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- PDB-8xm1: Phytase mutant APPAmut4 -

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Basic information

Entry
Database: PDB / ID: 8xm1
TitlePhytase mutant APPAmut4
ComponentsPhytase
KeywordsHYDROLASE / Phytase mutant APPAmut4
Function / homology
Function and homology information


4-phytase / 4-phytase activity / sugar-phosphatase activity / acid phosphatase activity / lysosome organization / dephosphorylation / outer membrane-bounded periplasmic space / lysosome
Similarity search - Function
Histidine acid phosphatases phosphohistidine signature. / Histidine acid phosphatase active site / Histidine phosphatase superfamily, clade-2 / Histidine phosphatase superfamily (branch 2) / Histidine phosphatase superfamily
Similarity search - Domain/homology
Biological speciesYersinia intermedia (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsTu, T. / Wang, Q.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32222082 China
Citation
Journal: To Be Published
Title: The mutant crystal structure of phytase APPAmut4 from Yersinia intermedia
Authors: Tu, T. / Wang, Q.
#1: Journal: To Be Published
Title: Enhancing the thermostability of phytase up to its boiling point through a structured-based computational approach
Authors: Tu, T. / Wang, Q.
History
DepositionDec 27, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 3, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phytase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,7422
Polymers45,6201
Non-polymers1221
Water7,224401
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.514, 46.016, 192.797
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Phytase


Mass: 45619.789 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia intermedia (bacteria) / Production host: Komagataella pastoris (fungus) / References: UniProt: Q000T0, 4-phytase
#2: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Feature type: SUBJECT OF INVESTIGATION / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 401 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.12 Å3/Da / Density % sol: 41.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 0.1 M Sodium acetate trihydrate pH 4.5; 30% w/v Polyethylene glycol 1,500

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 14, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→26.35 Å / Num. obs: 31168 / % possible obs: 98.22 % / Redundancy: 2 % / Biso Wilson estimate: 20.12 Å2 / CC1/2: 0.993 / Net I/σ(I): 8.95
Reflection shellResolution: 1.9→1.96 Å / Mean I/σ(I) obs: 2.46 / Num. unique obs: 2732 / CC1/2: 0.876

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→26.35 Å / SU ML: 0.2113 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 20.1005 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2081 1623 5.21 %
Rwork0.1581 29537 -
obs0.1607 31160 98.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.61 Å2
Refinement stepCycle: LAST / Resolution: 1.9→26.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3148 0 8 401 3557
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00653378
X-RAY DIFFRACTIONf_angle_d0.91814621
X-RAY DIFFRACTIONf_chiral_restr0.051508
X-RAY DIFFRACTIONf_plane_restr0.0052618
X-RAY DIFFRACTIONf_dihedral_angle_d2.71012764
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.950.30921300.2312101X-RAY DIFFRACTION87.08
1.95-2.010.24031330.20022333X-RAY DIFFRACTION94.7
2.01-2.090.25761310.17522460X-RAY DIFFRACTION99.54
2.09-2.170.23681260.16852469X-RAY DIFFRACTION99.62
2.17-2.270.22341240.16732458X-RAY DIFFRACTION99.5
2.27-2.390.24041340.1642476X-RAY DIFFRACTION99.92
2.39-2.540.22061350.16032509X-RAY DIFFRACTION99.96
2.54-2.730.21511280.15462502X-RAY DIFFRACTION99.96
2.73-3.010.17481310.1522511X-RAY DIFFRACTION99.96
3.01-3.440.17051540.14852484X-RAY DIFFRACTION99.81
3.44-4.340.19641450.12842567X-RAY DIFFRACTION99.93
4.34-26.350.20051520.16522667X-RAY DIFFRACTION98.84
Refinement TLS params.Method: refined / Origin x: -6.88853576911 Å / Origin y: 4.4864080037 Å / Origin z: -26.3278598937 Å
111213212223313233
T0.100091492884 Å20.00423071387375 Å2-0.00194845479745 Å2-0.0917171840345 Å20.00352661768242 Å2--0.103410738713 Å2
L0.285444988896 °20.00373659597089 °20.009447074302 °2-0.204763603589 °20.156268647233 °2--0.406289834218 °2
S-0.0085076111192 Å °-0.000609912968089 Å °-0.0196909195937 Å °0.0257820911631 Å °-0.000319031631124 Å °-0.00241517557689 Å °0.0185995349207 Å °-0.0251830483528 Å °2.98988482284E-5 Å °
Refinement TLS groupSelection details: all

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