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- PDB-3anu: Crystal structure of D-serine dehydratase from chicken kidney -

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Basic information

Entry
Database: PDB / ID: 3anu
TitleCrystal structure of D-serine dehydratase from chicken kidney
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 ...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 / MAD / Resolution: 1.9 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
DepositionSep 9, 2010Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 15, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 7, 2013Group: Database references

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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)40,7974
Polymers40,4491
Non-polymers3483
Water2,576143
1
A: D-serine dehydratase
hetero molecules

A: D-serine dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,5948
Polymers80,8982
Non-polymers6966
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Buried area4410 Å2
ΔGint-19 kcal/mol
Surface area25980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.578, 104.578, 81.449
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number89
Space group name H-MP422
Components on special symmetry positions
IDModelComponents
11A-450-

CL

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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


Mass: 247.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 143 / 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: 2.75 Å3/Da / Density % sol: 55.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 12-15% PEG 4000, 50mM MES-NaOH, 10% 2-propanol, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1.0000, 1.28179, 1.28284, 1.25510, 1.30300
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 12, 2010
RadiationMonochromator: Si 111 / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
21.281791
31.282841
41.25511
51.3031
ReflectionResolution: 1.9→17 Å / Num. all: 36209 / Num. obs: 35919 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.9 % / Net I/σ(I): 26.5
Reflection shellResolution: 1.9→2 Å / Redundancy: 6.7 % / Mean I/σ(I) obs: 3.5 / Num. unique all: 5021 / % possible all: 99.7

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SHARPphasing
REFMAC5.4.0078refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MAD / Resolution: 1.9→17 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.952 / SU B: 6.761 / SU ML: 0.088 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.122 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21486 1796 5 %RANDOM
Rwork0.18906 ---
all0.19035 34123 --
obs0.19035 34123 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: 35.334 Å2
Baniso -1Baniso -2Baniso -3
1--1.4 Å20 Å20 Å2
2---1.4 Å20 Å2
3---2.8 Å2
Refinement stepCycle: LAST / Resolution: 1.9→17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2778 0 17 143 2938
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0212873
X-RAY DIFFRACTIONr_angle_refined_deg1.3091.9653916
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8735365
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.41422.101119
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.88215433
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2551527
X-RAY DIFFRACTIONr_chiral_restr0.0960.2442
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212199
X-RAY DIFFRACTIONr_mcbond_it0.6471.51830
X-RAY DIFFRACTIONr_mcangle_it1.17622919
X-RAY DIFFRACTIONr_scbond_it1.89431043
X-RAY DIFFRACTIONr_scangle_it3.1084.5997
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.347 129 -
Rwork0.31 2449 -
obs-2449 100 %
Refinement TLS params.Method: refined / Origin x: 0.537 Å / Origin y: 67.602 Å / Origin z: 20.608 Å
111213212223313233
T0.0588 Å2-0.0163 Å2-0.02 Å2-0.0452 Å2-0.021 Å2--0.0584 Å2
L1.3269 °2-1.1619 °2-0.0746 °2-2.7554 °2-0.273 °2--0.5709 °2
S0.0256 Å °0.0586 Å °-0.0387 Å °-0.1854 Å °-0.0248 Å °0.0326 Å °-0.0342 Å °0.0107 Å °-0.0007 Å °

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