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- PDB-3nh4: Crystal structure of murine aminoacylase 3 -

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Basic information

Entry
Database: PDB / ID: 3nh4
TitleCrystal structure of murine aminoacylase 3
ComponentsAspartoacylase-2
KeywordsHYDROLASE / Mercapturates
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 / cytosol / cytoplasm
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
ACETATE ION / : / FORMIC ACID / 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 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 1.2Sep 6, 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_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)37,0018
Polymers36,4931
Non-polymers5077
Water1,71195
1
A: Aspartoacylase-2
hetero molecules

A: Aspartoacylase-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,00116
Polymers72,9872
Non-polymers1,01414
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_565-x,-y+1,z1
Buried area4600 Å2
ΔGint-248 kcal/mol
Surface area23880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.661, 93.661, 97.128
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number171
Space group name H-MP62

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 36493.414 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
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

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Non-polymers , 6 types, 102 molecules

#2: Chemical ChemComp-ZN / ZINC ION


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


Mass: 132.905 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cs
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 95 / 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: 3.26 Å3/Da / Density % sol: 62.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 2M Sodium formate, 0.1M Sodium acetate, pH5.0, 0.1M Cesium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.9774 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 24, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9774 Å / Relative weight: 1
ReflectionResolution: 2→46 Å / Num. all: 32766 / Num. obs: 32766 / % possible obs: 100 % / Redundancy: 4.9 % / Rmerge(I) obs: 0.064 / Χ2: 1.071 / Net I/σ(I): 14.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2-2.073.90.50532661.097100
2.07-2.154.50.35132461.118100
2.15-2.2550.28932911.163100
2.25-2.375.10.232491.068100
2.37-2.525.10.15132531.072100
2.52-2.715.10.11132661.098100
2.71-2.995.10.08432641.08100
2.99-3.425.10.06232911.02100
3.42-4.315.10.04832951.025100
4.31-5050.03933450.98299.9

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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
Starting model: PDB ENTRY 2GU2

2gu2


Resolution: 2→46 Å / Occupancy max: 1 / Occupancy min: 0.38 / FOM work R set: 0.8712 / SU ML: 0.24 / Isotropic thermal model: Isotropic plus TLS / Cross valid method: THROUGHOUT / σ(F): 1.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2069 1660 5.07 %random
Rwork0.1844 ---
all0.1855 32711 --
obs0.1855 32711 99.86 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 48.235 Å2 / ksol: 0.412 e/Å3
Displacement parametersBiso max: 166.88 Å2 / Biso mean: 39.1555 Å2 / Biso min: 19.02 Å2
Baniso -1Baniso -2Baniso -3
1--1.0866 Å2-0 Å20 Å2
2---1.0866 Å2-0 Å2
3---2.1731 Å2
Refinement stepCycle: LAST / Resolution: 2→46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2371 0 12 95 2478
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082441
X-RAY DIFFRACTIONf_angle_d1.0383318
X-RAY DIFFRACTIONf_chiral_restr0.066365
X-RAY DIFFRACTIONf_plane_restr0.005442
X-RAY DIFFRACTIONf_dihedral_angle_d15.33894
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2-2.05770.26671440.21772542268699
2.0577-2.12410.21231460.194625842730100
2.1241-2.20.2141350.186725852720100
2.2-2.28810.23791510.185825612712100
2.2881-2.39220.24561370.186525882725100
2.3922-2.51830.23481270.188225792706100
2.5183-2.67610.22381430.198625782721100
2.6761-2.88270.24241270.203825962723100
2.8827-3.17270.20931340.19925882722100
3.1727-3.63170.22171460.176226062752100
3.6317-4.57490.16151440.154925912735100
4.5749-46.84330.17121260.17526532779100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.5336-0.2864-0.75631.40510.08830.7786-0.2604-0.0954-0.2186-0.26110.0676-0.06440.11760.07490.15930.26760.06740.1150.22890.03630.2358-14.104422.0338-9.9338
20.2690.0869-0.44311.2221-0.20780.717-0.1404-0.1152-0.2318-0.07510.09250.4750.0343-0.12630.02080.22650.06060.04250.35820.06180.3329-36.15728.83610.1173
30.4035-0.70940.36731.6351-0.59260.412-0.1339-0.0367-0.3036-0.18960.11860.34820.1003-0.02840.01380.24390.05770.08180.31230.06390.3555-30.995621.5526-1.0049
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 7:213)A7 - 213
2X-RAY DIFFRACTION2(chain A and resid 214:269)A214 - 269
3X-RAY DIFFRACTION3(chain A and resid 270:314)A270 - 314

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