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- PDB-3awn: Crystal structure of D-serine dehydratase from chicken kidney (ED... -

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Basic information

Entry
Database: PDB / ID: 3awn
TitleCrystal structure of D-serine dehydratase from chicken kidney (EDTA treated)
ComponentsD-serine dehydratase
KeywordsLYASE / PLP-dependent fold-type III enzyme / D-serine dehydratase / PLP binding / Zinc binding
Function / homology
Function and homology information


D-serine ammonia-lyase / D-serine ammonia-lyase activity / D-serine catabolic process / pyridoxal phosphate binding / dendrite / zinc ion binding / cytoplasm
Similarity search - Function
D-serine dehydratase-like domain / D-serine dehydratase-like domain / D-serine dehydratase-like domain superfamily / Putative serine dehydratase domain / Putative serine dehydratase domain / Alanine racemase, N-terminal / Alanine racemase, N-terminal domain / Lyase, Ornithine Decarboxylase; Chain A, domain 1 / Alanine racemase / PLP-binding barrel ...D-serine dehydratase-like domain / D-serine dehydratase-like domain / D-serine dehydratase-like domain superfamily / Putative serine dehydratase domain / Putative serine dehydratase domain / Alanine racemase, N-terminal / Alanine racemase, N-terminal domain / Lyase, Ornithine Decarboxylase; Chain A, domain 1 / Alanine racemase / PLP-binding barrel / TIM Barrel / Alpha-Beta Barrel / Beta Barrel / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
PYRIDOXAL-5'-PHOSPHATE / D-serine dehydratase
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsTanaka, H. / Senda, M. / Venugopalan, N. / Yamamoto, A. / Senda, T. / Ishida, T. / Horiike, K.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Crystal structure of a zinc-dependent D-serine dehydratase from chicken kidney.
Authors: Tanaka, H. / Senda, M. / Venugopalan, N. / Yamamoto, A. / Senda, T. / Ishida, T. / Horiike, K.
History
DepositionMar 25, 2011Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 15, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 9, 2015Group: Database references
Revision 1.3Nov 1, 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: D-serine dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,6962
Polymers40,4491
Non-polymers2471
Water0
1
A: D-serine dehydratase
hetero molecules

A: D-serine dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,3934
Polymers80,8982
Non-polymers4942
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Buried area4320 Å2
ΔGint-20 kcal/mol
Surface area26190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.329, 105.329, 82.018
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number89
Space group name H-MP422

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Components

#1: Protein D-serine dehydratase


Mass: 40449.242 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / References: UniProt: A9CP13, D-serine ammonia-lyase
#2: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate / Pyridoxal phosphate


Mass: 247.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10NO6P

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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: 2.81 Å3/Da / Density % sol: 56.26 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop, micro-seeding / pH: 6.5
Details: 12-15% PEG 4000, 50mM MES-NaOH, 10% 2-propanol, pH 6.5, VAPOUR DIFFUSION, HANGING DROP, MICRO-SEEDING, temperature 293K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Mar 6, 2011
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→90 Å / Num. all: 11900 / Num. obs: 11883 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.9 % / Net I/σ(I): 12.6
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 6.7 % / Num. unique all: 1675 / % possible all: 99.7

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
REFMAC5.4.0078refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ANU

3anu


Resolution: 2.8→20 Å / Cor.coef. Fo:Fc: 0.914 / Cor.coef. Fo:Fc free: 0.885 / SU B: 13.41 / SU ML: 0.267 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.364 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25677 592 5 %RANDOM
Rwork0.21065 ---
all0.21293 11245 --
obs0.21293 11245 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.024 Å2
Baniso -1Baniso -2Baniso -3
1--0.65 Å20 Å20 Å2
2---0.65 Å20 Å2
3---1.3 Å2
Refinement stepCycle: LAST / Resolution: 2.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2767 0 15 0 2782
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0212848
X-RAY DIFFRACTIONr_angle_refined_deg1.4331.9653884
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1265364
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.7222.069116
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.0815420
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2021526
X-RAY DIFFRACTIONr_chiral_restr0.0870.2440
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212182
X-RAY DIFFRACTIONr_mcbond_it0.6021.51824
X-RAY DIFFRACTIONr_mcangle_it1.13622904
X-RAY DIFFRACTIONr_scbond_it1.48331024
X-RAY DIFFRACTIONr_scangle_it2.5984.5980
LS refinement shellResolution: 2.8→2.871 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.36 43 -
Rwork0.318 799 -
obs-799 100 %

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