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- PDB-1pwh: Rat Liver L-Serine Dehydratase- Complex with PYRIDOXYL-(O-METHYL-... -

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Basic information

Entry
Database: PDB / ID: 1pwh
TitleRat Liver L-Serine Dehydratase- Complex with PYRIDOXYL-(O-METHYL-SERINE)-5-MONOPHOSPHATE
ComponentsL-serine dehydratase
KeywordsLYASE / Rat Liver / L-Serine Dehydratase / Complex
Function / homology
Function and homology information


Threonine catabolism / threonine ammonia-lyase / threonine deaminase activity / L-serine ammonia-lyase / L-serine ammonia-lyase activity / pyruvate biosynthetic process / L-serine catabolic process / response to cobalamin / response to amino acid / gluconeogenesis ...Threonine catabolism / threonine ammonia-lyase / threonine deaminase activity / L-serine ammonia-lyase / L-serine ammonia-lyase activity / pyruvate biosynthetic process / L-serine catabolic process / response to cobalamin / response to amino acid / gluconeogenesis / response to nutrient levels / 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
: / Chem-PLV / L-serine dehydratase/L-threonine deaminase
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 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: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.5Aug 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_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_atom_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_atom_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 300BIOMOLECULE: 1, 2, 3, 4 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF ...BIOMOLECULE: 1, 2, 3, 4 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 4 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). THE AUTHORS STATE THAT CHAINS AB, CD 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

Downloads & links

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Assembly

Deposited unit
A: L-serine dehydratase
B: L-serine dehydratase
C: L-serine dehydratase
D: L-serine dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)139,58212
Polymers138,0254
Non-polymers1,5578
Water2,144119
1
A: L-serine dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,8953
Polymers34,5061
Non-polymers3892
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: L-serine dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,8953
Polymers34,5061
Non-polymers3892
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: L-serine dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,8953
Polymers34,5061
Non-polymers3892
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: L-serine dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,8953
Polymers34,5061
Non-polymers3892
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.241, 109.262, 98.940
Angle α, β, γ (deg.)90.00, 91.66, 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.: 4
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: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#3: Chemical
ChemComp-PLV / N-({3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYL)-O-METHYL-L-SERINE / PYRIDOXYL-(O-METHYL-SERINE)-5-MONOPHOSPHATE


Mass: 350.262 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C12H19N2O8P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 119 / 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: 2.44 Å3/Da / Density % sol: 49.49 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PEG 8000, potassium Acetate, TrisHCL, Dioxane, VAPOR DIFFUSION, HANGING DROP, temperature 22K
Crystal grow
*PLUS
Temperature: 22 ℃ / pH: 8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
150 mMHEPES1reservoirpH8.0
210 mMOMS1reservoir
3200 mMpotassium acetate1reservoir
41 mMdithiothreitol1reservoir
514 %(w/v)PEG80001reservoir
62 %1,4-dioxane1reservoir
720 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: Apr 5, 2003 / Details: mirrors
RadiationMonochromator: GRAPHITE + MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→100 Å / Num. obs: 40706 / % possible obs: 95.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.3 % / Biso Wilson estimate: 22.2 Å2 / Rmerge(I) obs: 0.078 / Rsym value: 0.078 / Net I/σ(I): 1692.5
Reflection shellResolution: 2.6→2.69 Å / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 491.7 / Num. unique all: 3051 / Rsym value: 0.28 / % possible all: 75.4
Reflection
*PLUS
Lowest resolution: 35 Å / Num. obs: 40796 / Num. measured all: 271545
Reflection shell
*PLUS
Rmerge(I) obs: 0.124

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Processing

Software
NameVersionClassification
CNS1.1refinement
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Apo Enzyme 1PWE

1pwe


Resolution: 2.6→25.01 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
Rfree0.26 3784 10 %RANDOM
Rwork0.23 ---
all0.26 37708 --
obs0.23 37708 92.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 15.7014 Å2 / ksol: 0.33981 e/Å3
Displacement parametersBiso mean: 20.3 Å2
Baniso -1Baniso -2Baniso -3
1-0.13 Å20 Å2-4.46 Å2
2---0.28 Å20 Å2
3---0.15 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.4 Å0.34 Å
Luzzati d res low-5 Å
Luzzati sigma a0.43 Å0.38 Å
Refinement stepCycle: LAST / Resolution: 2.6→25.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9668 0 96 119 9883
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_d22.8
X-RAY DIFFRACTIONc_improper_angle_d0.83
X-RAY DIFFRACTIONc_mcbond_it0.881.5
X-RAY DIFFRACTIONc_mcangle_it1.472
X-RAY DIFFRACTIONc_scbond_it1.312
X-RAY DIFFRACTIONc_scangle_it1.862.5
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 2.6→2.76 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.317 488 9.9 %
Rwork0.295 4452 -
obs--73.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAMION.TOP
X-RAY DIFFRACTION3WATER.PARAMWATER.TOP
X-RAY DIFFRACTION4PLSM.PARPLSM.TOP
Refinement
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 25 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.8
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.83
LS refinement shell
*PLUS
Rfactor Rfree: 0.32 / Rfactor Rwork: 0.3

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