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- PDB-1ve7: Crystal structure of an acylpeptide hydrolase/esterase from Aerop... -

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Basic information

Entry
Database: PDB / ID: 1ve7
TitleCrystal structure of an acylpeptide hydrolase/esterase from Aeropyrum pernix K1 in complex with p-nitrophenyl phosphate
ComponentsAcylamino-acid-releasing enzymeAcylaminoacyl-peptidase
KeywordsHYDROLASE / beta propeller domain / alpha/beta hydrolase domain
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
4-NITROPHENYL PHOSPHATE / Acylamino-acid-releasing enzyme
Similarity search - Component
Biological speciesAeropyrum pernix (archaea)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.7 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.
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
Revision 1.3Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

Downloads & links

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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)126,7475
Polymers126,2172
Non-polymers5303
Water3,369187
1
A: Acylamino-acid-releasing enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,4203
Polymers63,1091
Non-polymers3112
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Acylamino-acid-releasing enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,3282
Polymers63,1091
Non-polymers2191
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.883, 104.622, 168.004
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: 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-4NP / 4-NITROPHENYL PHOSPHATE / Para-Nitrophenylphosphate


Mass: 219.089 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H6NO6P
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 187 / 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: 2.22 Å3/Da / Density % sol: 44.7 %
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: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Sep 1, 2003 / Details: mirrors
RadiationProtocol: 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. obs: 31768 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.8 % / Rmerge(I) obs: 0.1 / Rsym value: 0.1 / Net I/σ(I): 6.9
Reflection shellResolution: 2.7→2.85 Å / Redundancy: 7 % / Rmerge(I) obs: 0.377 / Mean I/σ(I) obs: 2 / % possible all: 100

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
CNSrefinement
CCP4(SCALA)data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1VE6

1ve6


Resolution: 2.7→30 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.267 1555 RANDOM
Rwork0.207 --
all0.223 31690 -
obs0.223 30134 -
Refine analyze
FreeObs
Luzzati coordinate error0.42 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.45 Å0.25 Å
Refinement stepCycle: LAST / Resolution: 2.7→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8730 0 34 187 8951
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_dihedral_angle_d25.9
X-RAY DIFFRACTIONc_improper_angle_d1.04
LS refinement shellResolution: 2.7→2.87 Å / Rfactor Rfree error: 0.024
RfactorNum. reflection% reflection
Rfree0.34 254 -
Rwork0.276 --
obs-4922 100 %

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