers00
Water1,964109
1
A: L-serine dehydratase


Theoretical massNumber of molelcules
Total (without water)34,5061
Polymers34,5061
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: L-serine dehydratase


Theoretical massNumber of molelcules
Total (without water)34,5061
Polymers34,5061
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: L-serine dehydratase


Theoretical massNumber of molelcules
Total (without water)34,5061
Polymers34,5061
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: L-serine dehydratase


Theoretical massNumber of molelcules
Total (without water)34,5061
Polymers34,5061
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: L-serine dehydratase


Theoretical massNumber of molelcules
Total (without water)34,5061
Polymers34,5061
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: L-serine dehydratase


Theoretical massNumber of molelcules
Total (without water)34,5061
Polymers34,5061
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
A: L-serine dehydratase
B: L-serine dehydratase


Theoretical massNumber of molelcules
Total (without water)69,0122
Polymers69,0122
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4730 Å2
ΔGint-29 kcal/mol
Surface area23360 Å2
MethodPISA, PQS
8
C: L-serine dehydratase
D: L-serine dehydratase


Theoretical massNumber of molelcules
Total (without water)69,0122
Polymers69,0122
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4720 Å2
ΔGint-29 kcal/mol
Surface area23390 Å2
MethodPISA, PQS
9
E: L-serine dehydratase
F: L-serine dehydratase


Theoretical massNumber of molelcules
Total (without water)69,0122
Polymers69,0122
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4690 Å2
ΔGint-29 kcal/mol
Surface area23410 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)70.628, 169.843, 95.998
Angle α, β, γ (deg.)90.00, 92.75, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
L-serine dehydratase


Mass: 34506.129 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Plasmid: pCWOri+ / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: P09367, L-serine ammonia-lyase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 109 / 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: 2.78 Å3/Da / Density % sol: 55.7 %
Crystal grow
*PLUS
Temperature: 26 ℃ / pH: 7 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
150 mMTris-HCl1reservoirpH7.0
21 mMdithiothreitol1reservoir
32 %(w/v)PEG33501reservoir
420 %(v/v)ethylene glycol1reservoir
510 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Aug 19, 2002 / Details: mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.8→100 Å / Num. all: 617721 / Num. obs: 617721 / % possible obs: 89.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.9 % / Biso Wilson estimate: 19.7 Å2 / Rsym value: 0.07 / Net I/σ(I): 2655.8
Reflection shellResolution: 2.8→2.9 Å / Rmerge(I) obs: 0.261 / Mean I/σ(I) obs: 727.4 / Num. unique all: 4286 / Rsym value: 0.261 / % possible all: 77.5
Reflection
*PLUS
Lowest resolution: 35 Å / Num. obs: 22269 / Num. measured all: 617721 / Rmerge(I) obs: 0.07
Reflection shell
*PLUS
Rmerge(I) obs: 0.139

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: SIR / Resolution: 2.8→23.52 Å / Rfactor Rfree error: 0.004 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.247 4806 10 %RANDOM
Rwork0.218 ---
all-47906 --
obs-47906 86.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 11.7739 Å2 / ksol: 0.316064 e/Å3
Displacement parametersBiso mean: 25.2 Å2
Baniso -1Baniso -2Baniso -3
1-2.02 Å20 Å2-5.46 Å2
2---1.86 Å20 Å2
3----0.16 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.4 Å0.36 Å
Luzzati d res low-5 Å
Luzzati sigma a0.48 Å0.45 Å
Refinement stepCycle: LAST / Resolution: 2.8→23.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13956 0 0 109 14065
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d22.4
X-RAY DIFFRACTIONc_improper_angle_d0.82
X-RAY DIFFRACTIONc_mcbond_it1.241.5
X-RAY DIFFRACTIONc_mcangle_it2.222
X-RAY DIFFRACTIONc_scbond_it1.442
X-RAY DIFFRACTIONc_scangle_it2.252.5
LS refinement shellResolution: 2.8→2.98 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.331 628 9.5 %
Rwork0.307 5975 -
obs--71.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER.PARAMWATER.TOP
Refinement
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 23.6 Å / Rfactor Rfree: 0.25 / Rfactor Rwork: 0.22
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.82
LS refinement shell
*PLUS
Rfactor Rfree: 0.33 / Rfactor Rwork: 0.31

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