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- PDB-1m7j: Crystal structure of D-aminoacylase defines a novel subset of ami... -

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Basic information

Entry
Database: PDB / ID: 1m7j
TitleCrystal structure of D-aminoacylase defines a novel subset of amidohydrolases
ComponentsD-aminoacylase
KeywordsHYDROLASE / TIN-barrel / metal-dependent amidohydrolase
Function / homology
Function and homology information


N-acyl-D-amino-acid deacylase / N-acyl-D-amino-acid deacylase activity / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amides / metal ion binding / cytosol
Similarity search - Function
D-aminoacylase. Domain 3 / D-aminoacylase, insert domain superfamily / Amidohydrolase 3 / Amidohydrolase family / : / Urease, subunit C; domain 1 / Urease, subunit C, domain 1 / Metal-dependent hydrolase, composite domain superfamily / Metal-dependent hydrolases / Metal-dependent hydrolase ...D-aminoacylase. Domain 3 / D-aminoacylase, insert domain superfamily / Amidohydrolase 3 / Amidohydrolase family / : / Urease, subunit C; domain 1 / Urease, subunit C, domain 1 / Metal-dependent hydrolase, composite domain superfamily / Metal-dependent hydrolases / Metal-dependent hydrolase / Dna Ligase; domain 1 / Roll / TIM Barrel / Alpha-Beta Barrel / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / D-aminoacylase
Similarity search - Component
Biological speciesAlcaligenes faecalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.5 Å
AuthorsLiaw, S.-H. / Chen, S.-J. / Ko, T.-P. / Hsu, C.-S. / Wang, A.H.-J. / Tsai, Y.-C.
Citation
Journal: J.Biol.Chem. / Year: 2003
Title: Crystal Structure of D-Aminoacylase from Alcaligenes faecalis DA1. A NOVEL SUBSET OF AMIDOHYDROLASES AND INSIGHTS INTO THE ENZYME MECHANISM.
Authors: Liaw, S.-H. / Chen, S.-J. / Ko, T.-P. / Hsu, C.-S. / Chen, C.J. / Wang, A.H. / Tsai, Y.-C.
#1: Journal: Protein Sci. / Year: 2002
Title: Structural-based mutational analysis of D-aminoacylase from Alcaligenes faecalis DA1.
Authors: Hsu, C.-S. / Lai, W.-L. / Chang, W.-W. / Liaw, S.-H. / Tsai, Y.-C.
#2: Journal: Acta Crystallogr.,Sect.D / Year: 2002
Title: Crystallization and preliminary crystallographic analysis of a D-aminoacylase from Alcaligenes faecalis DA1
Authors: Hsu, C.-S. / Chen, S.-J. / Tsai, Y.-C. / Lin, T.-W. / Liaw, S.-H. / Wang, A.H.
History
DepositionJul 22, 2002Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 25, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.4Mar 13, 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_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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_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_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_conn.ptnr2_label_seq_id / _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: D-aminoacylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,3105
Polymers52,0611
Non-polymers2494
Water9,062503
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.102, 77.167, 135.744
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThis protein is monomeric.

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Components

#1: Protein D-aminoacylase / N-acyl-D-amino acid amidohydrolase


Mass: 52060.707 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Alcaligenes faecalis (bacteria) / Plasmid: pQE / Production host: Escherichia coli (E. coli) / Strain (production host): M15 / References: UniProt: Q9AGH8, N-acyl-D-amino-acid deacylase
#2: Chemical ChemComp-ZN / ZINC ION


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


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 503 / 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: 2.74 Å3/Da / Density % sol: 54.79 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: sodium citrate, ammonium acetate, PEG 4000, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal grow
*PLUS
Details: Hsu, C.-S., (2002) Acta Crystallogr., Sect.D, 58, 1482.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
125-30 %PEG40001reservoir
20.1 Msodium citrate1reservoirpH5.6
30.2 Mammonium acetate1reservoir
412-20 mg/mlprotein1drop

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSPring-8 BL41XU11
SYNCHROTRONPhoton Factory BL-18B20.9197
Detector
TypeIDDetectorDate
ADSC QUANTUM 41CCDApr 10, 2002
ADSC QUANTUM 42CCDMar 5, 2002
RadiationMonochromator: rotated-inclined double-crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.91971
ReflectionResolution: 1.5→50 Å / Num. all: 101683 / Num. obs: 100783 / % possible obs: 99.2 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 6.3 % / Rmerge(I) obs: 0.047 / Net I/σ(I): 50.5
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.116 / Mean I/σ(I) obs: 17.6 / Num. unique all: 9984 / % possible all: 100
Reflection
*PLUS
Lowest resolution: 150 Å
Reflection shell
*PLUS
Highest resolution: 1.5 Å / % possible obs: 100 % / Num. unique obs: 9984

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Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
CNSrefinement
WARPmodel building
HKL-2000data reduction
CNSphasing
ARP/wARPmodel building
RefinementMethod to determine structure: SAD / Resolution: 1.5→50 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.174 5056 -random
Rwork0.16 ---
all0.161 101683 --
obs0.161 100057 98.4 %-
Displacement parametersBiso mean: 10.8 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.15 Å0.13 Å
Luzzati d res low-5 Å
Luzzati sigma a-0.05 Å-0.06 Å
Refinement stepCycle: LAST / Resolution: 1.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3589 0 10 503 4102
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.77
X-RAY DIFFRACTIONc_bond_d0.015
LS refinement shellResolution: 1.5→1.55 Å
RfactorNum. reflection% reflection
Rfree0.173 --
Rwork0.159 --
obs-9984 100 %
Refinement
*PLUS
Lowest resolution: 150 Å / Rfactor Rwork: 0.16
Solvent computation
*PLUS
Displacement parameters
*PLUS

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