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- PDB-1b65: Structure of l-aminopeptidase d-ala-esterase/amidase from ochroba... -

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Basic information

Entry
Database: PDB / ID: 1b65
TitleStructure of l-aminopeptidase d-ala-esterase/amidase from ochrobactrum anthropi, a prototype for the serine aminopeptidases, reveals a new variant among the ntn hydrolase fold
ComponentsPROTEIN (AMINOPEPTIDASE)
KeywordsHYDROLASE / PEPTIDE DEGRADATION / NTN HYDROLASE
Function / homology
Function and homology information


D-stereospecific aminopeptidase / aminopeptidase activity
Similarity search - Function
Peptidase S58, DmpA / Peptidase family S58 / L-amino peptidase D-ALA esterase/amidase / L-amino peptidase D-ALA esterase/amidase / ArgJ-like domain superfamily / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesOchrobactrum anthropi (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.82 Å
AuthorsBompard-Gilles, C. / Villeret, V. / Davies, G.J. / Fanuel, L. / Joris, B. / Frere, J.M. / Van Beeumen, J.
Citation
Journal: Structure Fold.Des. / Year: 2000
Title: A new variant of the Ntn hydrolase fold revealed by the crystal structure of L-aminopeptidase D-ala-esterase/amidase from Ochrobactrum anthropi.
Authors: Bompard-Gilles, C. / Villeret, V. / Davies, G.J. / Fanuel, L. / Joris, B. / Frere, J.M. / Van Beeumen, J.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1999
Title: Crystallization and preliminary X-ray analysis of a new L-aminopeptidase-D-amidase/D-esterase activated by a Gly-Ser peptide bond hydrolysis.
Authors: Bompard-Gilles, C. / Villeret, V. / Fanuel, L. / Joris, B. / Frere, J.M. / Van Beeumen, J.
#2: Journal: To be Published
Title: Structure of L-Aminopeptidase D-Ala-Esterase/ Amidase from Ochrobactrum Anthropi, a Prototype for the Serine Aminopeptidases,Reveals a New Variant Among the Ntn Hydrolase Fold
Authors: Bompard-Gilles, C. / Villeret, V. / Davies, G.J. / Fanuel, L. / Joris, B. / Frere, J.M. / Van Beeumen, J.
History
DepositionJan 20, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Jul 23, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (AMINOPEPTIDASE)
B: PROTEIN (AMINOPEPTIDASE)
C: PROTEIN (AMINOPEPTIDASE)
D: PROTEIN (AMINOPEPTIDASE)
E: PROTEIN (AMINOPEPTIDASE)
F: PROTEIN (AMINOPEPTIDASE)


Theoretical massNumber of molelcules
Total (without water)242,7456
Polymers242,7456
Non-polymers00
Water23,4921304
1
A: PROTEIN (AMINOPEPTIDASE)
B: PROTEIN (AMINOPEPTIDASE)
C: PROTEIN (AMINOPEPTIDASE)
D: PROTEIN (AMINOPEPTIDASE)


Theoretical massNumber of molelcules
Total (without water)161,8304
Polymers161,8304
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18470 Å2
ΔGint-54 kcal/mol
Surface area40890 Å2
MethodPISA
2
E: PROTEIN (AMINOPEPTIDASE)
F: PROTEIN (AMINOPEPTIDASE)

E: PROTEIN (AMINOPEPTIDASE)
F: PROTEIN (AMINOPEPTIDASE)


Theoretical massNumber of molelcules
Total (without water)161,8304
Polymers161,8304
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Unit cell
Length a, b, c (Å)156.970, 96.220, 154.410
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.999, -0.033), (0.001, -1, -0.007), (-0.033, -0.007, 0.999)78.332, 57.996, 1.507
2given(-0.589, 0.808, 0.008), (0.808, 0.589, 0.021), (0.012, 0.019, -1)37.969, -19.946, 50.621
3given(0.59, -0.807, 0.024), (-0.807, -0.59, -0.01), (0.022, -0.014, -1)38.626, 77.501, 51.179
4given(-0.272, 0.962, -0.015), (-0.962, -0.272, -0.005), (-0.009, 0.013, 1)14.96, 117.801, -51.27
5given(-0.618, -0.786, 0.014), (-0.786, 0.618, 0.007), (-0.014, -0.007, -1)123.808, 60.394, 104.461

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Components

#1: Protein
PROTEIN (AMINOPEPTIDASE) / DMPA


Mass: 40457.516 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ochrobactrum anthropi (bacteria) / Strain: LMG7991 / Production host: Escherichia coli (E. coli) / References: UniProt: Q59632
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1304 / 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: 2.43 Å3/Da / Density % sol: 49 %
Crystal growpH: 9 / Details: pH 9.0
Crystal
*PLUS
Density % sol: 49 %
Crystal grow
*PLUS
Temperature: 294 K / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 mg/mlprotein1drop
213-16 %(w/v)PEG2000 MME1reservoir
3100 mMbicine1reservoir
41 M1reservoirLiCl

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Data collection

DiffractionMean temperature: 294 K
Diffraction sourceSource: SYNCHROTRON / Site: LURE / Beamline: DW32 / Wavelength: 0.9
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.82→12.5 Å / Num. obs: 56600 / % possible obs: 95.8 % / Observed criterion σ(I): 2 / Redundancy: 3.5 % / Rsym value: 0.058
Reflection
*PLUS
Num. measured all: 473750 / Rmerge(I) obs: 0.081
Reflection shell
*PLUS
Highest resolution: 1.82 Å / Lowest resolution: 1.9 Å / % possible obs: 91.9 % / Rmerge(I) obs: 0.288 / Mean I/σ(I) obs: 6.9

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CCP4model building
REFMACrefinement
CCP4phasing
RefinementMethod to determine structure: MIR / Resolution: 1.82→12.5 Å / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.206 -5 %
Rwork0.169 --
obs0.17 56600 95.8 %
Refinement stepCycle: LAST / Resolution: 1.82→12.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16482 0 0 1304 17786
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.013
X-RAY DIFFRACTIONp_angle_d0.034
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
σ(F): 0 / Rfactor obs: 0.169 / Num. reflection obs: 180391 / Num. reflection Rfree: 9535
Solvent computation
*PLUS
Displacement parameters
*PLUS

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