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- PDB-1q7l: Zn-binding domain of the T347G mutant of human aminoacylase-I -

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Basic information

Entry
Database: PDB / ID: 1q7l
TitleZn-binding domain of the T347G mutant of human aminoacylase-I
Components(Aminoacylase-1) x 2
KeywordsHYDROLASE / aminoacylase-1 / catalysis / enzyme dimerization / site-directed mutagenesis / structure comparison / zinc
Function / homology
Function and homology information


N-acyl-aliphatic-L-amino acid amidohydrolase / Defective ACY1 causes encephalopathy / aminoacylase activity / Aflatoxin activation and detoxification / Paracetamol ADME / amino acid metabolic process / extracellular exosome / metal ion binding / identical protein binding / cytosol
Similarity search - Function
DNA polymerase; domain 1 - #900 / N-acyl-L-amino-acid amidohydrolase / : / ArgE / dapE / ACY1 / CPG2 / yscS family signature 1. / ArgE / dapE / ACY1 / CPG2 / yscS family signature 2. / ArgE/DapE/ACY1/CPG2/YscS, conserved site / Bacterial exopeptidase dimerisation domain / Peptidase M20, dimerisation domain / Peptidase dimerisation domain / Peptidase M20 ...DNA polymerase; domain 1 - #900 / N-acyl-L-amino-acid amidohydrolase / : / ArgE / dapE / ACY1 / CPG2 / yscS family signature 1. / ArgE / dapE / ACY1 / CPG2 / yscS family signature 2. / ArgE/DapE/ACY1/CPG2/YscS, conserved site / Bacterial exopeptidase dimerisation domain / Peptidase M20, dimerisation domain / Peptidase dimerisation domain / Peptidase M20 / Peptidase family M20/M25/M40 / Zn peptidases / Aminopeptidase / DNA polymerase; domain 1 / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
GLYCINE / Aminoacylase-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.4 Å
AuthorsLindner, H.A. / Lunin, V.V. / Alary, A. / Hecker, R. / Cygler, M. / Menard, R.
CitationJournal: J.Biol.Chem. / Year: 2003
Title: Essential roles of zinc ligation and enzyme dimerization for catalysis in the aminoacylase-1/M20 family.
Authors: Lindner, H.A. / Lunin, V.V. / Alary, A. / Hecker, R. / Cygler, M. / Menard, R.
History
DepositionAug 19, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 20, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...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_asym_id / _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_asym_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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Aminoacylase-1
B: Aminoacylase-1
C: Aminoacylase-1
D: Aminoacylase-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,10910
Polymers64,6984
Non-polymers4126
Water12,016667
1
A: Aminoacylase-1
B: Aminoacylase-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,4804
Polymers32,3492
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7500 Å2
ΔGint-122 kcal/mol
Surface area12180 Å2
MethodPISA
2
C: Aminoacylase-1
D: Aminoacylase-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,6306
Polymers32,3492
Non-polymers2814
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7010 Å2
ΔGint-105 kcal/mol
Surface area12030 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17600 Å2
ΔGint-264 kcal/mol
Surface area21130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.528, 67.249, 146.479
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsA dimer formed without dimerization domains. This dimer is not biologically relevant.

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Components

#1: Protein Aminoacylase-1 / N-acyl-L-amino-acid amidohydrolase / ACY-1


Mass: 22556.510 Da / Num. of mol.: 2 / Fragment: Zn-binding domain (residues 1-198)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ACY1 / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Sf21
References: UniProt: Q03154, N-acyl-aliphatic-L-amino acid amidohydrolase
#2: Protein Aminoacylase-1 / N-acyl-L-amino-acid amidohydrolase / ACY-1


Mass: 9792.244 Da / Num. of mol.: 2 / Fragment: residues 321-408 / Mutation: T347G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ACY1 / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Sf21
References: UniProt: Q03154, N-acyl-aliphatic-L-amino acid amidohydrolase
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-GLY / GLYCINE


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H5NO2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 667 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.04 Å3/Da / Density % sol: 39.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: PEG8000, (NH4)2SO4, CoCl2, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
15-8 mg/mlprotein1drop
220 mMTris-HCl1droppH7.5
320 %(w/v)PEG80001reservoir
40.2 Mammonium sulfate1reservoir
52 mM1reservoirCoCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 1.005685 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 20, 2002
RadiationMonochromator: GRAPHITE / Protocol: SAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.005685 Å / Relative weight: 1
Reflection
*PLUS
Highest resolution: 1.5 Å / Lowest resolution: 50 Å / Num. obs: 158345 / % possible obs: 95.8 % / Num. measured all: 529534 / Rmerge(I) obs: 0.074
Reflection shell
*PLUS
Highest resolution: 1.5 Å / Lowest resolution: 1.55 Å / % possible obs: 81.9 % / Rmerge(I) obs: 0.344

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Processing

Software
NameVersionClassification
REFMAC5.1.08refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: SIRAS / Resolution: 1.4→33.71 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.969 / SU B: 0.787 / SU ML: 0.031 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.056 / ESU R Free: 0.054 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17208 1037 1 %RANDOM
Rwork0.1326 ---
all0.133 102135 --
obs0.13299 102135 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 15.204 Å2
Baniso -1Baniso -2Baniso -3
1--0.55 Å20 Å20 Å2
2--0.65 Å20 Å2
3----0.1 Å2
Refinement stepCycle: LAST / Resolution: 1.4→33.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4446 0 14 667 5127
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0214608
X-RAY DIFFRACTIONr_angle_refined_deg1.891.9366253
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1865551
X-RAY DIFFRACTIONr_dihedral_angle_2_deg11.2515700
X-RAY DIFFRACTIONr_chiral_restr0.1420.2670
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.023600
X-RAY DIFFRACTIONr_nbd_refined0.2080.22145
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1440.2430
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3680.255
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.30.235
X-RAY DIFFRACTIONr_mcbond_it1.9271.52793
X-RAY DIFFRACTIONr_mcangle_it2.7224519
X-RAY DIFFRACTIONr_scbond_it3.61631815
X-RAY DIFFRACTIONr_scangle_it5.1134.51734
X-RAY DIFFRACTIONr_rigid_bond_restr1.85924608
X-RAY DIFFRACTIONr_sphericity_free6.6552667
X-RAY DIFFRACTIONr_sphericity_bonded4.73324460
LS refinement shellResolution: 1.4→1.436 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.321 67
Rwork0.23 6373
Refinement
*PLUS
Highest resolution: 1.4 Å / Lowest resolution: 50 Å / Rfactor Rfree: 0.172 / Rfactor Rwork: 0.133
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.023
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.89

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