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- PDB-3k4p: Aspergillus niger Phytase -

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Basic information

Entry
Database: PDB / ID: 3k4p
TitleAspergillus niger Phytase
Components3-phytase A
KeywordsHYDROLASE / Phytase / PhyA / 3-Phosphotase / myo-inositol hexakis phosphate phosphohydrolase / 37288-11-2 / Disulfide bond / Glycoprotein / Secreted
Function / homology
Function and homology information


3-phytase / inositol hexakisphosphate 3-phosphatase 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 niger (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsOakley, A.J.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2010
Title: The structure of Aspergillus niger phytase PhyA in complex with a phytate mimetic
Authors: Oakley, A.J.
History
DepositionOct 6, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 30, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / 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_leaving_atom_flag / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 3-phytase A
B: 3-phytase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,1058
Polymers97,7782
Non-polymers1,3276
Water5,693316
1
A: 3-phytase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,5534
Polymers48,8891
Non-polymers6643
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: 3-phytase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,5534
Polymers48,8891
Non-polymers6643
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)71.066, 87.457, 82.185
Angle α, β, γ (deg.)90.00, 110.98, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: 1 / Auth seq-ID: 7 - 444 / Label seq-ID: 7 - 444

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein 3-phytase A / 3 phytase A / Myo-inositol-hexaphosphate 3-phosphohydrolase A / Myo-inositol hexakisphosphate ...3 phytase A / Myo-inositol-hexaphosphate 3-phosphohydrolase A / Myo-inositol hexakisphosphate phosphohydrolase A


Mass: 48888.996 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus niger (mold) / Gene: phyA / Production host: Aspergillus niger (mold) / References: UniProt: P34752, 3-phytase
#2: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


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


Mass: 18.015 Da / Num. of mol.: 316 / 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: 2.44 Å3/Da / Density % sol: 49.57 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 25% (w/v) PEG 3350, 0.4M ammonium nitrate, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.953715 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 28, 2009 / Details: BEAMLINE OPTICS
RadiationMonochromator: BEAMLINE OPTICS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953715 Å / Relative weight: 1
ReflectionResolution: 2.4→76.74 Å / Num. all: 35613 / Num. obs: 35613 / % possible obs: 96.6 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Biso Wilson estimate: 35.4 Å2 / Rmerge(I) obs: 0.138 / Net I/σ(I): 6.6
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.542 / Mean I/σ(I) obs: 2.4 / Num. unique all: 5338 / % possible all: 99.8

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Processing

Software
NameVersionClassification
Blu-Icedata collection
MOLREPphasing
REFMAC5.5.0102refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1IHP

1ihp


Resolution: 2.4→66.36 Å / Cor.coef. Fo:Fc: 0.919 / Cor.coef. Fo:Fc free: 0.873 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 9.744 / SU ML: 0.229 / Cross valid method: THROUGHOUT / σ(F): -1 / σ(I): -1 / ESU R: 0.635 / ESU R Free: 0.314 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27548 1770 5 %RANDOM
Rwork0.21528 ---
all0.21825 33827 --
obs0.21825 33827 96.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 57.71 Å2 / Biso mean: 26.967 Å2 / Biso min: 2.05 Å2
Baniso -1Baniso -2Baniso -3
1--0.3 Å20 Å2-3.04 Å2
2--0.08 Å20 Å2
3----1.95 Å2
Refinement stepCycle: LAST / Resolution: 2.4→66.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6777 0 84 316 7177
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0227060
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.681.9629629
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7225880
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.04724.224322
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.495151078
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.611537
X-RAY DIFFRACTIONr_chiral_restr0.1110.21085
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0215455
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7271.54373
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.3327086
X-RAY DIFFRACTIONr_scbond_it2.02332687
X-RAY DIFFRACTIONr_scangle_it3.2474.52540
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 3363 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
tight positional0.040.05
tight thermal0.120.5
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.353 124 -
Rwork0.249 2559 -
obs-2559 99.7 %

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