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- PDB-4tsr: The Complex Structure of Mutant Phytase with IHS -

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Basic information

Entry
Database: PDB / ID: 4tsr
TitleThe Complex Structure of Mutant Phytase with IHS
ComponentsPeriplasmic AppA protein
KeywordsHYDROLASE/HYDROLASE Inhibitor / Phytase / Synchrotron radiation / HYDROLASE-HYDROLASE Inhibitor complex
Function / homology
Function and homology information


4-phytase activity / inositol phosphate phosphatase activity / cellular response to anoxia / nucleotidase activity / sugar-phosphatase activity / acid phosphatase activity / Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases / cellular response to phosphate starvation / lysosome organization / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides ...4-phytase activity / inositol phosphate phosphatase activity / cellular response to anoxia / nucleotidase activity / sugar-phosphatase activity / acid phosphatase activity / Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases / cellular response to phosphate starvation / lysosome organization / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / dephosphorylation / outer membrane-bounded periplasmic space / lysosome / GTPase activity
Similarity search - Function
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 / NICKEL (II) ION / Phytase AppA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.07 Å
AuthorsWu, T.H. / Chen, C.C. / Huang, C.H. / Guo, R.T.
CitationJournal: To Be Published
Title: The Complex Structure of mutant Phytase with IHS
Authors: Wu, T.H. / Chen, C.C. / Huang, C.H. / Guo, R.T.
History
DepositionJun 19, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 6, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Source and taxonomy / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / entity_src_gen / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_struct_oper_list / refine_hist / struct_conn / struct_keywords
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.symmetry_operation / _refine_hist.number_atoms_solvent / _refine_hist.pdbx_number_atoms_ligand / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_keywords.text

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Periplasmic AppA protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,6436
Polymers44,7481
Non-polymers8955
Water5,386299
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)63.796, 47.500, 65.632
Angle α, β, γ (deg.)90.00, 100.51, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Periplasmic AppA protein / Phosphoanhydride phosphohydrolase / 4-phytase


Mass: 44747.680 Da / Num. of mol.: 1 / Mutation: V89T and S206A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Komagataella pastoris CBS 7435 (fungus) / References: UniProt: P07102, acid phosphatase, 4-phytase
#2: Chemical
ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ni
#3: Chemical ChemComp-IHS / D-MYO-INOSITOL-HEXASULPHATE


Mass: 660.535 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H12O24S6
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 299 / 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: 2.19 Å3/Da / Density % sol: 43.71 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.01 M NiCl2, 0.1 M HEPES, 20% PEG 3350 and 2% PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13C1 / Wavelength: 0.97622 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 1, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97622 Å / Relative weight: 1
ReflectionResolution: 2.07→25 Å / Num. obs: 23694 / % possible obs: 99.7 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.129 / Net I/σ(I): 10.9

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Processing

SoftwareName: REFMAC / Version: 5.8.0071 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1DKQ

1dkq


Resolution: 2.07→25 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.916 / SU B: 9.64 / SU ML: 0.133 / Cross valid method: THROUGHOUT / ESU R: 0.223 / ESU R Free: 0.179 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21818 1182 5 %RANDOM
Rwork0.17181 ---
obs0.17419 22501 99.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.096 Å2
Baniso -1Baniso -2Baniso -3
1-1.62 Å20 Å20.23 Å2
2---1.12 Å20 Å2
3----0.55 Å2
Refinement stepCycle: 1 / Resolution: 2.07→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3054 0 40 299 3393
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0193158
X-RAY DIFFRACTIONr_bond_other_d0.0010.023018
X-RAY DIFFRACTIONr_angle_refined_deg1.7921.9794322
X-RAY DIFFRACTIONr_angle_other_deg0.9253.0026941
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1125397
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.59824.275131
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.37515509
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6971522
X-RAY DIFFRACTIONr_chiral_restr0.1150.2507
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213556
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02694
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_it1.1421.4571594
X-RAY DIFFRACTIONr_mcbond_other1.1381.4571593
X-RAY DIFFRACTIONr_mcangle_it1.8172.1771989
X-RAY DIFFRACTIONr_mcangle_other1.8182.1781990
X-RAY DIFFRACTIONr_scbond_it2.0461.7441564
X-RAY DIFFRACTIONr_scbond_other2.0261.7421560
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.0522.5312328
X-RAY DIFFRACTIONr_long_range_B_refined5.4112.873806
X-RAY DIFFRACTIONr_long_range_B_other5.24212.5123702
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.07→2.125 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.269 72 -
Rwork0.214 1653 -
obs--99.48 %
Refinement TLS params.Method: refined / Origin x: -12.8012 Å / Origin y: -4.5073 Å / Origin z: -21.3597 Å
111213212223313233
T0.0057 Å20.0017 Å2-0.0023 Å2-0.0398 Å2-0.0022 Å2--0.001 Å2
L0.1514 °20.0091 °2-0.0779 °2-0.1858 °20.148 °2--0.4034 °2
S-0.0166 Å °0.011 Å °0.0044 Å °0.0243 Å °0.0251 Å °-0.0119 Å °0.0195 Å °0.0098 Å °-0.0085 Å °

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