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- PDB-2w4c: Human common-type acylphosphatase variant, A99 -

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Basic information

Entry
Database: PDB / ID: 2w4c
TitleHuman common-type acylphosphatase variant, A99
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: 1.52 Å
AuthorsLam, S.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 25, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 22, 2009Provider: repository / Type: Initial release
Revision 1.1Feb 1, 2012Group: Database references / Derived calculations / Version format compliance
Revision 1.2Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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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)11,2201
Polymers11,2201
Non-polymers00
Water1,928107
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)24.604, 57.861, 59.095
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 / HUMAN COMMON-TYPE ACYLPHOSPHATASE / ACYLPHOSPHATE PHOSPHOHYDROLASE 1 / ACYLPHOSPHATASE ORGAN-COMMON ...HUMAN COMMON-TYPE ACYLPHOSPHATASE / ACYLPHOSPHATE PHOSPHOHYDROLASE 1 / ACYLPHOSPHATASE ORGAN-COMMON TYPE ISOZYME / ACYLPHOSPHATASE ERYTHROCYTE ISOZYME


Mass: 11219.737 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Organ: LIVER / Plasmid: PET3A / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P07311, acylphosphatase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 107 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, LYS 99 TO ALA

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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: 1.87 Å3/Da / Density % sol: 34.38 % / Description: NONE
Crystal growpH: 6
Details: 16MG/ML K99A IN 20MMTRIS, 0.2MNACL, PH7.5 K99A WAS CRYSTALLIZED IN 0.1M BIS-TRIS, 0.1M NAOAC, PH6.0 WITH 25% PEG3350 AS CYROPROTECTANT

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Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5
DetectorType: RIGAKU IMAGE PLATE / Detector: IMAGE PLATE / Date: Sep 30, 2006 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5 Å / Relative weight: 1
ReflectionResolution: 1.52→14.31 Å / Num. obs: 13607 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 2 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 30.7
Reflection shellResolution: 1.52→1.52 Å / Rmerge(I) obs: 0.18 / Mean I/σ(I) obs: 9.2 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2VH7

2vh7


Resolution: 1.52→41.34 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.949 / SU B: 1.65 / SU ML: 0.062 / Cross valid method: THROUGHOUT / ESU R: 0.092 / ESU R Free: 0.092 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.228 671 4.9 %RANDOM
Rwork0.196 ---
obs0.198 12894 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.18 Å2
Baniso -1Baniso -2Baniso -3
1-0.22 Å20 Å20 Å2
2---0.66 Å20 Å2
3---0.44 Å2
Refinement stepCycle: LAST / Resolution: 1.52→41.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms765 0 0 107 872
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.022780
X-RAY DIFFRACTIONr_bond_other_d0.0010.02700
X-RAY DIFFRACTIONr_angle_refined_deg1.3531.9311050
X-RAY DIFFRACTIONr_angle_other_deg0.7431636
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.015594
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.00324.87239
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.90215144
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.212154
X-RAY DIFFRACTIONr_chiral_restr0.090.2113
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02865
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02157
X-RAY DIFFRACTIONr_nbd_refined0.20.2116
X-RAY DIFFRACTIONr_nbd_other0.180.2664
X-RAY DIFFRACTIONr_nbtor_refined0.1760.2379
X-RAY DIFFRACTIONr_nbtor_other0.0850.2443
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1670.263
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1270.28
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2350.236
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1410.29
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2451.5605
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.5292755
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.3433366
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.434.5295
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: 1.52→1.56 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.311 44
Rwork0.286 931

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