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- PDB-1u25: Crystal structure of Selenomonas ruminantium phytase complexed wi... -

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Basic information

Entry
Database: PDB / ID: 1u25
TitleCrystal structure of Selenomonas ruminantium phytase complexed with persulfated phytate in the C2221 crystal form
Componentsmyo-inositol hexaphosphate phosphohydrolase
KeywordsHYDROLASE / PTP / P-loop / phytase
Function / homology
Function and homology information


dephosphorylation / hydrolase activity
Similarity search - Function
Alpha-Beta Plaits - #1690 / Inositol hexakisphosphate / Inositol hexakisphosphate / Protein tyrosine phosphatase superfamily / Protein-Tyrosine Phosphatase; Chain A / Tyrosine specific protein phosphatases active site. / Protein-tyrosine phosphatase, active site / Tyrosine-specific protein phosphatases domain / Tyrosine specific protein phosphatases domain profile. / Protein-tyrosine phosphatase-like ...Alpha-Beta Plaits - #1690 / Inositol hexakisphosphate / Inositol hexakisphosphate / Protein tyrosine phosphatase superfamily / Protein-Tyrosine Phosphatase; Chain A / Tyrosine specific protein phosphatases active site. / Protein-tyrosine phosphatase, active site / Tyrosine-specific protein phosphatases domain / Tyrosine specific protein phosphatases domain profile. / Protein-tyrosine phosphatase-like / Alpha-Beta Plaits / Alpha-Beta Complex / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
D-MYO-INOSITOL-HEXASULPHATE / Myo-inositol hexaphosphate phosphohydrolase
Similarity search - Component
Biological speciesSelenomonas ruminantium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsChu, H.M. / Guo, R.T. / Lin, T.W. / Chou, C.C. / Shr, H.L. / Lai, H.L. / Tang, T.Y. / Cheng, K.J. / Selinger, B.L. / Wang, A.H.-J.
CitationJournal: STRUCTURE / Year: 2004
Title: Structures of Selenomonas ruminantium Phytase in Complex with Persulfated Phytate; DSP Phytase Fold and Mechanism for Sequential Substrate Hydrolysis
Authors: Chu, H.M. / Guo, R.T. / Lin, T.W. / Chou, C.C. / Shr, H.L. / Lai, H.L. / Tang, T.Y. / Cheng, K.J. / Selinger, B.L. / Wang, A.H.-J.
History
DepositionJul 16, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 9, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: myo-inositol hexaphosphate phosphohydrolase
B: myo-inositol hexaphosphate phosphohydrolase
C: myo-inositol hexaphosphate phosphohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,0046
Polymers117,0233
Non-polymers1,9823
Water16,952941
1
A: myo-inositol hexaphosphate phosphohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,3293
Polymers39,0081
Non-polymers1,3212
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: myo-inositol hexaphosphate phosphohydrolase


Theoretical massNumber of molelcules
Total (without water)39,0081
Polymers39,0081
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: myo-inositol hexaphosphate phosphohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,6682
Polymers39,0081
Non-polymers6611
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)128.376, 228.745, 91.778
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-2404-

HOH

21A-2581-

HOH

31A-2763-

HOH

41A-2779-

HOH

51A-2985-

HOH

61A-3200-

HOH

71C-2551-

HOH

81C-2931-

HOH

91C-3204-

HOH

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Components

#1: Protein myo-inositol hexaphosphate phosphohydrolase / phytase


Mass: 39007.547 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Selenomonas ruminantium (bacteria) / Plasmid: pET23b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q7WUJ1, EC: 3.1.3.72
#2: Chemical ChemComp-IHS / D-MYO-INOSITOL-HEXASULPHATE


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


Mass: 18.015 Da / Num. of mol.: 941 / 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: 3.035 Å3/Da / Density % sol: 57.91 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 0.1M LiCl, 0.05M CAPSO, 12% PEG6000, 2% PEG200, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL12B2 / Wavelength: 1.0362 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 15, 2003 / Details: mirror
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0362 Å / Relative weight: 1
ReflectionResolution: 2.44→50 Å / Num. all: 47108 / Num. obs: 37388 / % possible obs: 84 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.078 / Net I/σ(I): 13
Reflection shellResolution: 2.44→2.53 Å

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→35.21 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.265 1878 random
Rwork0.179 --
all-47108 -
obs-37388 -
Refine analyze
FreeObs
Luzzati coordinate error0.39 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.4 Å0.28 Å
Refinement stepCycle: LAST / Resolution: 2.5→35.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7603 0 108 941 8652
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.98
X-RAY DIFFRACTIONc_bond_d0.017
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.024
RfactorNum. reflection% reflection
Rfree0.366 133 -
Rwork0.266 --
obs-4744 64.3 %

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