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- PDB-6ayu: Crystal structure of fructose-1,6-bisphosphatase T84S from Mycoba... -

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Basic information

Entry
Database: PDB / ID: 6ayu
TitleCrystal structure of fructose-1,6-bisphosphatase T84S from Mycobacterium tuberculosis
ComponentsFructose-1,6-bisphosphatase class 2
KeywordsHYDROLASE / Fructose-1 / 6-bisphosphatase / gluconeogenesis / Class II phosphatase / Mycobacterium tuberculosis
Function / homology
Function and homology information


glycerol metabolic process / fructose-bisphosphatase / fructose 1,6-bisphosphate 1-phosphatase activity / gluconeogenesis / metal ion binding / cytoplasm
Similarity search - Function
D-Maltodextrin-Binding Protein; domain 2 - #90 / Fructose-1,6-bisphosphatase class 2/Sedoheputulose-1,7-bisphosphatase / Bacterial fructose-1,6-bisphosphatase, glpX-encoded / 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
6-O-phosphono-beta-D-fructofuranose / MALONATE ION / Fructose-1,6-bisphosphatase class 2
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsAbad-Zapatero, C. / Wolf, N. / Gutka, H.J. / Movahedzadeh, F.
Funding support United States, 1items
OrganizationGrant numberCountry
PottsG3541 United States
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2018
Title: Structures of the Mycobacterium tuberculosis GlpX protein (class II fructose-1,6-bisphosphatase): implications for the active oligomeric state, catalytic mechanism and citrate inhibition.
Authors: Wolf, N.M. / Gutka, H.J. / Movahedzadeh, F. / Abad-Zapatero, C.
History
DepositionSep 8, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 14, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 25, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_special_symmetry / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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.ptnr2_auth_asym_id / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fructose-1,6-bisphosphatase class 2
B: Fructose-1,6-bisphosphatase class 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,63315
Polymers73,2932
Non-polymers1,34013
Water2,954164
1
A: Fructose-1,6-bisphosphatase class 2
B: Fructose-1,6-bisphosphatase class 2
hetero molecules

A: Fructose-1,6-bisphosphatase class 2
B: Fructose-1,6-bisphosphatase class 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,26530
Polymers146,5864
Non-polymers2,68026
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_664-y+1,-x+1,-z-1/61
Buried area16900 Å2
ΔGint-48 kcal/mol
Surface area44020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)130.890, 130.890, 142.848
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-561-

HOH

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Components

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Protein / Sugars , 2 types, 4 molecules AB

#1: Protein Fructose-1,6-bisphosphatase class 2 / FBPase class 2 / D-fructose-1 / 6-bisphosphate 1-phosphohydrolase class 2


Mass: 36646.406 Da / Num. of mol.: 2 / Fragment: UNP residues 35-362 / Mutation: T84S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: ATCC 25177 / H37Ra / Gene: glpX, MRA_1110 / Plasmid: pET15b / Cell (production host): BL21 (DE3) / Production host: Escherichia coli (E. coli) / References: UniProt: A5U1E6, fructose-bisphosphatase
#2: Sugar ChemComp-F6P / 6-O-phosphono-beta-D-fructofuranose / FRUCTOSE-6-PHOSPHATE / 6-O-phosphono-beta-D-fructose / 6-O-phosphono-D-fructose / 6-O-phosphono-fructose


Type: D-saccharide, beta linking / Mass: 260.136 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H13O9P
IdentifierTypeProgram
b-D-Fruf6PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 4 types, 175 molecules

#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H2O4
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 164 / 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: 2.41 Å3/Da / Density % sol: 48.96 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 2.4 M sodium malonate pH 6.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97872 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 14, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.2→40 Å / Num. obs: 37421 / % possible obs: 99.86 % / Redundancy: 10.8 % / Biso Wilson estimate: 49.2 Å2 / CC1/2: 0.948 / Rpim(I) all: 0.025 / Rsym value: 0.082 / Net I/σ(I): 35.7
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 10.6 % / Rmerge(I) obs: 1.326 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 1825 / CC1/2: 0.907 / Rpim(I) all: 0.425 / Rsym value: 1.326 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3d1r

3d1r


Resolution: 2.2→38.5 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.73
RfactorNum. reflection% reflection
Rfree0.252 1839 4.91 %
Rwork0.204 --
obs0.206 37420 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.2→38.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4611 0 84 164 4859
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084767
X-RAY DIFFRACTIONf_angle_d1.026445
X-RAY DIFFRACTIONf_dihedral_angle_d11.5613371
X-RAY DIFFRACTIONf_chiral_restr0.063735
X-RAY DIFFRACTIONf_plane_restr0.005847
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.2540.27291490.25312641X-RAY DIFFRACTION99
2.254-2.32030.31531200.25562686X-RAY DIFFRACTION100
2.3203-2.39520.34281450.25252682X-RAY DIFFRACTION100
2.3952-2.48080.32251400.24872711X-RAY DIFFRACTION100
2.4808-2.58010.28891470.24842684X-RAY DIFFRACTION100
2.5801-2.69750.2571370.23232701X-RAY DIFFRACTION100
2.6975-2.83970.29761290.23542737X-RAY DIFFRACTION100
2.8397-3.01760.24671230.22742724X-RAY DIFFRACTION100
3.0176-3.25040.28831410.22262728X-RAY DIFFRACTION100
3.2504-3.57730.25531520.2112750X-RAY DIFFRACTION100
3.5773-4.09450.24271580.18112750X-RAY DIFFRACTION100
4.0945-5.15660.19981570.17012801X-RAY DIFFRACTION100
5.1566-38.50920.24831410.19232986X-RAY DIFFRACTION100

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