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- PDB-8xm2: The mutant crystal structure of phytase APPAmut9 from Yersinia in... -

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Basic information

Entry
Database: PDB / ID: 8xm2
TitleThe mutant crystal structure of phytase APPAmut9 from Yersinia intermedia
ComponentsPhytase
KeywordsHYDROLASE / The mutant crystal structure of phytase APPAmut9 from Yersinia intermedia
Function / homology
Function and homology information


4-phytase / inositol hexakisphosphate 4-phosphatase activity / sugar-phosphatase activity / outer membrane-bounded periplasmic space
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: 1.77 Å
AuthorsTu, T. / Dong, R.Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32222082 China
Citation
Journal: J.Biol.Chem. / Year: 2024
Title: Achieving thermostability of a phytase with resistance up to 100 °C.
Authors: Tu, T. / Wang, Q. / Dong, R. / Liu, X. / Penttinen, L. / Hakulinen, N. / Tian, J. / Zhang, W. / Wang, Y. / Luo, H. / Yao, B. / Huang, H.
#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
Revision 1.1Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Revision 1.2Jan 15, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phytase


Theoretical massNumber of molelcules
Total (without water)45,7001
Polymers45,7001
Non-polymers00
Water10,791599
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.500, 70.450, 103.540
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: 45700.242 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 599 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.13 Å3/Da / Density % sol: 42.38 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 5% pentanediol, 10% PEG 10000, 0.1M HEPES buffer pH7.5

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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: Aug 26, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.77→47.53 Å / Num. obs: 38446 / % possible obs: 98.88 % / Redundancy: 9.3 % / Biso Wilson estimate: 19.08 Å2 / CC1/2: 0.998 / Net I/σ(I): 17.49
Reflection shellResolution: 1.77→1.83 Å / Mean I/σ(I) obs: 3.82 / Num. unique obs: 3452 / CC1/2: 0.955

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.77→47.53 Å / SU ML: 0.1982 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 20.2993 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2125 1937 5.04 %
Rwork0.1616 36505 -
obs0.1641 38442 98.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.85 Å2
Refinement stepCycle: LAST / Resolution: 1.77→47.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3155 0 0 599 3754
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00573290
X-RAY DIFFRACTIONf_angle_d0.83984490
X-RAY DIFFRACTIONf_chiral_restr0.0593500
X-RAY DIFFRACTIONf_plane_restr0.0052592
X-RAY DIFFRACTIONf_dihedral_angle_d2.47032732
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.77-1.810.32961030.22612316X-RAY DIFFRACTION89
1.81-1.860.26691150.2042520X-RAY DIFFRACTION96.52
1.86-1.920.27981340.19492586X-RAY DIFFRACTION99.09
1.92-1.980.21841370.18622597X-RAY DIFFRACTION99.89
1.98-2.050.24251590.18032578X-RAY DIFFRACTION99.93
2.05-2.130.20961330.18172620X-RAY DIFFRACTION99.93
2.13-2.230.26121440.17512614X-RAY DIFFRACTION100
2.23-2.350.21571630.16772583X-RAY DIFFRACTION99.96
2.35-2.490.23441410.16522603X-RAY DIFFRACTION100
2.49-2.690.20841510.16652642X-RAY DIFFRACTION100
2.69-2.960.21531490.16712638X-RAY DIFFRACTION100
2.96-3.390.20391390.15552672X-RAY DIFFRACTION100
3.39-4.270.1711300.13722704X-RAY DIFFRACTION100
4.27-47.530.18541390.14012832X-RAY DIFFRACTION99.76
Refinement TLS params.Method: refined / Origin x: 7.2987966704 Å / Origin y: -2.48928008283 Å / Origin z: -14.5791506101 Å
111213212223313233
T0.0397398219102 Å20.00206118789953 Å2-0.00373254792891 Å2-0.0397585364341 Å20.014104243043 Å2--0.0523857122864 Å2
L0.067745711586 °2-0.0293520131575 °2-0.0772365597936 °2-0.131740926996 °20.0187807755577 °2--0.321028332001 °2
S0.0262062394283 Å °-0.00558285892577 Å °0.01721741508 Å °-0.0335150816545 Å °0.0428355506038 Å °0.0394436490404 Å °0.00081986874798 Å °0.0011785903439 Å °0.253158351486 Å °
Refinement TLS groupSelection details: all

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