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- PDB-3nh8: Crystal structure of murine aminoacylase 3 in complex with N-acet... -

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Basic information

Entry
Database: PDB / ID: 3nh8
TitleCrystal structure of murine aminoacylase 3 in complex with N-acetyl-S-1,2-dichlorovinyl-L-cysteine
ComponentsAspartoacylase-2
KeywordsHYDROLASE / N-acetyl-S-1 / 2-dichlorovinyl-L-cysteine
Function / homology
Function and homology information


N-acyl-aromatic-L-amino acid amidohydrolase / Aflatoxin activation and detoxification / aminoacylase activity / hydrolase activity, acting on ester bonds / apical plasma membrane / membrane / identical protein binding / metal ion binding / cytoplasm / 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
N-acetyl-S-[(1S)-1,2-dichloroethyl]-L-cysteine / N-acyl-aromatic-L-amino acid amidohydrolase (carboxylate-forming)
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.802 Å
AuthorsHsieh, J.M. / Tsirulnikov, K. / Sawaya, M.R. / Magilnick, N. / Abuladze, N. / Kurtz, I. / Abramson, J. / Pushkin, A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: Structures of aminoacylase 3 in complex with acetylated substrates.
Authors: Hsieh, J.M. / Tsirulnikov, K. / Sawaya, M.R. / Magilnick, N. / Abuladze, N. / Kurtz, I. / Abramson, J. / Pushkin, A.
History
DepositionJun 14, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 20, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 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_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.pdbx_dist_value / _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_ref_seq_dif.details / _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

Downloads & links

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Assembly

Deposited unit
A: Aspartoacylase-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,8325
Polymers36,4351
Non-polymers3964
Water25214
1
A: Aspartoacylase-2
hetero molecules

A: Aspartoacylase-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,66410
Polymers72,8712
Non-polymers7938
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_445-x-1,-y-1,z1
Buried area2830 Å2
ΔGint-60 kcal/mol
Surface area24640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.407, 93.407, 97.637
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number171
Space group name H-MP62

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Components

#1: Protein Aspartoacylase-2 / Aminoacylase-3 / ACY-3 / Aminoacylase III / Acylase III / Hepatitis C virus core-binding protein 1 / HCBP1


Mass: 36435.379 Da / Num. of mol.: 1 / Mutation: E177A
Source method: isolated from a genetically manipulated source
Details: E177A mutation / Source: (gene. exp.) Mus musculus (house mouse) / Gene: ACY-3, Acy3, Aspa2 / Plasmid: pRSET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS
References: UniProt: Q91XE4, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-DC2 / N-acetyl-S-[(1S)-1,2-dichloroethyl]-L-cysteine


Type: L-peptide linking / Mass: 260.138 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H11Cl2NO3S
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / 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: 3.27 Å3/Da / Density % sol: 62.38 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 15% PEG 4000, 0.1M Sodium cacodylate, pH 5.0, vapor diffusion, hanging drop, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 14, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. all: 11756 / Num. obs: 11756 / % possible obs: 98.2 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.154 / Χ2: 1.028 / Net I/σ(I): 8.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.8-2.93.80.4811601.07298
2.9-3.023.90.3811891.01398.7
3.02-3.1540.32411591.07898.3
3.15-3.324.20.26611730.99299.1
3.32-3.534.30.23711731.00598.6
3.53-3.84.30.17711780.99798.7
3.8-4.184.30.14211801.06898.7
4.18-4.794.30.11511791.02298.2
4.79-6.034.30.12311771.0597.4
6.03-504.50.09711880.99796.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHASERphasing
PHENIX1.5_2refinement
PDB_EXTRACT3.1data extraction
BOSdata collection
DENZOdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.802→42.132 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8474 / SU ML: 0.36 / σ(F): 0.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2235 565 5.09 %
Rwork0.1752 --
all0.1776 11107 -
obs0.1776 11107 92.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 23.784 Å2 / ksol: 0.341 e/Å3
Displacement parametersBiso max: 94.54 Å2 / Biso mean: 41.5913 Å2 / Biso min: 22.38 Å2
Baniso -1Baniso -2Baniso -3
1--1.7577 Å20 Å20 Å2
2---1.7577 Å2-0 Å2
3---3.5155 Å2
Refinement stepCycle: LAST / Resolution: 2.802→42.132 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2389 0 17 14 2420
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112460
X-RAY DIFFRACTIONf_angle_d1.473344
X-RAY DIFFRACTIONf_chiral_restr0.077370
X-RAY DIFFRACTIONf_plane_restr0.006444
X-RAY DIFFRACTIONf_dihedral_angle_d18.147900
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.8021-3.0840.3171340.23872473260788
3.084-3.53010.26471440.1922603274792
3.5301-4.44670.19511600.15352723288396
4.4467-42.13630.18841270.15852743287095

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