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- PDB-2w4p: Human common-type acylphosphatase variant, A99G -

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Basic information

Entry
Database: PDB / ID: 2w4p
TitleHuman common-type acylphosphatase variant, A99G
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: 1.7 Å
AuthorsLam, S.Y. / Sze, K.H. / 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.H. / 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 29, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 29, 2009Provider: repository / Type: Initial release
Revision 1.1Feb 1, 2012Group: Database references / Derived calculations / Version format compliance
Revision 1.2May 1, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,2982
Polymers11,2061
Non-polymers921
Water1,53185
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)24.206, 57.339, 58.777
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 ACYLPHOSPHATA / ACYLPHOSPHATE PHOSPHOHYDROLASE 1 / ACYLPHOSPHATASE ORGAN-COMMON ...HUMAN COMMON-TYPE ACYLPHOSPHATA / ACYLPHOSPHATE PHOSPHOHYDROLASE 1 / ACYLPHOSPHATASE ORGAN-COMMON TYPE ISOZYME / ACYLPHOSPHATASE ERYTHROCYTE ISOZYME


Mass: 11205.712 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: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 85 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, LYS 99 TO GLY

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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: 1.85 Å3/Da / Density % sol: 33.7 % / Description: NONE
Crystal growpH: 7 / Details: 2.4M SODIUM MALONATE, PH7.0 25% GLYCEROL

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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: Aug 4, 2006 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5 Å / Relative weight: 1
ReflectionResolution: 1.7→41 Å / Num. obs: 9498 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 6.36 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 8.5
Reflection shellResolution: 1.7→1.74 Å / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 2.1 / % possible all: 98.4

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: HUMAN COMMON-TYPE ACYPHOSPHATASE WILD TYPE

Resolution: 1.7→41.03 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.92 / SU B: 2.353 / SU ML: 0.08 / Cross valid method: THROUGHOUT / ESU R: 0.127 / ESU R Free: 0.129 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.241 453 4.8 %RANDOM
Rwork0.187 ---
obs0.19 9045 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.24 Å2
Baniso -1Baniso -2Baniso -3
1--1.02 Å20 Å20 Å2
2---1.14 Å20 Å2
3---2.16 Å2
Refinement stepCycle: LAST / Resolution: 1.7→41.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms768 0 6 85 859
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.022788
X-RAY DIFFRACTIONr_bond_other_d0.0020.02707
X-RAY DIFFRACTIONr_angle_refined_deg1.551.9381058
X-RAY DIFFRACTIONr_angle_other_deg0.84831653
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8595
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.09624.87239
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.64215144
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.829154
X-RAY DIFFRACTIONr_chiral_restr0.1040.2112
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02872
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02158
X-RAY DIFFRACTIONr_nbd_refined0.1960.2121
X-RAY DIFFRACTIONr_nbd_other0.1970.2691
X-RAY DIFFRACTIONr_nbtor_refined0.1770.2382
X-RAY DIFFRACTIONr_nbtor_other0.0850.2472
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1930.261
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.110.25
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2270.229
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.220.27
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0971.5614
X-RAY DIFFRACTIONr_mcbond_other0.2541.5203
X-RAY DIFFRACTIONr_mcangle_it1.32758
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.2983372
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.4174.5300
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: 1.7→1.74 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.293 36 -
Rwork0.23 648 -
obs--98.42 %

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