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- PDB-3gip: Crystal structure of N-acyl-D-Glutamate Deacylase from Bordetella... -

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Basic information

Entry
Database: PDB / ID: 3gip
TitleCrystal structure of N-acyl-D-Glutamate Deacylase from Bordetella Bronchiseptica complexed with zinc, acetate and formate ions.
ComponentsN-acyl-D-glutamate deacylase
KeywordsHYDROLASE / N-acyl-D-Glutamate Deacylase / Amidohydrolase family
Function / homology
Function and homology information


N-acyl-D-glutamate deacylase / N-acyl-D-glutamate deacylase activity / metal ion binding
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 / Dna Ligase; domain 1 ...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
ACETIC ACID / FORMIC ACID / N-acyl-D-glutamate deacylase / N-acyl-D-glutamate deacylase
Similarity search - Component
Biological speciesBordetella bronchiseptica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsFedorov, A.A. / Fedorov, E.V. / Cummings, J. / Raushel, F.M. / Almo, S.C.
CitationJournal: Biochemistry / Year: 2009
Title: Annotating enzymes of uncertain function: the deacylation of D-amino acids by members of the amidohydrolase superfamily.
Authors: Cummings, J.A. / Fedorov, A.A. / Xu, C. / Brown, S. / Fedorov, E. / Babbitt, P.C. / Almo, S.C. / Raushel, F.M.
History
DepositionMar 5, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 1, 2009Provider: 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 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_label_asym_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

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Assembly

Deposited unit
A: N-acyl-D-glutamate deacylase
B: N-acyl-D-glutamate deacylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,79110
Polymers102,3562
Non-polymers4358
Water12,322684
1
A: N-acyl-D-glutamate deacylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,3955
Polymers51,1781
Non-polymers2184
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: N-acyl-D-glutamate deacylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,3955
Polymers51,1781
Non-polymers2184
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)90.988, 90.988, 507.134
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein N-acyl-D-glutamate deacylase /


Mass: 51177.965 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bordetella bronchiseptica (bacteria) / Gene: BB3285 / Production host: Escherichia coli (E. coli)
References: UniProt: Q7WHC3, UniProt: A0A0H3LXD5*PLUS, N-acyl-D-glutamate deacylase
#2: Chemical ChemComp-ACY / ACETIC ACID / Acetic acid


Mass: 60.052 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H4O2
#3: Chemical
ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CH2O2
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 684 / 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: 2.96 Å3/Da / Density % sol: 58.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 2.0M sodium formate, 0.1M sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 6, 2008
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 1.5→25 Å / Num. all: 190443 / Num. obs: 190443 / % possible obs: 95.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 18.4 Å2 / Rmerge(I) obs: 0.074

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
BALBESphasing
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→24.95 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 2563033.1 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.215 9565 5 %RANDOM
Rwork0.205 ---
obs0.205 190443 95.4 %-
all-190443 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 50.3345 Å2 / ksol: 0.386183 e/Å3
Displacement parametersBiso mean: 19.2 Å2
Baniso -1Baniso -2Baniso -3
1-3.59 Å21.94 Å20 Å2
2--3.59 Å20 Å2
3----7.18 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.2 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.19 Å0.18 Å
Refinement stepCycle: LAST / Resolution: 1.5→24.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7110 0 2 704 7816
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d23.5
X-RAY DIFFRACTIONc_improper_angle_d0.84
X-RAY DIFFRACTIONc_mcbond_it0.881.5
X-RAY DIFFRACTIONc_mcangle_it1.292
X-RAY DIFFRACTIONc_scbond_it1.742
X-RAY DIFFRACTIONc_scangle_it2.382.5
LS refinement shellResolution: 1.5→1.55 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.347 751 5 %
Rwork0.343 14121 -
obs-14121 76.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION4cis_peptide.param&_1_TOPOLOGY_INFILE_4
X-RAY DIFFRACTION5inh_par.txt&_1_TOPOLOGY_INFILE_5

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