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- PDB-2qzp: Crystal structure of mutation of an acylptide hydrolase/esterase ... -

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Basic information

Entry
Database: PDB / ID: 2qzp
TitleCrystal structure of mutation of an acylptide hydrolase/esterase from Aeropyrum pernix K1
ComponentsAcylamino-acid-releasing enzymeAcylaminoacyl-peptidase
KeywordsHYDROLASE / truncated / acylpeptide hydrolase / Aeropyrum pernix K1 / Cytoplasm
Function / homology
Function and homology information


acylaminoacyl-peptidase / serine-type peptidase activity / omega peptidase activity / proteolysis / cytoplasm
Similarity search - Function
Peptidase/esterase 'gauge' domain / Peptidase S9, prolyl oligopeptidase, catalytic domain / Prolyl oligopeptidase family / 7 Propeller / Methylamine Dehydrogenase; Chain H / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Acylamino-acid-releasing enzyme
Similarity search - Component
Biological speciesAeropyrum pernix (archaea)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsZhang, H.F. / Zheng, B.S. / Rao, Z.
CitationJournal: to be published
Title: Expression, purification and crystal structure of a truncated acylpeptide hydrolase from Aeropyrum pernix K1
Authors: Zhang, H.F. / Zheng, B.S. / Rao, Z.
History
DepositionAug 17, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 2, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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


Theoretical massNumber of molelcules
Total (without water)121,2992
Polymers121,2992
Non-polymers00
Water6,593366
1
A: Acylamino-acid-releasing enzyme


Theoretical massNumber of molelcules
Total (without water)60,6491
Polymers60,6491
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Acylamino-acid-releasing enzyme


Theoretical massNumber of molelcules
Total (without water)60,6491
Polymers60,6491
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.117, 102.183, 163.594
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 Acylamino-acid-releasing enzyme / Acylaminoacyl-peptidase / AARE / Acyl-peptide hydrolase / APH / Acylaminoacyl-peptidase


Mass: 60649.496 Da / Num. of mol.: 2 / Fragment: residues 21-582
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aeropyrum pernix (archaea) / Plasmid: pET11a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9YBQ2, acylaminoacyl-peptidase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 366 / 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: 2.33 Å3/Da / Density % sol: 47.13 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: NaAc, PEG3000, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Nov 5, 2004 / Details: osmic mirror
RadiationMonochromator: osmic mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. all: 35191 / Num. obs: 35191 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.8 % / Biso Wilson estimate: 45 Å2 / Rmerge(I) obs: 0.177
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.777 / Num. unique all: 3463 / % possible all: 99

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Processing

Software
NameClassification
HKL-2000data collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1VE6

1ve6


Resolution: 2.7→48.11 Å / Rfactor Rfree error: 0.007 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.277 1393 5.1 %random
Rwork0.226 ---
obs0.226 27467 92 %-
Solvent computationSolvent model: CNS BULK SOLVENT MODEL USED / Bsol: 67.97 Å2 / ksol: 0.34 e/Å3
Displacement parametersBiso mean: 30.14 Å2
Baniso -1Baniso -2Baniso -3
1--1.44 Å20 Å20 Å2
2---6.83 Å20 Å2
3---8.27 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.4 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.52 Å0.41 Å
Refinement stepCycle: LAST / Resolution: 2.7→48.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8515 0 0 366 8881
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_bond_d0.009
LS refinement shellResolution: 2.7→2.82 Å / Rfactor Rfree error: 0.03
RfactorNum. reflection% reflection
Rfree0.403 176 5.4 %
Rwork0.316 3106 -
obs--89.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER_REP.TOP

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