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- PDB-1ihp: STRUCTURE OF PHOSPHOMONOESTERASE -

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Basic information

Entry
Database: PDB / ID: 1ihp
TitleSTRUCTURE OF PHOSPHOMONOESTERASE
ComponentsPHYTASE
KeywordsPHOSPHOMONOESTERASE / HYDROLASE / GLYCOPROTEIN
Function / homology
Function and homology information


3-phytase / 3-phytase 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 ficuum (mold)
MethodX-RAY DIFFRACTION / SIRAS / Resolution: 2.5 Å
AuthorsKostrewa, D.
CitationJournal: Nat.Struct.Biol. / Year: 1997
Title: Crystal structure of phytase from Aspergillus ficuum at 2.5 A resolution.
Authors: Kostrewa, D. / Gruninger-Leitch, F. / D'Arcy, A. / Broger, C. / Mitchell, D. / van Loon, A.P.
History
DepositionFeb 4, 1997Processing site: BNL
Revision 1.0Mar 18, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type

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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)48,3402
Polymers48,2441
Non-polymers961
Water2,072115
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: PHYTASE
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)290,04212
Polymers289,4666
Non-polymers5766
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation4_555y,x,-z1
crystal symmetry operation5_555x-y,-y,-z1
crystal symmetry operation6_555-x,-x+y,-z1
Buried area11810 Å2
ΔGint-125 kcal/mol
Surface area95260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.250, 92.250, 100.890
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321
DetailsTHE ASYMMETRIC UNIT OF THE CRYSTAL CONTAINS ONE DEGLYCOSYLATED PROTEIN MONOMER.

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Components

#1: Protein PHYTASE / / MYO-INOSITOL-HEXAKISPHOSPHATE-3-PHOSPHOHYDROLASE


Mass: 48244.348 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: ALSO CALLED ASPERGILLUS NIGER STRAIN NRRL3135 / Source: (natural) Aspergillus ficuum (mold) / References: UniProt: P34752, 3-phytase
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 115 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.57 Å3/Da / Density % sol: 52.09 %
Crystal grow
*PLUS
Method: unknown

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Data collection

DiffractionMean temperature: 273 K
Diffraction sourceSource: ROTATING ANODE / Type: OTHER / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→25 Å / Num. obs: 17223 / % possible obs: 97.7 % / Observed criterion σ(I): 0 / Redundancy: 4.6 % / Rsym value: 0.056 / Net I/σ(I): 28
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 3.1 % / Mean I/σ(I) obs: 7 / Rsym value: 0.204 / % possible all: 93.8
Reflection
*PLUS
Num. measured all: 79917 / Rmerge(I) obs: 0.056
Reflection shell
*PLUS
% possible obs: 93.8 %

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Processing

Software
NameVersionClassification
XDSdata scaling
XDSdata reduction
X-PLOR3.1model building
X-PLOR3.1refinement
X-PLOR3.1phasing
RefinementMethod to determine structure: SIRAS / Resolution: 2.5→25 Å / Cross valid method: FREE R / σ(F): 0
Details: AMINO ACIDS 249 - 252 ARE COMPLETELY DISORDERED. THE FOLLOWING AMINO ACID SIDE CHAINS ARE DISORDERED: GLU 43, LYS 70, GLU 77, GLN 81, LYS 94, GLN 392, GLN 395, ARG 428 THE ELECTRON DENSITY ...Details: AMINO ACIDS 249 - 252 ARE COMPLETELY DISORDERED. THE FOLLOWING AMINO ACID SIDE CHAINS ARE DISORDERED: GLU 43, LYS 70, GLU 77, GLN 81, LYS 94, GLN 392, GLN 395, ARG 428 THE ELECTRON DENSITY OF THE SULFATE IS NOT WELL DEFINED.
RfactorNum. reflection% reflectionSelection details
Rfree0.211 -5 %RANDOM
Rwork0.155 ---
obs0.155 17223 97.7 %-
Displacement parametersBiso mean: 30.7 Å2
Refinement stepCycle: LAST / Resolution: 2.5→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3368 0 5 115 3488
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.5
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d22.8
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.9
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.5
X-RAY DIFFRACTIONx_mcangle_it2
X-RAY DIFFRACTIONx_scbond_it2
X-RAY DIFFRACTIONx_scangle_it2.5
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg22.8
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.9

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