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

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Basic information

Entry
Database: PDB / ID: 3tnv
TitleAcylphosphatase with thermophilic surface and mesophilic core
ComponentsAcylphosphatase
KeywordsHYDROLASE / Alpha and beta proteins / STABILITY / AMYLOID / PHOSPHATASE
Function / homology
Function and homology information


acylphosphatase / acylphosphatase activity / hydrolase activity
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
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsYu, T.H. / Chan, C.H.
CitationJournal: To be Published
Title: Protein surface is a preferred site for thermostability engineering
Authors: Yu, T.H. / Wong, K.B.
History
DepositionSep 2, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 5, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 1, 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_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

Downloads & links

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Assembly

Deposited unit
A: Acylphosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,4662
Polymers10,3711
Non-polymers951
Water2,504139
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)28.087, 44.438, 30.813
Angle α, β, γ (deg.)90.00, 100.99, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Acylphosphatase / Acylphosphate phosphohydrolase


Mass: 10370.921 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.) Pyrococcus horikoshii (archaea) / Strain: OT-3 / Gene: acyP, PH0305.1 / Production host: Escherichia coli (E. coli) / References: UniProt: P84142, 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.: 139 / 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: 1.82 Å3/Da / Density % sol: 32.42 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.3
Details: 0.2M Sodium citrate tribasic dehydrate, 20% w/v PEG 3350 , pH 8.3, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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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: May 11, 2009
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.6→15.86 Å / Num. all: 9923 / Num. obs: 9923 / % possible obs: 99.9 % / Observed criterion σ(F): 1.4 / Observed criterion σ(I): 3
Reflection shell
Resolution (Å)Diffraction-ID% possible all
1.6-1.691100
1.69-1.791100
1.91-2.071100
2.07-2.261100
2.26-2.531100
2.53-2.921100
2.92-3.581100
3.58-5.06197

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHENIX(phenix.automr)model building
PHENIX(phenix.refine)refinement
MOSFLMdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1W2I

1w2i


Resolution: 1.6→15.858 Å / SU ML: 0.18 / σ(F): 1.4 / Phase error: 15.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.167 990 9.99 %Random
Rwork0.1463 ---
all0.1485 9923 --
obs0.1485 9907 99.97 %-
Solvent computationShrinkage radii: 0.04 Å / VDW probe radii: 0.4 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 73.581 Å2 / ksol: 0.474 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.1255 Å2-0 Å21.7703 Å2
2---0.6408 Å2-0 Å2
3---0.5153 Å2
Refinement stepCycle: LAST / Resolution: 1.6→15.858 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms724 0 5 139 868
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006756
X-RAY DIFFRACTIONf_angle_d0.951023
X-RAY DIFFRACTIONf_dihedral_angle_d13.016288
X-RAY DIFFRACTIONf_chiral_restr0.071102
X-RAY DIFFRACTIONf_plane_restr0.004134
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
1.6001-1.68430.25331400.23141266
1.6843-1.78970.21411400.16021265
1.7897-1.92770.17371420.13931275
1.9277-2.12130.18211390.14261259
2.1213-2.42730.15211420.14511266
2.4273-3.05460.17071420.14521286
3.0546-15.85830.14031450.13331300

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