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- PDB-1iw8: Crystal Structure of a mutant of acid phosphatase from Escherichi... -

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Basic information

Entry
Database: PDB / ID: 1iw8
TitleCrystal Structure of a mutant of acid phosphatase from Escherichia blattae (G74D/I153T)
Componentsacid phosphatase
KeywordsHYDROLASE / ALL ALPHA
Function / homology
Function and homology information


acid phosphatase / acid phosphatase activity / outer membrane-bounded periplasmic space
Similarity search - Function
Acid phosphatase, class A, bacterial, conserved site / Class A bacterial acid phosphatases signature. / Acid phosphatase, class A, bacterial / Acid phosphatase homologues / Phosphatidic acid phosphatase type 2/haloperoxidase / Vanadium-containing Chloroperoxidase; domain 1 / Phosphatidic acid phosphatase type 2/haloperoxidase / PAP2 superfamily / Phosphatidic acid phosphatase type 2/haloperoxidase superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesEscherichia blattae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsIshikawa, K. / Mihara, Y. / Shimba, N. / Ohtsu, N. / Kawasaki, H. / Suzuki, E. / Asano, Y.
Citation
Journal: PROTEIN ENG. / Year: 2002
Title: Enhancement of nucleoside phosphorylation activity in an acid phosphatase
Authors: Ishikawa, K. / Mihara, Y. / Shimba, N. / Ohtsu, N. / Kawasaki, H. / Suzuki, E. / Asano, Y.
#1: Journal: Embo J. / Year: 2000
Title: X-ray structures of a novel acid phosphatase from Escherichia blattae and its complex with the transition-state analog molybdate
Authors: Ishikawa, K. / Mihara, Y. / Gondoh, K. / Suzuki, E. / Asano, Y.
History
DepositionApr 22, 2002Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 11, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.classification
Revision 1.4Nov 10, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: acid phosphatase
B: acid phosphatase
C: acid phosphatase
D: acid phosphatase
E: acid phosphatase
F: acid phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)151,05112
Polymers150,4746
Non-polymers5766
Water5,657314
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12800 Å2
ΔGint-184 kcal/mol
Surface area49440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)137.800, 168.200, 58.400
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
acid phosphatase


Mass: 25079.078 Da / Num. of mol.: 6 / Fragment: residues 1-231 / Mutation: G74D, I153T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia blattae (bacteria) / Plasmid: pUC118 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9S1A6, acid phosphatase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 314 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.25 Å3/Da / Density % sol: 45.28 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.4
Details: PEG400, pH 8.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
120 mg/mlprotein1drop
220 mMTris1droppH8.0
338 %PEG4001reservoir
420 mMTris-HCl1reservoirpH8.4

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Data collection

DiffractionMean temperature: 288 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6B / Wavelength: 1 Å
DetectorType: FUJI / Detector: IMAGE PLATE / Date: Dec 3, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→10 Å / Num. all: 45889 / Num. obs: 45889 / % possible obs: 97.5 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Biso Wilson estimate: 28.6 Å2 / Rmerge(I) obs: 0.084
Reflection shellResolution: 2.5→2.55 Å / % possible all: 91.2
Reflection
*PLUS
Lowest resolution: 10 Å

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Processing

Software
NameVersionClassification
WEISdata scaling
SCALAdata scaling
AMoREphasing
CNX2000.1refinement
WEISdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1D2T

1d2t


Resolution: 2.5→10 Å / Isotropic thermal model: Isotropic / σ(F): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.284 2298 -RANDOM
Rwork0.243 ---
all0.243 45889 --
obs0.243 45889 97.5 %-
Displacement parametersBiso mean: 36.3 Å2
Refine analyzeLuzzati coordinate error obs: 0.32 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.48 Å
Refinement stepCycle: LAST / Resolution: 2.5→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9897 0 30 314 10241
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.3
LS refinement shellResolution: 2.5→2.65 Å / Rfactor Rfree error: 0.021
RfactorNum. reflection% reflection
Rfree0.381 335 -
Rwork0.338 --
obs-6867 92.4 %
Refinement
*PLUS
Lowest resolution: 10 Å / σ(F): 1 / Rfactor Rfree: 0.285 / Rfactor Rwork: 0.242
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: c_angle_deg / Dev ideal: 1.31

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