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- PDB-2acy: ACYL-PHOSPHATASE (COMMON TYPE) FROM BOVINE TESTIS -

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Basic information

Entry
Database: PDB / ID: 2acy
TitleACYL-PHOSPHATASE (COMMON TYPE) FROM BOVINE TESTIS
ComponentsACYLPHOSPHATASE
KeywordsACYLPHOSPHATASE / PHOSPHORIC MONOESTER HYDROLASE
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 speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / MIR / Resolution: 1.8 Å
AuthorsThunnissen, M.M.G.M. / Nordlund, P.
CitationJournal: Structure / Year: 1997
Title: Crystal structure of common type acylphosphatase from bovine testis.
Authors: Thunnissen, M.M. / Taddei, N. / Liguri, G. / Ramponi, G. / Nordlund, P.
History
DepositionNov 8, 1996Processing site: BNL
Revision 1.0Nov 12, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.source
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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)11,3264
Polymers11,0991
Non-polymers2283
Water1,35175
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.200, 36.200, 45.300
Angle α, β, γ (deg.)90.00, 104.10, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein ACYLPHOSPHATASE / ACP


Mass: 11098.529 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Cellular location: CYTOPLASM / Organ: TESTIS / References: UniProt: P41500, acylphosphatase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 75 / 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: 2.3 Å3/Da / Density % sol: 45 %
Crystal growpH: 3.5
Details: PROTEIN WAS CRYSTALLIZED FROM 30% PEG8000 OR 4000, 25 MM ACETATE BUFFER PH 3.5, 0.2 M AMMONIUM-SULFATE
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
125 mMacetate1reservoir
230 %PEG40001reservoir
30.2 Mammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: ROTATING ANODE / Type: SIEMENS / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 1, 1995
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 8949 / % possible obs: 98.8 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.059 / Net I/σ(I): 36.98
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.215 / Mean I/σ(I) obs: 10.52 / % possible all: 92.4
Reflection
*PLUS
Num. measured all: 41285

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Processing

Software
NameVersionClassification
DMmodel building
MLPHAREphasing
TNT5Erefinement
MARXDSdata reduction
MARSCALEdata scaling
DMphasing
RefinementMethod to determine structure: MIR / Resolution: 1.8→15 Å / Isotropic thermal model: TNT BCORREL / σ(F): 0 / Stereochemistry target values: TNT PROTGEO (ENGH & HUBER)
Details: REFINED WITH FREE SET UNTIL CONVERGENCE OCCURRED, THEN REFINED WITH ALL DATA TO FINAL R-FACTOR.
RfactorNum. reflection% reflection
Rfree0.23 905 10 %
Rwork0.179 --
all0.17 9119 -
obs0.17 9119 95 %
Solvent computationSolvent model: BABINET SCALING / Bsol: 158.1 Å2 / ksol: 0.697 e/Å3
Refinement stepCycle: LAST / Resolution: 1.8→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms784 0 11 75 870
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.018161.2
X-RAY DIFFRACTIONt_angle_deg1.710980.9
X-RAY DIFFRACTIONt_dihedral_angle_d16.94790
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.009243
X-RAY DIFFRACTIONt_gen_planes0.0111310
X-RAY DIFFRACTIONt_it5.48005
X-RAY DIFFRACTIONt_nbd0.0321818
Software
*PLUS
Name: TNT / Version: 5E / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.235
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_dihedral_angle_deg16.90
X-RAY DIFFRACTIONt_planar_d0.0093
X-RAY DIFFRACTIONt_plane_restr0.0110

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