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- PDB-4oix: Crystal structure of truncated Acylphosphatase from S. sulfataricus -

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Basic information

Entry
Database: PDB / ID: 4oix
TitleCrystal structure of truncated Acylphosphatase from S. sulfataricus
ComponentsAcylphosphatase
KeywordsHYDROLASE / native-like aggregation / acylphosphatase
Function / homology
Function and homology information


acylphosphatase / acylphosphatase 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
Biological speciesSulfolobus solfataricus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsDilovic, I. / Bolognesi, M. / Ricagno, S.
CitationJournal: TO BE PUBLISHED
Title: Crystal structure of truncated Acylphosphatase from S. sulfataricus
Authors: Dilovic, I. / Bolognesi, M. / Ricagno, S.
History
DepositionJan 20, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 5, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 20, 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: Acylphosphatase


Theoretical massNumber of molelcules
Total (without water)11,6521
Polymers11,6521
Non-polymers00
Water1,65792
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)31.780, 39.510, 64.130
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 Acylphosphatase / Acylphosphate phosphohydrolase


Mass: 11652.300 Da / Num. of mol.: 1 / Fragment: Delta-11 AcP
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Strain: ATCC 35092 / DSM 1617 / JCM 11322 / P2 / Gene: acyP, SSO0887 / Plasmid: pGEX-2T / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q97ZL0, acylphosphatase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 92 / 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: 1.73 Å3/Da / Density % sol: 28.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 10% PEG 8000, 8% ethylene glycol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 1.0716 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Mar 12, 2013 / Details: bent collimating mirror and toroid
RadiationMonochromator: Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0716 Å / Relative weight: 1
ReflectionResolution: 1.55→31.78 Å / Num. all: 12271 / Num. obs: 11780 / % possible obs: 96 % / Redundancy: 4.7 % / Biso Wilson estimate: 10.8 Å2 / Rmerge(I) obs: 0.044 / Net I/σ(I): 23.1
Reflection shellResolution: 1.55→1.63 Å / Redundancy: 3 % / Rmerge(I) obs: 0.061 / Mean I/σ(I) obs: 10.7 / Num. unique all: 1398 / % possible all: 80.3

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Processing

Software
NameVersionClassification
MxCuBEdata collection
PHASERphasing
REFMAC5.7.0029refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 2BJE

2bje


Resolution: 1.55→28.49 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.957 / SU B: 2.581 / SU ML: 0.043 / Cross valid method: THROUGHOUT / ESU R: 0.115 / ESU R Free: 0.079 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17795 814 6.9 %RANDOM
Rwork0.14742 ---
obs0.1496 10928 95.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.493 Å2
Baniso -1Baniso -2Baniso -3
1--0.94 Å20 Å20 Å2
2--1.56 Å20 Å2
3----0.62 Å2
Refinement stepCycle: LAST / Resolution: 1.55→28.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms725 0 0 92 817
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.019747
X-RAY DIFFRACTIONr_bond_other_d0.0010.02725
X-RAY DIFFRACTIONr_angle_refined_deg1.0581.9841003
X-RAY DIFFRACTIONr_angle_other_deg0.63931673
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.952591
X-RAY DIFFRACTIONr_dihedral_angle_2_deg24.09523.61136
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.89715138
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.155155
X-RAY DIFFRACTIONr_chiral_restr0.0650.2103
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02839
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02172
X-RAY DIFFRACTIONr_rigid_bond_restr2.3931472
X-RAY DIFFRACTIONr_sphericity_free24.304520
X-RAY DIFFRACTIONr_sphericity_bonded5.23451528
LS refinement shellResolution: 1.55→1.59 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.214 34 -
Rwork0.14 645 -
obs--74.53 %

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