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- PDB-1qwo: Crystal structure of a phosphorylated phytase from Aspergillus fu... -

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Basic information

Entry
Database: PDB / ID: 1qwo
TitleCrystal structure of a phosphorylated phytase from Aspergillus fumigatus, revealing the structural basis for its heat resilience and catalytic pathway
Componentsphytase
KeywordsHYDROLASE / Alpha Barrel / Beta Sandwich / Orthogonal Bundle / Glycoprotein / phosphohistidine
Function / homology
Function and homology information


3-phytase / 3-phytase activity / acid phosphatase activity / Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases / extracellular region
Similarity search - Function
Histidine acid phosphatase, eukaryotic / Histidine acid phosphatases active site signature. / Histidine acid phosphatases phosphohistidine signature. / Histidine acid phosphatase active site / Histidine phosphatase superfamily, clade-2 / Histidine phosphatase superfamily (branch 2) / Phosphoglycerate mutase-like / Histidine phosphatase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesAspergillus fumigatus (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsXiang, T. / Liu, Q. / Deacon, A.M. / Koshy, M. / Kriksunov, I.A. / Lei, X.G. / Hao, Q. / Thiel, D.J.
CitationJournal: J.Mol.Biol. / Year: 2004
Title: Crystal Structure of a Heat-resilient Phytase from Aspergillus fumigatus, Carrying a Phosphorylated Histidine
Authors: Xiang, T. / Liu, Q. / Deacon, A.M. / Koshy, M. / Kriksunov, I.A. / Lei, X.G. / Hao, Q. / Thiel, D.J.
History
DepositionSep 3, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 1, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Jul 29, 2020Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Structure summary
Category: chem_comp / database_PDB_caveat ...chem_comp / database_PDB_caveat / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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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)49,9457
Polymers48,6171
Non-polymers1,3276
Water11,061614
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.340, 70.340, 186.673
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-954-

HOH

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Components

#1: Protein phytase /


Mass: 48617.449 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus fumigatus (mold) / Production host: Pichia pastoris (fungus) / References: UniProt: O00092, 3-phytase
#2: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 614 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.37 Å3/Da / Density % sol: 48.2 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG4000, magnesium chloride hexahydrate, HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 300K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.92 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 10, 2000
RadiationMonochromator: Silicon / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.5→20 Å / Num. all: 69199 / Num. obs: 69199 / % possible obs: 90.4 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 5.73 % / Rmerge(I) obs: 0.038
Reflection shellResolution: 1.5→1.53 Å / % possible all: 90.4

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→20 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.958 / SU B: 1.188 / SU ML: 0.044 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.073 / ESU R Free: 0.073 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18561 3529 5.1 %RANDOM
Rwork0.16116 ---
obs0.16242 65670 91.11 %-
all-69199 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 13.851 Å2
Baniso -1Baniso -2Baniso -3
1-0.2 Å20 Å20 Å2
2--0.2 Å20 Å2
3----0.4 Å2
Refinement stepCycle: LAST / Resolution: 1.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3378 0 84 614 4076
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0213552
X-RAY DIFFRACTIONr_bond_other_d0.0020.023105
X-RAY DIFFRACTIONr_angle_refined_deg1.4951.9764823
X-RAY DIFFRACTIONr_angle_other_deg0.90237216
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0055433
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_chiral_restr0.0950.2538
X-RAY DIFFRACTIONr_gen_planes_refined0.010.023907
X-RAY DIFFRACTIONr_gen_planes_other0.0130.02727
X-RAY DIFFRACTIONr_nbd_refined0.2530.2757
X-RAY DIFFRACTIONr_nbd_other0.250.23705
X-RAY DIFFRACTIONr_nbtor_other0.0830.21928
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1580.2420
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.280.26
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3450.238
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2090.237
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.791.52163
X-RAY DIFFRACTIONr_mcangle_it1.4323477
X-RAY DIFFRACTIONr_scbond_it2.41731389
X-RAY DIFFRACTIONr_scangle_it3.7354.51346
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.5→1.538 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.243 119
Rwork0.243 2420

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