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- PDB-4ir8: 1.85 Angstrom Crystal Structure of Putative Sedoheptulose-1,7 bis... -

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Basic information

Entry
Database: PDB / ID: 4ir8
Title1.85 Angstrom Crystal Structure of Putative Sedoheptulose-1,7 bisphosphatase from Toxoplasma gondii
ComponentsSedoheptulose-1,7 bisphosphatase, putative
KeywordsHYDROLASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / FBPase/IMPase/glpX-like domain / Fructose-1 / 6-bisphospatase / NIAID / National Institute of Allergy and Infectious Diseases
Function / homology
Function and homology information


sedoheptulose-bisphosphatase / sedoheptulose-bisphosphatase activity / sucrose biosynthetic process / fructose 1,6-bisphosphate 1-phosphatase activity / fructose 1,6-bisphosphate metabolic process / fructose metabolic process / fructose 6-phosphate metabolic process / gluconeogenesis / cytoplasm
Similarity search - Function
Sedoheptulose-1,7-bisphosphatase / 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 ...Sedoheptulose-1,7-bisphosphatase / 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
ACETATE ION / DI(HYDROXYETHYL)ETHER / Sedoheptulose-1,7 bisphosphatase, putative
Similarity search - Component
Biological speciesToxoplasma gondii (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsMinasov, G. / Ruan, J. / Wawrzak, Z. / Halavaty, A. / Shuvalova, L. / Harb, O.S. / Ngo, H. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: TO BE PUBLISHED
Title: 1.85 Angstrom Crystal Structure of Putative Sedoheptulose-1,7 bisphosphatase from Toxoplasma gondii.
Authors: Minasov, G. / Ruan, J. / Wawrzak, Z. / Halavaty, A. / Shuvalova, L. / Harb, O.S. / Ngo, H. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionJan 14, 2013Deposition site: RCSB / Processing site: RCSB
SupersessionJan 23, 2013ID: 3UKS
Revision 1.0Jan 23, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sedoheptulose-1,7 bisphosphatase, putative
B: Sedoheptulose-1,7 bisphosphatase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,1927
Polymers75,7082
Non-polymers4845
Water9,728540
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5320 Å2
ΔGint-1 kcal/mol
Surface area22720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.400, 64.400, 591.610
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein Sedoheptulose-1,7 bisphosphatase, putative


Mass: 37854.074 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Toxoplasma gondii (eukaryote) / Strain: ME49 / Gene: TGGT1_070070, TGME49_035700, TGVEG_061570 / Plasmid: pCCK-N' / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3 Magic / References: UniProt: B9PW60, sedoheptulose-bisphosphatase
#2: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 540 / 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: 2.34 Å3/Da / Density % sol: 47.41 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: Protein: 20.0mG/mL, 0.5M Sodium chloride, 0.01M Tris-HCl (pH 8.3); Screen: PEG's (A2), 0.1M Sodium acetate (pH 4.6), 30% (v/v) PEG 300, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.97903 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 6, 2011 / Details: Mirrors
RadiationMonochromator: Si {1,1,1} / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97903 Å / Relative weight: 1
ReflectionResolution: 1.85→30 Å / Num. all: 64336 / Num. obs: 64336 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 14.3 % / Biso Wilson estimate: 23.6 Å2 / Rmerge(I) obs: 0.088 / Net I/σ(I): 29.6
Reflection shellResolution: 1.85→1.88 Å / Redundancy: 15 % / Rmerge(I) obs: 0.606 / Mean I/σ(I) obs: 5.3 / Num. unique all: 3115 / % possible all: 99.3

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Processing

Software
NameVersionClassification
Blu-IceMaxdata collection
PHENIXmodel building
REFMAC5.5.0102refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KBZ

3kbz


Resolution: 1.85→29.52 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.956 / SU B: 3.354 / SU ML: 0.047
Isotropic thermal model: Thermal Factors Individually Refined
Cross valid method: THROUGHOUT / ESU R: 0.114 / ESU R Free: 0.108 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18465 3242 5 %RANDOM
Rwork0.15425 ---
all0.1558 61040 --
obs0.1558 61040 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: 20.557 Å2
Baniso -1Baniso -2Baniso -3
1-0.59 Å20.29 Å2-0 Å2
2--0.59 Å2-0 Å2
3----0.88 Å2
Refinement stepCycle: LAST / Resolution: 1.85→29.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4828 0 32 540 5400
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0225392
X-RAY DIFFRACTIONr_bond_other_d0.0010.023638
X-RAY DIFFRACTIONr_angle_refined_deg1.3231.9617342
X-RAY DIFFRACTIONr_angle_other_deg0.8338947
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.2785721
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.95424.936233
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.44915950
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.8091533
X-RAY DIFFRACTIONr_chiral_restr0.0870.2822
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026234
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021043
X-RAY DIFFRACTIONr_mcbond_it0.9661.53431
X-RAY DIFFRACTIONr_mcbond_other0.3041.51403
X-RAY DIFFRACTIONr_mcangle_it1.67625550
X-RAY DIFFRACTIONr_scbond_it2.71531961
X-RAY DIFFRACTIONr_scangle_it4.3594.51792
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.253 229 -
Rwork0.191 4335 -
obs-4335 98 %
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)
11.01030.3791-0.10191.43470.10971.2753-0.00930.10830.0497-0.0886-0.02920.1665-0.007-0.12520.03850.0827-0.0168-0.02940.0437-0.0310.094435.048718.36319.0412
20.94630.5068-0.26411.16090.01020.97-0.0436-0.0576-0.01010.0852-0.00120.14710.1362-0.06750.04480.0859-0.01940.00470.0318-0.0180.078838.159717.959729.2132
30.830.2470.32060.86840.51461.73250.0219-0.054-0.07360.086-0.0003-0.04160.04770.1833-0.02150.0664-0.0082-0.01410.0374-0.00070.025654.991722.683234.4454
41.35060.26190.35870.77970.29821.3224-0.0082-0.2210.0450.1734-0.05270.1250.0141-0.09780.06090.1307-0.02250.01550.0504-0.020.048344.024623.879841.5726
51.49970.0598-0.43461.04540.28691.5207-0.02640.0579-0.1438-0.0177-0.0331-0.04890.24880.02250.05950.122-0.00620.01880.0273-0.03620.069471.487529.85627.7832
60.89320.2401-0.3450.6711-0.32550.9187-0.0059-0.02270.0414-0.09970.0132-0.10850.02460.0847-0.00730.0738-0.01050.01280.0347-0.04270.078973.317638.785113.1699
70.70410.0256-0.33810.8310.13091.8633-0.0047-0.09910.01840.0923-0.03530.0356-0.02630.00930.040.0922-0.0355-0.0080.0544-0.04110.071760.582240.777826.3013
80.79870.0279-0.73460.5460.19681.26840.0031-0.2547-0.04590.11290.0155-0.16660.03360.2983-0.01870.1156-0.0293-0.03720.1195-0.02190.100273.528642.248927.6161
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 110
2X-RAY DIFFRACTION2A111 - 178
3X-RAY DIFFRACTION3A179 - 252
4X-RAY DIFFRACTION4A253 - 330
5X-RAY DIFFRACTION5B6 - 110
6X-RAY DIFFRACTION6B111 - 178
7X-RAY DIFFRACTION7B179 - 252
8X-RAY DIFFRACTION8B253 - 329

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