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- PDB-4ojh: The crystal structure of truncated, Y86E mutant of S. solfataricu... -

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Basic information

Entry
Database: PDB / ID: 4ojh
TitleThe crystal structure of truncated, Y86E 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: 1.6 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 21, 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)23,9099
Polymers23,2362
Non-polymers6727
Water2,216123
1
A: Acylphosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,9064
Polymers11,6181
Non-polymers2883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Acylphosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,0025
Polymers11,6181
Non-polymers3844
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)41.680, 45.190, 44.120
Angle α, β, γ (deg.)90.00, 93.20, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Acylphosphatase / Acylphosphate phosphohydrolase


Mass: 11618.239 Da / Num. of mol.: 2 / Mutation: Y86E
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 / Production host: Escherichia coli (E. coli) / References: UniProt: Q97ZL0, acylphosphatase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 123 / 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: 1.79 Å3/Da / Density % sol: 31.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.3
Details: 0.2M ammonium sulfate, 30% PEG 8000, pH 8.3, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.98 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Dec 16, 2013
RadiationMonochromator: Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.6→31.54 Å / Num. obs: 21048 / % possible obs: 96.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.5 % / Biso Wilson estimate: 12.864 Å2 / Rmerge(I) obs: 0.079 / Net I/σ(I): 10.1
Reflection shellResolution: 1.6→1.69 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 2.7 / Num. unique all: 6340 / % possible all: 80.5

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Processing

Software
NameVersionClassification
MXcube2data collection
PHASERphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4OJ3

4oj3


Resolution: 1.6→31.54 Å / SU ML: 0.18 / σ(F): 1.35 / Phase error: 23.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2376 1999 9.5 %lattice symmetry 10%
Rwork0.1911 ---
obs0.1956 21033 96.54 %-
all-21786 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.6→31.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1423 0 35 123 1581
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0121479
X-RAY DIFFRACTIONf_angle_d1.3991991
X-RAY DIFFRACTIONf_dihedral_angle_d13.03545
X-RAY DIFFRACTIONf_chiral_restr0.098204
X-RAY DIFFRACTIONf_plane_restr0.007254
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.640.28231110.21051035X-RAY DIFFRACTION74
1.64-1.68440.25691180.19861194X-RAY DIFFRACTION85
1.6844-1.73390.24851360.19821327X-RAY DIFFRACTION94
1.7339-1.78990.22461490.19191366X-RAY DIFFRACTION99
1.7899-1.85380.2361440.18731397X-RAY DIFFRACTION100
1.8538-1.92810.21821520.1751400X-RAY DIFFRACTION100
1.9281-2.01580.27411530.18191398X-RAY DIFFRACTION100
2.0158-2.1220.20831440.18621403X-RAY DIFFRACTION100
2.122-2.2550.24821510.18071405X-RAY DIFFRACTION100
2.255-2.4290.25381500.17861394X-RAY DIFFRACTION100
2.429-2.67330.23691450.20251411X-RAY DIFFRACTION100
2.6733-3.05990.25911460.19691421X-RAY DIFFRACTION100
3.0599-3.85410.24151530.19551423X-RAY DIFFRACTION100
3.8541-31.54990.20511470.19381460X-RAY DIFFRACTION100
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)
14.6003-3.01964.38796.7141-5.04086.98180.20570.3125-0.0206-0.6517-0.0121-0.15250.25120.0433-0.16490.13960.01110.04130.15260.00020.085622.0202-6.52687.2762
21.2229-0.39450.54735.9793-0.86671.20940.01490.00360.0131-0.2352-0.0027-0.0010.006-0.0066-0.01010.0431-0.00260.02180.069-0.00570.079618.2236-5.234216.9216
34.907-0.73821.37964.3393-1.54485.38790.00140.32160.3604-0.303-0.0963-0.1702-0.24270.30370.08990.11890.0070.03920.09940.01080.093122.41760.13779.1926
41.8044-0.37352.36770.4066-0.77863.36560.21950.3818-0.0147-0.3538-0.2045-0.12230.0610.09320.04480.17180.03840.01320.1690.0150.086727.9302-7.150912.7861
52.6824-0.99081.6352.8639-2.90863.68220.0410.0695-0.2528-0.46990.05740.32640.2957-0.7021-0.07370.17770.0072-0.04240.1859-0.03660.206310.2977-3.89788.1434
64.26833-3.95025.964-3.78274.88870.0807-0.2125-0.03790.49380.0625-0.0481-0.1034-0.1998-0.10530.1248-0.0047-0.01160.15210.0240.07211.0386-1.370836.4787
71.31390.9666-0.56285.8868-1.16391.0796-0.0113-0.0442-0.08450.12950.05690.0850.0336-0.0974-0.04560.0384-0.0016-0.00420.09020.00230.0944-2.5894-3.242727.1396
84.65931.2963-1.44086.1916-1.49145.9197-0.0247-0.2676-0.49810.25780.0378-0.09690.44260.2186-0.00050.1068-0.0088-0.03820.11040.01470.1241.5437-8.553634.8909
93.02770.2839-2.92412.28920.51016.10480.0633-0.32650.0170.2154-0.1354-0.14730.09650.23330.0570.07610.0004-0.00890.10640.01990.09976.9154-1.141931.3093
103.50430.4755-0.86172.9763-0.6033.0251-0.0274-0.4672-0.14060.51290.09950.542-0.0203-0.8427-0.04090.16520.00070.0740.29620.02520.2496-10.8468-4.791436.0354
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 12 through 23 )
2X-RAY DIFFRACTION2chain 'A' and (resid 24 through 53 )
3X-RAY DIFFRACTION3chain 'A' and (resid 54 through 74 )
4X-RAY DIFFRACTION4chain 'A' and (resid 75 through 89 )
5X-RAY DIFFRACTION5chain 'A' and (resid 90 through 101 )
6X-RAY DIFFRACTION6chain 'B' and (resid 12 through 23 )
7X-RAY DIFFRACTION7chain 'B' and (resid 24 through 53 )
8X-RAY DIFFRACTION8chain 'B' and (resid 54 through 74 )
9X-RAY DIFFRACTION9chain 'B' and (resid 75 through 89 )
10X-RAY DIFFRACTION10chain 'B' and (resid 90 through 101 )

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