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- PDB-5iz3: P. patens sedoheptulose-1,7-bisphosphatase -

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Basic information

Entry
Database: PDB / ID: 5iz3
TitleP. patens sedoheptulose-1,7-bisphosphatase
Components
  • Predicted protein
  • sedoheptulose-1,7-bisphosphatase
KeywordsHYDROLASE / Physcomitrella patens carbon metabolism sedoheptulose bisphophatase
Function / homology
Function and homology information


phosphatase activity / carbohydrate metabolic process / metal ion binding
Similarity search - Function
Sedoheptulose-1,7-bisphosphatase / Fructose-1,6-bisphosphatase, active site / Fructose-1-6-bisphosphatase active site. / Fructose-1,6-bisphosphatase class 1 / Fructose-1-6-bisphosphatase class I, N-terminal / Fructose-1-6-bisphosphatase class 1, C-terminal / Fructose-1-6-bisphosphatase, N-terminal domain / Fructose-1-6-bisphosphatase, C-terminal domain / D-Maltodextrin-Binding Protein; domain 2 - #80 / Fructose-1,6-Bisphosphatase, subunit A, domain 1 ...Sedoheptulose-1,7-bisphosphatase / Fructose-1,6-bisphosphatase, active site / Fructose-1-6-bisphosphatase active site. / Fructose-1,6-bisphosphatase class 1 / Fructose-1-6-bisphosphatase class I, N-terminal / Fructose-1-6-bisphosphatase class 1, C-terminal / Fructose-1-6-bisphosphatase, N-terminal domain / Fructose-1-6-bisphosphatase, C-terminal domain / D-Maltodextrin-Binding Protein; domain 2 - #80 / Fructose-1,6-Bisphosphatase, subunit A, domain 1 / Fructose-1,6-Bisphosphatase; Chain A, domain 1 / D-Maltodextrin-Binding Protein; domain 2 / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
IMIDAZOLE / PHOSPHATE ION / Predicted protein
Similarity search - Component
Biological speciesPhyscomitrella patens (plant)
Physcomitrella patens subsp. patens (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsEinsle, O. / Guetle, D.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2016
Title: Chloroplast FBPase and SBPase are thioredoxin-linked enzymes with similar architecture but different evolutionary histories.
Authors: Gutle, D.D. / Roret, T. / Muller, S.J. / Couturier, J. / Lemaire, S.D. / Hecker, A. / Dhalleine, T. / Buchanan, B.B. / Reski, R. / Einsle, O. / Jacquot, J.P.
History
DepositionMar 24, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jun 8, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 22, 2016Group: Database references
Revision 1.2Oct 16, 2019Group: Data collection / Category: reflns_shell
Revision 1.3Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Nov 20, 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: sedoheptulose-1,7-bisphosphatase
B: Predicted protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,6686
Polymers69,3402
Non-polymers3284
Water10,989610
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5340 Å2
ΔGint-26 kcal/mol
Surface area22640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.180, 70.417, 197.245
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number17
Space group name H-MP2221
Components on special symmetry positions
IDModelComponents
11A-517-

HOH

21B-776-

HOH

31B-789-

HOH

41B-809-

HOH

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Components

#1: Protein sedoheptulose-1,7-bisphosphatase


Mass: 34655.113 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Physcomitrella patens (plant) / Gene: PHYPADRAFT_122707 / Production host: Physcomitrella patens (plant) / References: UniProt: A9S1S8
#2: Protein Predicted protein


Mass: 34685.137 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Physcomitrella patens subsp. patens (plant)
Gene: PHYPADRAFT_122707 / Production host: Physcomitrella patens (plant) / References: UniProt: A9S1S8
#3: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H5N2
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 610 / 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: 2.26 Å3/Da / Density % sol: 45.66 %
Crystal growTemperature: 281 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 40 % PEG 600 0.2 M imidazole/malate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.0001 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 10, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0001 Å / Relative weight: 1
ReflectionResolution: 1.3→100 Å / Num. obs: 155382 / % possible obs: 99.3 % / Observed criterion σ(F): 2 / Redundancy: 10.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.067 / Net I/σ(I): 30.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1D9Q

1d9q


Resolution: 1.3→98.62 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.959 / SU B: 1.797 / SU ML: 0.036 / Cross valid method: THROUGHOUT / ESU R: 0.053 / ESU R Free: 0.058 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1908 6340 4.9 %RANDOM
Rwork0.15969 ---
obs0.1612 122301 82.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 19.237 Å2
Baniso -1Baniso -2Baniso -3
1--0.08 Å2-0 Å20 Å2
2--0.06 Å2-0 Å2
3---0.01 Å2
Refinement stepCycle: 1 / Resolution: 1.3→98.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4863 0 20 610 5493
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.0195112
X-RAY DIFFRACTIONr_bond_other_d0.0020.024847
X-RAY DIFFRACTIONr_angle_refined_deg2.3171.9716938
X-RAY DIFFRACTIONr_angle_other_deg0.985311178
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7475659
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.46424.425226
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.2815884
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.81531
X-RAY DIFFRACTIONr_chiral_restr0.1470.2786
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.025876
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021143
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_it1.811.2342597
X-RAY DIFFRACTIONr_mcbond_other1.8071.2312596
X-RAY DIFFRACTIONr_mcangle_it2.8321.8423269
X-RAY DIFFRACTIONr_mcangle_other2.8331.8463270
X-RAY DIFFRACTIONr_scbond_it3.1951.6232514
X-RAY DIFFRACTIONr_scbond_other3.1831.6222507
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.9542.2853658
X-RAY DIFFRACTIONr_long_range_B_refined6.97113.03923390
X-RAY DIFFRACTIONr_long_range_B_other6.97113.0423391
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.3→1.334 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.315 110 -
Rwork0.248 1797 -
obs--16.71 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.4623-0.1772-0.06020.53720.12180.0372-0.0412-0.0559-0.08230.01170.02910.08760.00010.0220.01210.01450.00450.02190.03010.00590.0435-15.1835-64.0043-27.6999
20.1649-0.04310.0190.2150.00630.1649-0.012-0.01910.06180.0168-0.0190.00830.01160.0020.0310.01990.005-0.00290.0145-0.01550.0336-16.0532-33.0321-27.385
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A79 - 394
2X-RAY DIFFRACTION2B79 - 393

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