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- PDB-2q4z: Ensemble refinement of the protein crystal structure of an aspart... -

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Basic information

Entry
Database: PDB / ID: 2q4z
TitleEnsemble refinement of the protein crystal structure of an aspartoacylase from Rattus norvegicus
ComponentsAspartoacylase
KeywordsHYDROLASE / Ensemble Refinement / Refinement Methodology Development / Aspartoacylase family / Aminoacylase-2 / ACY-2 / ACY2_RAT / Structural Genomics / Protein Structure Initiative / PSI / Center for Eukaryotic Structural Genomics / CESG
Function / homology
Function and homology information


Aspartate and asparagine metabolism / aspartoacylase / aspartoacylase activity / acetate metabolic process / aspartate metabolic process / central nervous system myelination / 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 ...Aspartate and asparagine metabolism / aspartoacylase / aspartoacylase activity / acetate metabolic process / aspartate metabolic process / central nervous system myelination / 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 / metal ion binding / nucleus / 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
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / Re-refinement using ensemble model / Resolution: 1.8 Å
AuthorsLevin, E.J. / Kondrashov, D.A. / Wesenberg, G.E. / Phillips Jr., G.N. / Center for Eukaryotic Structural Genomics (CESG)
Citation
Journal: Structure / Year: 2007
Title: Ensemble refinement of protein crystal structures: validation and application.
Authors: Levin, E.J. / Kondrashov, D.A. / Wesenberg, G.E. / Phillips, G.N.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 2006
Title: Structure of Aspartoacylase, the Brain Enzyme Impaired in Canavan Disease.
Authors: Bitto, E. / Bingman, C.A. / Wesenberg, G.E. / Mccoy, J.G. / Phillips Jr., G.N.
History
DepositionMay 31, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2007Provider: repository / Type: Initial release
Revision 1.1Sep 25, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 10, 2011Group: Other
Revision 1.4Dec 21, 2022Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_conn_type / 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 / _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_conn_type.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 1.5Sep 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.6Nov 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)71,5569
Polymers70,9452
Non-polymers6117
Water9,944552
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)92.581, 135.778, 54.033
Angle α, β, γ (deg.)90.000, 101.490, 90.000
Int Tables number5
Space group name H-MC121
Number of models16
Components on special symmetry positions
IDModelComponents
11A-744-

HOH

21B-777-

HOH

32A-743-

HOH

42B-778-

HOH

53A-741-

HOH

63B-780-

HOH

74A-742-

HOH

84B-778-

HOH

95A-740-

HOH

105B-782-

HOH

116A-742-

HOH

126B-778-

HOH

137A-744-

HOH

147B-777-

HOH

158A-745-

HOH

168B-775-

HOH

179A-745-

HOH

189B-775-

HOH

1910A-743-

HOH

2010B-779-

HOH

2111A-745-

HOH

2211B-777-

HOH

2312A-742-

HOH

2412B-778-

HOH

2513A-743-

HOH

2613B-777-

HOH

2714A-743-

HOH

2814B-778-

HOH

2915A-743-

HOH

3015B-778-

HOH

3116A-744-

HOH

3216B-777-

HOH

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Components

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


Mass: 35472.438 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Aspa / Plasmid: PVP16 / Production host: Escherichia coli (E. coli) / Strain (production host): BL834 P(RARE2) / References: UniProt: Q9R1T5, aspartoacylase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 552 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.33 Å3/Da / Density % sol: 47.27 % / Description: AUTHOR USED THE SF DATA FROM ENTRY 2GU2.

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Data collection

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

Software
NameVersionClassificationNB
CNS1.1refinement
PDB_EXTRACT2data extraction
CNS1.1phasing
RefinementMethod to determine structure: Re-refinement using ensemble model
Starting model: PDB entry 2GU2

2gu2


Resolution: 1.8→40.5 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 3110357 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Stereochemistry target values: maximum likelihood using amplitudes
Details: This PDB entry is a re-refinement using an ensemble model of the previously deposited single-conformer structure 2gu2 and the first data set in the deposited structure factor file for 2gu2 ...Details: This PDB entry is a re-refinement using an ensemble model of the previously deposited single-conformer structure 2gu2 and the first data set in the deposited structure factor file for 2gu2 along with the R-free set defined therein. The coordinates were generated by an automated protocol from an initial model consisting of 16 identical copies of the protein and non-water hetero-atoms assigned fractional occupancies adding up to one, and a single copy of the solvent molecules. Refinement was carried out with all the conformers present simultaneously and with the potential energy terms corresponding to interactions between the different conformers excluded. The helix and sheet records were calculated using coordinates from the first conformer only. The structure visualization program PYMOL is well-suited for directly viewing the ensemble model presented in this PDB file.
RfactorNum. reflection% reflectionSelection details
Rfree0.191 2955 5.1 %RANDOM
Rwork0.138 ---
obs0.138 58207 97.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 54.219 Å2 / ksol: 0.371 e/Å3
Displacement parametersBiso mean: 19.4 Å2
Baniso -1Baniso -2Baniso -3
1--0.14 Å20 Å20.61 Å2
2--0.13 Å20 Å2
3---0.01 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.19 Å0.13 Å
Luzzati d res low-5 Å
Luzzati sigma a0.11 Å0.08 Å
Refinement stepCycle: LAST / Resolution: 1.8→40.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4862 0 27 552 5441
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d23.8
X-RAY DIFFRACTIONc_improper_angle_d0.95
X-RAY DIFFRACTIONc_mcbond_it1.491.5
X-RAY DIFFRACTIONc_mcangle_it2.132
X-RAY DIFFRACTIONc_scbond_it2.252
X-RAY DIFFRACTIONc_scangle_it3.192.5
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRfactor Rfree errorNum. reflection allNum. reflection obs% reflection obs (%)
1.8-1.920.2424575.10.19284850.0119939894290
1.92-2.070.1884524.60.12493040.00910003975697.5
2.07-2.270.1815045.20.11492720.0089952977698.2
2.27-2.60.18449450.11693250.0089956981998.6
2.6-3.280.1935165.20.13293620.0099975987899
3.28-40.50.1875325.30.15195040.008100721003699.6
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.param

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