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- PDB-4oj3: The crystal structure of V84P mutant of S. solfataricus Acylphosp... -

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Basic information

Entry
Database: PDB / ID: 4oj3
TitleThe crystal structure of V84P mutant of S. solfataricus Acylphosphatase
ComponentsAcylphosphatase
KeywordsHYDROLASE / native-like aggregation / amyloid 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: 2.2 Å
Authorsde Rosa, M. / Bolognesi, M. / Ricagno, S.
CitationJournal: Febs J. / Year: 2014
Title: Edge strand engineering prevents native-like aggregation in Sulfolobus solfataricus acylphosphatase.
Authors: de Rosa, M. / Bemporad, F. / Pellegrino, S. / Chiti, F. / Bolognesi, M. / Ricagno, S.
History
DepositionJan 20, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 4, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 18, 2014Group: Database references
Revision 1.2Oct 1, 2014Group: Database references
Revision 1.3Sep 20, 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
B: Acylphosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,8698
Polymers23,3012
Non-polymers5686
Water1,00956
1
A: Acylphosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,9354
Polymers11,6501
Non-polymers2843
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Acylphosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,9354
Polymers11,6501
Non-polymers2843
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)112.190, 45.270, 41.470
Angle α, β, γ (deg.)90.00, 105.39, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.859692, 0.01087, 0.510697), (0.009886, -0.99994, 0.004641), (0.510717, 0.001058, -0.859748)1.24972, 54.15409, -5.67901

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Components

#1: Protein Acylphosphatase / Acylphosphate phosphohydrolase


Mass: 11650.283 Da / Num. of mol.: 2 / Mutation: V84 to Pro
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: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 56 / 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: 2.18 Å3/Da / Density % sol: 43.55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.2M ammonium sulphate, 25% PEG 4K, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8729 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 14, 2013 / Details: Pt coated mirrors
RadiationMonochromator: Si (111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8729 Å / Relative weight: 1
ReflectionResolution: 2.2→30.48 Å / Num. obs: 9635 / % possible obs: 93.9 % / Redundancy: 2.3 % / Biso Wilson estimate: 19.4 Å2 / Rmerge(I) obs: 0.153 / Net I/σ(I): 5
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.573 / Mean I/σ(I) obs: 2.1 / Num. unique all: 1400 / % possible all: 93.5

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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: 4OIX

4oix


Resolution: 2.2→30.5 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.89 / SU B: 11.837 / SU ML: 0.161 / Cross valid method: THROUGHOUT / ESU R: 0.386 / ESU R Free: 0.248 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25575 670 7 %RANDOM
Rwork0.21464 ---
obs0.21751 8964 93.09 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.347 Å2
Baniso -1Baniso -2Baniso -3
1-2.57 Å20 Å20.52 Å2
2---1.71 Å20 Å2
3----0.88 Å2
Refinement stepCycle: LAST / Resolution: 2.2→30.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1493 0 32 56 1581
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0191558
X-RAY DIFFRACTIONr_bond_other_d0.0020.021480
X-RAY DIFFRACTIONr_angle_refined_deg1.1442.0032094
X-RAY DIFFRACTIONr_angle_other_deg0.72333418
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1765185
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.28523.73375
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.67815275
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2831510
X-RAY DIFFRACTIONr_chiral_restr0.0640.2217
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0211723
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02351
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.22 52 -
Rwork0.242 668 -
obs--93.75 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.42840.01940.48850.8099-0.49752.20950.01210.0467-0.03770.08-0.1802-0.01310.0570.27540.16810.0149-0.00760.01360.08730.0460.0648-17.764415.95931.9184
21.3240.0393-1.13120.63290.17091.03570.0685-0.17810.0307-0.0335-0.0404-0.0551-0.06960.1478-0.02810.0082-0.01410.00410.05660.03120.0834-12.86837.9834-16.4198
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A12 - 20
2X-RAY DIFFRACTION1A21 - 63
3X-RAY DIFFRACTION1A64 - 101
4X-RAY DIFFRACTION2B12 - 20
5X-RAY DIFFRACTION2B21 - 63
6X-RAY DIFFRACTION2B64 - 101

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