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- PDB-1ei5: CRYSTAL STRUCTURE OF A D-AMINOPEPTIDASE FROM OCHROBACTRUM ANTHROPI -

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Basic information

Entry
Database: PDB / ID: 1ei5
TitleCRYSTAL STRUCTURE OF A D-AMINOPEPTIDASE FROM OCHROBACTRUM ANTHROPI
ComponentsD-AMINOPEPTIDASE
KeywordsHYDROLASE / D-AMINOPEPTIDASE / PENICILLIN BINDING PROTEIN / ALPHA/BETA DOMAIN / BETA BARREL DOMAIN
Function / homology
Function and homology information


D-stereospecific aminopeptidase / aminopeptidase activity / proteolysis
Similarity search - Function
D-aminopeptidase, domain B / D-aminopeptidase / D-aminopeptidase, domain B / Lipocalin - #50 / D-aminopeptidase/lipoprotein domain superfamily / : / Beta-lactamase-related / Beta-lactamase / Beta-lactamase / DD-peptidase/beta-lactamase superfamily ...D-aminopeptidase, domain B / D-aminopeptidase / D-aminopeptidase, domain B / Lipocalin - #50 / D-aminopeptidase/lipoprotein domain superfamily / : / Beta-lactamase-related / Beta-lactamase / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Lipocalin / Beta-lactamase/transpeptidase-like / Beta Barrel / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesOchrobactrum anthropi (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.9 Å
AuthorsBompard-Gilles, C. / Remaut, H. / Villeret, V. / Prange, T. / Fanuel, L. / Joris, J. / Frere, J.-M. / Van Beeumen, J.
CitationJournal: Structure Fold.Des. / Year: 2000
Title: Crystal structure of a D-aminopeptidase from Ochrobactrum anthropi, a new member of the 'penicillin-recognizing enzyme' family.
Authors: Bompard-Gilles, C. / Remaut, H. / Villeret, V. / Prange, T. / Fanuel, L. / Delmarcelle, M. / Joris, B. / Frere, J. / Van Beeumen, J.
History
DepositionFeb 24, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 4, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: 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: D-AMINOPEPTIDASE


Theoretical massNumber of molelcules
Total (without water)57,4591
Polymers57,4591
Non-polymers00
Water6,630368
1
A: D-AMINOPEPTIDASE

A: D-AMINOPEPTIDASE


Theoretical massNumber of molelcules
Total (without water)114,9182
Polymers114,9182
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Unit cell
Length a, b, c (Å)82.860, 82.860, 204.650
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
DetailsThe biological assembly is a dimer constructed from chain A a symmetry partner generated by the two-fold.

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Components

#1: Protein D-AMINOPEPTIDASE / DAP


Mass: 57458.754 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ochrobactrum anthropi (bacteria) / Strain: SCRC C1-38 / Plasmid: PUC18 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9ZBA9, D-stereospecific aminopeptidase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 368 / 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: 3.06 Å3/Da / Density % sol: 59.75 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 5
Details: PEG 400, sodium acetate, pH 5, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Crystal grow
*PLUS
Temperature: 21 ℃ / pH: 8
Details: drop consists of equal amounts of protein and reservoir solutions
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
19 mg/mlprotein1drop
210 mMTris-HCl1drop
310 mMdithiothreitol1drop
40.1 mMEDTA1drop
51 mMsodium azide1drop
630 %PEG4001reservoir
70.1 Msodium acetate1reservoir

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: SYNCHROTRON / Site: LURE / Beamline: DW32 / Wavelength: 0.97
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 4, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.82→15 Å / Num. all: 62212 / Num. obs: 62212 / % possible obs: 96.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 12.99 % / Biso Wilson estimate: 17.93 Å2 / Rmerge(I) obs: 0.092 / Net I/σ(I): 14.6
Reflection shellResolution: 1.82→1.89 Å / Redundancy: 4.76 % / Rmerge(I) obs: 0.346 / Num. unique all: 5161 / % possible all: 81
Reflection
*PLUS
% possible obs: 93.2 % / Redundancy: 7.9 % / Rmerge(I) obs: 0.052
Reflection shell
*PLUS
% possible obs: 81 % / Mean I/σ(I) obs: 3.5

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Processing

Software
NameClassification
SHARPphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 1.9→12.5 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.192 2735 RANDOM 5%
Rwork0.163 --
all-54705 -
obs-54705 -
Refinement stepCycle: LAST / Resolution: 1.9→12.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3961 0 0 368 4329
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.012
X-RAY DIFFRACTIONp_angle_d2.4
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Num. reflection all: 54802
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: p_angle_d / Dev ideal: 0.031

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