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- PDB-1dkp: CRYSTAL STRUCTURE OF PHYTATE COMPLEX OF ESCHERICHIA COLI PHYTASE ... -

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Basic information

Entry
Database: PDB / ID: 1dkp
TitleCRYSTAL STRUCTURE OF PHYTATE COMPLEX OF ESCHERICHIA COLI PHYTASE AT PH 6.6. PHYTATE IS BOUND WITH ITS 3-PHOSPHATE IN THE ACTIVE SITE. HG2+ CATION ACTS AS AN INTERMOLECULAR BRIDGE
ComponentsPHYTASE
KeywordsHYDROLASE / HISTIDINE ACID PHOSPHATASE FOLD
Function / homology
Function and homology information


inositol phosphate phosphatase activity / inositol hexakisphosphate 4-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 / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / outer membrane-bounded periplasmic space / 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
: / INOSITOL HEXAKISPHOSPHATE / Phytase AppA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 2.28 Å
AuthorsLim, D. / Golovan, S. / Forsberg, C.W. / Jia, Z.
Citation
Journal: Nat.Struct.Biol. / Year: 2000
Title: Crystal structures of Escherichia coli phytase and its complex with phytate.
Authors: Lim, D. / Golovan, S. / Forsberg, C.W. / Jia, Z.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1998
Title: Purification, Crystallization and Preliminary X-ray Analysis of the Escherichia coli Phytase
Authors: Jia, Z. / Golovan, S. / Ye, Q. / Forsberg, C.W.
#2: Journal: J.Bacteriol. / Year: 1990
Title: The Complete Nucleotide Sequence of the Escherichia coli Gene appA Reveals Significant Homology Between pH 2.5 Acid Phosphatase and Glucose-1-phosphatase
Authors: Dassa, J. / Marck, C. / Boquet, P.L.
History
DepositionDec 8, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 3, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 24, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.4Oct 14, 2020Group: Derived calculations / Structure summary
Category: chem_comp / pdbx_struct_conn_angle ...chem_comp / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _chem_comp.pdbx_synonyms / _pdbx_struct_conn_angle.ptnr1_auth_comp_id ..._chem_comp.pdbx_synonyms / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _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 / _struct_conn.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 3, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.6Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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: PHYTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,1596
Polymers44,6971
Non-polymers1,4625
Water4,900272
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.573, 75.127, 90.393
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is the single molecule in the asymmetric unit.

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Components

#1: Protein PHYTASE / PH 2.5 ACID PHOSPHATASE


Mass: 44696.609 Da / Num. of mol.: 1 / Mutation: A116T, H17A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PET21A / Production host: Escherichia coli (E. coli) / References: UniProt: P07102, acid phosphatase
#2: Chemical
ChemComp-HG / MERCURY (II) ION


Mass: 200.590 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Hg
#3: Chemical ChemComp-IHP / INOSITOL HEXAKISPHOSPHATE / MYO-INOSITOL HEXAKISPHOSPHATE / INOSITOL 1,2,3,4,5,6-HEXAKISPHOSPHATE


Mass: 660.035 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H18O24P6
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 272 / 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: 2.68 Å3/Da / Density % sol: 54.08 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.6
Details: ETHYLENE GLYCOL, GLYCEROL, 2-MORPHOLINOPROPANESULFONIC ACID, MERCURIC CHLORIDE, pH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
172 mg/mlprotein1drop
22.5 mM1dropHgCl2
31.5 mM1dropNa2WO4
428 %ethylene glycol1reservoir
518 %glycerol1reservoir
633 mMMops1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 20, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.28→25 Å / Num. all: 94671 / Num. obs: 41377 / % possible obs: 97.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.3 % / Biso Wilson estimate: 22.3 Å2 / Rmerge(I) obs: 0.031 / Net I/σ(I): 22.38
Reflection shellResolution: 2.28→2.36 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.088 / % possible all: 89.6
Reflection
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 25 Å / Num. all: 48024 / Num. obs: 30534 / % possible obs: 93.7 % / Rmerge(I) obs: 0.039

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Processing

Software
NameVersionClassification
CNS0.5refinement
SCALEPACKdata scaling
XTALVIEWrefinement
DENZOdata reduction
RefinementResolution: 2.28→25 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1443774.67 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH & HUBER / Details: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.227 2052 5 %RANDOM
Rwork0.189 ---
all0.189 41317 --
obs0.189 41317 97.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 41.44 Å2 / ksol: 0.349 e/Å3
Displacement parametersBiso mean: 35.2 Å2
Baniso -1Baniso -2Baniso -3
1-3.41 Å20 Å20 Å2
2---6.26 Å20 Å2
3---2.84 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.29 Å0.19 Å
Refinement stepCycle: LAST / Resolution: 2.28→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3140 0 39 272 3451
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.82
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.971.5
X-RAY DIFFRACTIONc_mcangle_it2.782
X-RAY DIFFRACTIONc_scbond_it3.342
X-RAY DIFFRACTIONc_scangle_it4.312.5
LS refinement shellResolution: 2.28→2.42 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.281 288 4.3 %
Rwork0.22 6363 -
obs--94.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PAPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAWATER_REP.TOP
X-RAY DIFFRACTION3ION.TOP
X-RAY DIFFRACTION4PHYTATE.TO
Software
*PLUS
Name: CNS / Version: 0.5 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 5 % / Highest resolution: 2.5 Å / Lowest resolution: 25 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 35.2 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.82
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.281 / % reflection Rfree: 4.3 % / Rfactor Rwork: 0.22

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