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- PDB-2i3c: Crystal Structure of an Aspartoacylase from Homo Sapiens -

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Basic information

Entry
Database: PDB / ID: 2i3c
TitleCrystal Structure of an Aspartoacylase from Homo Sapiens
ComponentsAspartoacylase
KeywordsHYDROLASE / Canavan disease / N-acetyl-L-aspartate / Zinc-dependent hydrolase / Aspartoacylase family / Aminoacylase-2 / ACY2 / ASPA / PROTEIN STRUCTURE INITIATIVE / PSI / CENTER FOR EUKARYOTIC STRUCTURAL GENOMICS / CESG
Function / homology
Function and homology information


aspartoacylase / aspartoacylase activity / acetate metabolic process / aspartate metabolic process / central nervous system myelination / Aspartate and asparagine metabolism / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides / hydrolase activity, acting on ester bonds / positive regulation of oligodendrocyte differentiation / identical protein binding ...aspartoacylase / aspartoacylase activity / acetate metabolic process / aspartate metabolic process / central nervous system myelination / Aspartate and asparagine metabolism / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides / hydrolase activity, acting on ester bonds / positive regulation of oligodendrocyte differentiation / identical protein binding / nucleus / metal ion binding / cytosol
Similarity search - Function
N-terminal domain of TfIIb - #160 / Aspartoacylase / Succinylglutamate desuccinylase/aspartoacylase / Succinylglutamate desuccinylase / Aspartoacylase family / N-terminal domain of TfIIb / Zn peptidases / Single Sheet / Aminopeptidase / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Aspartoacylase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsBitto, E. / Wesenberg, G.E. / Phillips Jr., G.N. / Mccoy, J.G. / Bingman, C.A. / Center for Eukaryotic Structural Genomics (CESG)
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2007
Title: Structure of aspartoacylase, the brain enzyme impaired in Canavan disease.
Authors: Bitto, E. / Bingman, C.A. / Wesenberg, G.E. / McCoy, J.G. / Phillips, G.N.
History
DepositionAug 17, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 29, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Aug 30, 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_ncs_dom_lim / struct_ref_seq_dif / 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_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_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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_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_asym_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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Aspartoacylase
B: Aspartoacylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,27012
Polymers72,3792
Non-polymers89110
Water64936
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4500 Å2
ΔGint-150 kcal/mol
Surface area25860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)145.551, 145.551, 103.396
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / End auth comp-ID: CYS / End label comp-ID: CYS / Refine code: 2 / Auth seq-ID: 9 - 310 / Label seq-ID: 11 - 312

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
DetailsThe biological unit is a dimer (chains A & B in ASU).

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Components

#1: Protein Aspartoacylase / Aminoacylase-2 / ACY-2


Mass: 36189.566 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ASPA, ACY2, ASP / Plasmid: PVP 33K / Production host: Escherichia coli (E. coli) / Strain (production host): BL834 P(RARE2) / References: UniProt: P45381, aspartoacylase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 36 / 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: 3.8 Å3/Da / Density % sol: 67.6 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: PROTEIN SOLUTION (10 MG/ML PROTEIN, 0.050 M SODIUM CHLORIDE, 0.0003 M TCEP, 0.005 M Tris PH 8.0) MIXED IN A 1:1 RATIO WITH THE WELL SOLUTION (1.344 M K2HPO4, 0.056 M NaH2PO4) CRYOPROTECTED ...Details: PROTEIN SOLUTION (10 MG/ML PROTEIN, 0.050 M SODIUM CHLORIDE, 0.0003 M TCEP, 0.005 M Tris PH 8.0) MIXED IN A 1:1 RATIO WITH THE WELL SOLUTION (1.344 M K2HPO4, 0.056 M NaH2PO4) CRYOPROTECTED WITH WELL SOLUTION WITH 25% Ethylene glycol, vapor diffusion, hanging drop, temperature 277K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 22-ID10.97926
2
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 5, 2006
Details: HORIZONTAL SAGITALLY FOCUSING 2ND BENT MONOCHROMATOR CRYSTAL, VERTICAL BENT FOCUSING MIRROR
RadiationMonochromator: CRYOGENICALLY COOLED SI (220) DOUBLE BOUNCE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 2.8→48.716 Å / Num. obs: 27367 / % possible obs: 97.9 % / Redundancy: 13.3 % / Rmerge(I) obs: 0.164 / Χ2: 1.238 / Net I/σ(I): 10.612
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
2.8-2.96.20.5821.86622071.17481.4
2.9-3.028.10.53626661.00697
3.02-3.1511.80.47427571.012100
3.15-3.3214.40.37327681.061100
3.32-3.5315.20.2927291.157100
3.53-3.815.30.21127881.296100
3.8-4.1815.40.14727841.261100
4.18-4.7915.30.1228061.353100
4.79-6.0315.10.11628511.352100
6.03-48.71614.20.08730111.46899.8

