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- PDB-3k4q: Aspergillus niger Phytase in complex with myo-inositol hexakis sulfate -

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Basic information

Entry
Database: PDB / ID: 3k4q
TitleAspergillus niger Phytase in complex with myo-inositol hexakis sulfate
Components3-phytase A
KeywordsHYDROLASE / Phytase / PhyA / 3-Phosphotase / myo-inositol hexakis phosphate phosphohydrolase / 37288-11-2 / myo-Inositol hexakis sulfate / 70701-62-1 / 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
D-MYO-INOSITOL-HEXASULPHATE / Phytase A
Similarity search - Component
Biological speciesAspergillus niger (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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)100,86912
Polymers97,7782
Non-polymers3,09110
Water6,539363
1
A: 3-phytase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,4346
Polymers48,8891
Non-polymers1,5455
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: 3-phytase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,4346
Polymers48,8891
Non-polymers1,5455
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)70.699, 87.571, 81.765
Angle α, β, γ (deg.)90.00, 110.61, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B
13A
23B

NCS domain segments:

Component-ID: 1 / Refine code: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERALAALAAA7 - 357 - 35
21SERSERALAALABB7 - 357 - 35
12GLUGLUHISHISAA37 - 26437 - 264
22GLUGLUHISHISBB37 - 26437 - 264
13GLUGLUPHEPHEAA266 - 443266 - 443
23GLUGLUPHEPHEBB266 - 443266 - 443

NCS ensembles :
ID
1
2
3

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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: Chemical ChemComp-IHS / D-MYO-INOSITOL-HEXASULPHATE


Mass: 660.535 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H12O24S6
#3: 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.: 8
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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 363 / 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: 2.42 Å3/Da / Density % sol: 49.23 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 25% (w/v) PEG 3350, 0.2M 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: 2.2→76.53 Å / Num. all: 46790 / Num. obs: 46790 / % possible obs: 96.1 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 26 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 8.8
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.442 / Mean I/σ(I) obs: 2.4 / Num. unique all: 6741 / % possible all: 97.9

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Processing

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

1ihp


Resolution: 2.2→62.01 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.91 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 6.891 / SU ML: 0.172 / Cross valid method: THROUGHOUT / σ(F): -1 / σ(I): -1 / ESU R: 0.311 / ESU R Free: 0.232 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25367 2377 5.1 %RANDOM
Rwork0.19727 ---
all0.20013 44411 --
obs0.20013 44411 98.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 65.15 Å2 / Biso mean: 27.148 Å2 / Biso min: 8.88 Å2
Baniso -1Baniso -2Baniso -3
1--0.14 Å20 Å2-3.67 Å2
2--0.7 Å20 Å2
3----3.15 Å2
Refinement stepCycle: LAST / Resolution: 2.2→62.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6772 0 184 363 7319
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0227172
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8611.9799808
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.455884
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.95324.18323
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.407151079
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8581538
X-RAY DIFFRACTIONr_chiral_restr0.1250.21107
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0215488
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_it0.9061.54379
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.66727097
X-RAY DIFFRACTIONr_scbond_it2.51632793
X-RAY DIFFRACTIONr_scangle_it3.8874.52706
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 / Refine-ID: X-RAY DIFFRACTION

Ens-IDNumberTypeRms dev position (Å)Weight position
1231TIGHT POSITIONAL0.070.05
1231TIGHT THERMAL0.170.5
21761TIGHT POSITIONAL0.050.05
21761TIGHT THERMAL0.20.5
31365TIGHT POSITIONAL0.050.05
31365TIGHT THERMAL0.180.5
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.335 185 -
Rwork0.263 3218 -
obs--97.9 %

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