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- PDB-3toq: Acylphosphatase with mesophilic surface and thermophilic core -

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Basic information

Entry
Database: PDB / ID: 3toq
TitleAcylphosphatase with mesophilic surface and thermophilic core
ComponentsAcylphosphatase-1
KeywordsHYDROLASE / acylphosphatase / thermophilic / amyloid
Function / homology
Function and homology information


acylphosphatase / acylphosphatase activity / phosphate-containing compound metabolic process
Similarity search - Function
Acylphosphatase signature 2. / Acylphosphatase / Acylphosphatase signature 1. / Acylphosphatase, conserved site / Acylphosphatase / Acylphosphatase-like domain / Acylphosphatase-like domain profile. / Acylphosphatase-like domain superfamily / Alpha-Beta Plaits - #100 / Alpha-Beta Plaits ...Acylphosphatase signature 2. / Acylphosphatase / Acylphosphatase signature 1. / Acylphosphatase, conserved site / Acylphosphatase / Acylphosphatase-like domain / Acylphosphatase-like domain profile. / Acylphosphatase-like domain superfamily / Alpha-Beta Plaits - #100 / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Acylphosphatase-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsYu, T.H.
CitationJournal: To be Published
Title: Protein surface is the preferred region for thermostability engineering
Authors: Yu, T.H. / Wong, K.B.
History
DepositionSep 6, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 5, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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

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Assembly

Deposited unit
A: Acylphosphatase-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,2792
Polymers11,1841
Non-polymers951
Water2,072115
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)78.100, 78.100, 65.577
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11A-215-

HOH

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Components

#1: Protein Acylphosphatase-1 / Acylphosphatase / erythrocyte isozyme / Acylphosphatase / organ-common type isozyme / Acylphosphate ...Acylphosphatase / erythrocyte isozyme / Acylphosphatase / organ-common type isozyme / Acylphosphate phosphohydrolase 1


Mass: 11183.771 Da / Num. of mol.: 1 / Mutation: A6V, L8Y, M23T, A27G, V32L, A46G, L58M, A62L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ACYP1, ACYPE / Production host: Escherichia coli (E. coli) / References: UniProt: P07311, acylphosphatase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 115 / 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: 3.44 Å3/Da / Density % sol: 64.26 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.2
Details: 1.4 M Sodium Potassium, Phosphate pH 8.2 (Hampton Research, Index Screen B7 condition), 289 K , VAPOR DIFFUSION, SITTING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Mar 12, 2009
RadiationMonochromator: mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2→30.057 Å / Num. all: 10065 / Num. obs: 10063 / % possible obs: 99.8 % / Observed criterion σ(F): 2.06 / Observed criterion σ(I): 3 / Biso Wilson estimate: 22.31 Å2

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHENIX(phenix.automr)model building
PHENIX(phenix.refine: 1.6.4_486)refinement
MOSFLMdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→20.161 Å / SU ML: 0.27 / σ(F): 2.06 / Phase error: 18.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2089 1013 10.08 %
Rwork0.1672 --
obs0.1714 10048 99.78 %
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.198 Å2 / ksol: 0.406 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.0576 Å20 Å2-0 Å2
2--1.0576 Å20 Å2
3----2.1152 Å2
Refinement stepCycle: LAST / Resolution: 2→20.161 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms762 0 5 115 882
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006786
X-RAY DIFFRACTIONf_angle_d0.9181060
X-RAY DIFFRACTIONf_dihedral_angle_d14.034294
X-RAY DIFFRACTIONf_chiral_restr0.064116
X-RAY DIFFRACTIONf_plane_restr0.003136
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.0001-2.10540.23541440.1907126999
2.1054-2.23720.20521450.16031290100
2.2372-2.40960.22821410.17021307100
2.4096-2.65170.19461490.16441302100
2.6517-3.03420.21931430.1781276100
3.0342-3.81860.22471490.16491300100
3.8186-20.16170.18241420.1601129199

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