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Phasing

Phasing MRRfactor: 0.434 / Cor.coef. Fo:Fc: 0.498
Highest resolutionLowest resolution
Rotation4 Å48.69 Å
Translation4 Å48.69 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMAC5.2.0005refinement
PDB_EXTRACT2data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2gu2

2gu2


Resolution: 2.8→48.716 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.899 / WRfactor Rfree: 0.215 / WRfactor Rwork: 0.175 / SU B: 23.555 / SU ML: 0.217 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.501 / ESU R Free: 0.305 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.243 1374 5.032 %RANDOM
Rwork0.195 ---
all0.197 ---
obs0.197 27305 97.794 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 47.682 Å2
Baniso -1Baniso -2Baniso -3
1-0.567 Å20 Å20 Å2
2--0.567 Å20 Å2
3----1.133 Å2
Refinement stepCycle: LAST / Resolution: 2.8→48.716 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4860 0 42 36 4938
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0225014
X-RAY DIFFRACTIONr_angle_refined_deg1.5511.9726800
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2375602
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.42624.492236
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.84315874
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.2021524
X-RAY DIFFRACTIONr_chiral_restr0.0990.2738
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023788
X-RAY DIFFRACTIONr_nbd_refined0.2290.22122
X-RAY DIFFRACTIONr_nbtor_refined0.3210.23395
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1230.2113
X-RAY DIFFRACTIONr_metal_ion_refined0.2140.26
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1930.228
X-RAY DIFFRACTIONr_mcbond_it1.39923094
X-RAY DIFFRACTIONr_mcangle_it2.41544914
X-RAY DIFFRACTIONr_scbond_it4.44162142
X-RAY DIFFRACTIONr_scangle_it6.16681886
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
1208TIGHT POSITIONAL0.050.05
1222MEDIUM POSITIONAL0.40.5
1208TIGHT THERMAL0.110.5
1222MEDIUM THERMAL0.952
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.8-2.8730.419900.3541502201778.929
2.873-2.9510.409960.3371731197692.46
2.951-3.0370.345810.2931824192998.756
3.037-3.130.2871070.2521756186699.839
3.13-3.2330.264910.2111718181199.89
3.233-3.3460.262950.19416551750100
3.346-3.4720.267780.1971623170399.883
3.472-3.6140.245760.1915531629100
3.614-3.7750.25790.1841503158399.937
3.775-3.9580.228850.17714331518100
3.958-4.1720.198640.1671376144199.931
4.172-4.4250.206670.14112941361100
4.425-4.730.178600.13612271287100
4.73-5.1080.165660.14211381204100
5.108-5.5940.24660.17110591125100
5.594-6.2520.249450.1889671012100
6.252-7.2150.256470.207864911100
7.215-8.8250.243330.2751784100
8.825-12.4360.156300.166594624100
12.436-48.7160.32180.33936339097.692

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