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- PDB-2vh7: Crystal structure of human common-type acylphosphatase -

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Basic information

Entry
Database: PDB / ID: 2vh7
TitleCrystal structure of human common-type acylphosphatase
ComponentsACYLPHOSPHATASE-1
KeywordsHYDROLASE / ACETYLATION
Function / homology
Function and homology information


acylphosphatase / acylphosphatase activity / phosphate-containing compound metabolic process
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 speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsYeung, R.C.Y. / Lam, Y. / Wong, K.B.
Citation
Journal: Plos Biol. / Year: 2011
Title: A Rigidifying Salt-Bridge Favors the Activity of Thermophilic Enzyme at High Temperatures at the Expense of Low-Temperature Activity.
Authors: Lam, S.Y. / Yeung, R.C.Y. / Yu, T. / Sze, K. / Wong, K.B.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2006
Title: Crystallization and Preliminary Crystallographic Analysis of Human Common-Type Acylphosphatase.
Authors: Yeung, R.C.Y. / Lam, S.Y. / Wong, K.
History
DepositionNov 19, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 17, 2009Provider: repository / Type: Initial release
Revision 1.1Feb 1, 2012Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Version format compliance
Revision 1.2Dec 13, 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

Downloads & links

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Assembly

Deposited unit
A: ACYLPHOSPHATASE-1


Theoretical massNumber of molelcules
Total (without water)11,2781
Polymers11,2781
Non-polymers00
Water2,126118
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)42.577, 47.235, 57.261
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-1 / ACYLPHOSPHATE PHOSPHOHYDROLASE 1 / ACYLPHOSPHATASE / ORGAN-COMMON TYPE ISOZYME / ERYTHROCYTE ISOZYME


Mass: 11277.840 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P07311, acylphosphatase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 118 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.6 Å3/Da / Density % sol: 52 % / Description: NONE
Crystal growpH: 7.5
Details: 10%(V/V) 2-PROPANOL, 20%(W/V) PEG 4000, 0.1 M NA HEPES BUFFER PH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.45
DetectorType: RIGAKU-MSC / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.45 Å / Relative weight: 1
ReflectionResolution: 1.45→17.7 Å / Num. obs: 20888 / % possible obs: 99.1 % / Observed criterion σ(I): 1.45 / Redundancy: 4.28 % / Rmerge(I) obs: 0.03 / Net I/σ(I): 19.8
Reflection shellResolution: 1.45→1.5 Å / Redundancy: 2.97 % / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 2.9 / % possible all: 95.4

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2ACY

2acy


Resolution: 1.45→36.44 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.945 / SU B: 1.392 / SU ML: 0.053 / Cross valid method: THROUGHOUT / ESU R: 0.072 / ESU R Free: 0.072 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.228 1074 5.1 %RANDOM
Rwork0.209 ---
obs0.209 19814 99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.98 Å2
Baniso -1Baniso -2Baniso -3
1-1.87 Å20 Å20 Å2
2---0.99 Å20 Å2
3----0.88 Å2
Refinement stepCycle: LAST / Resolution: 1.45→36.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms761 0 0 118 879
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.022788
X-RAY DIFFRACTIONr_bond_other_d0.0010.02711
X-RAY DIFFRACTIONr_angle_refined_deg1.3251.9391059
X-RAY DIFFRACTIONr_angle_other_deg1.61731672
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.845593
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.17724.87239
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.45115154
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.952154
X-RAY DIFFRACTIONr_chiral_restr0.0830.2115
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02858
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02156
X-RAY DIFFRACTIONr_nbd_refined0.1950.2131
X-RAY DIFFRACTIONr_nbd_other0.1840.2674
X-RAY DIFFRACTIONr_nbtor_refined0.1790.2386
X-RAY DIFFRACTIONr_nbtor_other0.0830.2451
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1310.281
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0650.27
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2710.236
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1720.27
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0431.5608
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.1942756
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.093387
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.9794.5303
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.45→1.49 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.564 90 -
Rwork0.482 1345 -
obs--94.04 %

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