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- PDB-4oj1: Crystal structure of truncated Acylphosphatase from S. sulfataricus -

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Basic information

Entry
Database: PDB / ID: 4oj1
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: 1.7 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 ...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_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _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
B: Acylphosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,4697
Polymers23,3052
Non-polymers1655
Water1,946108
1
A: Acylphosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,7825
Polymers11,6521
Non-polymers1294
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Acylphosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,6882
Polymers11,6521
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)41.150, 41.330, 91.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: TYR / End label comp-ID: TYR / Refine code: _ / Auth seq-ID: 12 - 101 / Label seq-ID: 12 - 101

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Acylphosphatase / Acylphosphate phosphohydrolase


Mass: 11652.300 Da / Num. of mol.: 2 / 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: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 108 / 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: 1.67 Å3/Da / Density % sol: 26.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 2.0 M NaCl, 10% PEG 6000, pH 8.0, 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: Apr 5, 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
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.663
11K, H, -L20.337
ReflectionResolution: 1.7→24.58 Å / Num. all: 17814 / Num. obs: 17297 / % possible obs: 97.1 % / Redundancy: 5.3 % / Biso Wilson estimate: 14 Å2 / Rmerge(I) obs: 0.129 / Net I/σ(I): 11.4
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.404 / Mean I/σ(I) obs: 4.4 / Num. unique all: 2328 / % possible all: 91.2

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Processing

Software
NameVersionClassification
MxCuBEdata collection
PHASERphasing
REFMAC5.7.0029refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4OIX

4oix


Resolution: 1.7→24.58 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.903 / SU B: 4.998 / SU ML: 0.079 / Cross valid method: THROUGHOUT / ESU R: 0.055 / ESU R Free: 0.025 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21968 861 5 %RANDOM
Rwork0.16682 ---
obs0.16939 16390 95.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.483 Å2
Baniso -1Baniso -2Baniso -3
1--9.76 Å20 Å20 Å2
2---10.8 Å20 Å2
3---20.56 Å2
Refinement stepCycle: LAST / Resolution: 1.7→24.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1450 0 5 108 1563
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0191521
X-RAY DIFFRACTIONr_bond_other_d0.0050.021468
X-RAY DIFFRACTIONr_angle_refined_deg1.4221.9842049
X-RAY DIFFRACTIONr_angle_other_deg1.08633394
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0245190
X-RAY DIFFRACTIONr_dihedral_angle_2_deg25.45723.68476
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.66615282
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9941511
X-RAY DIFFRACTIONr_chiral_restr0.0820.2210
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021723
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02352
X-RAY DIFFRACTIONr_rigid_bond_restr4.82932989
X-RAY DIFFRACTIONr_sphericity_free18.039535
X-RAY DIFFRACTIONr_sphericity_bonded4.85853031
Refine LS restraints NCS

Ens-ID: 1 / Number: 5187 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.17 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.694→1.738 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.302 54 -
Rwork0.2 947 -
obs--76.88 %

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