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- PDB-3anv: Crystal structure of D-serine dehydratase from chicken kidney (2,... -

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Basic information

Entry
Database: PDB / ID: 3anv
TitleCrystal structure of D-serine dehydratase from chicken kidney (2,3-DAP complex)
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
3-amino-D-alanine / PYRIDOXAL-5'-PHOSPHATE / D-serine dehydratase
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.09 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
Revision 1.3May 14, 2014Group: Non-polymer description
Revision 1.4Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr2_label_alt_id / _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_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)40,9015
Polymers40,4491
Non-polymers4524
Water1,53185
1
A: D-serine dehydratase
hetero molecules

A: D-serine dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,80310
Polymers80,8982
Non-polymers9048
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Buried area4500 Å2
ΔGint-20 kcal/mol
Surface area26090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.712, 104.712, 81.879
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

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Protein , 1 types, 1 molecules A

#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

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Non-polymers , 5 types, 89 molecules

#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: Chemical ChemComp-2RA / 3-amino-D-alanine / diaminopropanoic acid


Type: D-peptide linking / Mass: 104.108 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8N2O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 85 / 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: 2.77 Å3/Da / Density % sol: 55.67 %
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: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: May 5, 2010
RadiationMonochromator: Si 111 / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.09→19.92 Å / Num. all: 27589 / Num. obs: 27396 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.1 % / Net I/σ(I): 22.5
Reflection shellResolution: 2.09→2.21 Å / Redundancy: 7.3 % / Mean I/σ(I) obs: 5.7 / Num. unique all: 4158 / % possible all: 99.6

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Processing

Software
NameVersionClassification
Blu-IceGUI interface to EPICS controldata collection
SHARPphasing
REFMAC5.4.0078refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.09→17 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.938 / SU B: 4.225 / SU ML: 0.114 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.166 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23379 1370 5 %RANDOM
Rwork0.19949 ---
all0.20119 26026 --
obs0.20119 26026 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: 37.213 Å2
Baniso -1Baniso -2Baniso -3
1--1.21 Å20 Å20 Å2
2---1.21 Å20 Å2
3---2.42 Å2
Refinement stepCycle: LAST / Resolution: 2.09→17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2796 0 24 85 2905
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0212887
X-RAY DIFFRACTIONr_angle_refined_deg1.2341.9643935
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9425371
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.221.966117
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.96815424
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2591527
X-RAY DIFFRACTIONr_chiral_restr0.0870.2443
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212219
X-RAY DIFFRACTIONr_mcbond_it0.7971.51853
X-RAY DIFFRACTIONr_mcangle_it1.48822948
X-RAY DIFFRACTIONr_scbond_it2.00431034
X-RAY DIFFRACTIONr_scangle_it3.3734.5987
LS refinement shellResolution: 2.09→2.144 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.26 99 -
Rwork0.239 1887 -
obs-1887 100 %

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