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- PDB-1ve6: Crystal structure of an acylpeptide hydrolase/esterase from Aerop... -

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Basic information

Entry
Database: PDB / ID: 1ve6
TitleCrystal structure of an acylpeptide hydrolase/esterase from Aeropyrum pernix K1
ComponentsAcylamino-acid-releasing enzyme
KeywordsHYDROLASE / beta propeller domain / alpha/beta hydrolase domain
Function / homologyPeptidase S9, prolyl oligopeptidase, catalytic domain / Alpha/Beta hydrolase fold / Prolyl oligopeptidase family / acylaminoacyl-peptidase / serine-type peptidase activity / cytoplasm / Acylamino-acid-releasing enzyme
Function and homology information
Biological speciesAeropyrum pernix (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 Å
AuthorsBartlam, M. / Wang, G. / Gao, R. / Yang, H. / Zhao, X. / Xie, G. / Cao, S. / Feng, Y. / Rao, Z.
CitationJournal: STRUCTURE / Year: 2004
Title: Crystal structure of an acylpeptide hydrolase/esterase from Aeropyrum pernix K1
Authors: Bartlam, M. / Wang, G. / Yang, H. / Gao, R. / Zhao, X. / Xie, G. / Cao, S. / Feng, Y. / Rao, Z.
Validation Report
SummaryFull reportAbout validation report
History
DepositionMar 27, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 2, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Acylamino-acid-releasing enzyme
B: Acylamino-acid-releasing enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,9866
Polymers126,2172
Non-polymers7694
Water9,890549
1
A: Acylamino-acid-releasing enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,4933
Polymers63,1091
Non-polymers3842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Acylamino-acid-releasing enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,4933
Polymers63,1091
Non-polymers3842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
γ
α
β
Length a, b, c (Å)64.730, 104.739, 170.944
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein/peptide Acylamino-acid-releasing enzyme / AARE / Acyl-peptide hydrolase / APH / Acylaminoacyl-peptidase


Mass: 63108.551 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aeropyrum pernix (archaea) / Production host: Escherichia coli (E. coli) / References: UniProt: Q9YBQ2, acylaminoacyl-peptidase
#2: Chemical ChemComp-BOG / B-OCTYLGLUCOSIDE


Mass: 292.369 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C14H28O6 / Octyl glucoside / Comment: detergent *YM
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3 / Glycerol
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 549 / Source method: isolated from a natural source / Formula: H2O / Water

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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: 2.3 Å3/Da / Density % sol: 46.42 % / Description: the file contains Friedel pairs
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: PEG 4000, NaAC, DTT, EDTA, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.9795, 0.9799, 0.9800
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Mar 30, 2003 / Details: mirrors
RadiationMonochromator: double-crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97951
20.97991
30.981
ReflectionResolution: 2.1→50 Å / Num. obs: 118700 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.4 % / Rmerge(I) obs: 0.079 / Rsym value: 0.079 / Net I/σ(I): 16.6
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.212 / Mean I/σ(I) obs: 6.1 / % possible all: 97.5

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Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
CNSrefinement
HKL-2000data reduction
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 2.1→29.77 Å / Isotropic thermal model: restrained / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: the file contains Friedel pairs
RfactorNum. reflection% reflectionSelection details
Rfree0.229 6134 -RANDOM
Rwork0.193 ---
All0.207 124834 --
Obs0.207 118700 95.3 %-
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.18 Å0.08 Å
Refinement stepCycle: LAST / Resolution: 2.1→29.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8748 0 52 549 9349
Refine LS restraints
Refinement-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d25.1
X-RAY DIFFRACTIONc_improper_angle_d0.93
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.008
RfactorNum. reflection% reflection
Rfree0.255 950 -
Rwork0.192 --
Obs-18473 88.7 %

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