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- PDB-4h46: Crystal Structure of AMP complexes of NEM modified Porcine Liver ... -

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Basic information

Entry
Database: PDB / ID: 4h46
TitleCrystal Structure of AMP complexes of NEM modified Porcine Liver Fructose-1,6-bisphosphatase
ComponentsFructose-1,6-bisphosphatase 1
KeywordsHYDROLASE / allosteric enzymes / FBPase / NEM modification
Function / homology
Function and homology information


Gluconeogenesis / sucrose biosynthetic process / fructose-bisphosphatase / fructose 1,6-bisphosphate 1-phosphatase activity / cellular response to magnesium ion / negative regulation of Ras protein signal transduction / fructose 6-phosphate metabolic process / fructose metabolic process / monosaccharide binding / fructose 1,6-bisphosphate metabolic process ...Gluconeogenesis / sucrose biosynthetic process / fructose-bisphosphatase / fructose 1,6-bisphosphate 1-phosphatase activity / cellular response to magnesium ion / negative regulation of Ras protein signal transduction / fructose 6-phosphate metabolic process / fructose metabolic process / monosaccharide binding / fructose 1,6-bisphosphate metabolic process / negative regulation of glycolytic process / regulation of gluconeogenesis / dephosphorylation / AMP binding / gluconeogenesis / negative regulation of cell growth / cellular response to xenobiotic stimulus / identical protein binding / metal ion binding / cytosol / cytoplasm
Similarity search - Function
Fructose-1,6-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 / 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
ADENOSINE MONOPHOSPHATE / 6-O-phosphono-beta-D-fructofuranose / 1-ETHYL-PYRROLIDINE-2,5-DIONE / PHOSPHATE ION / Fructose-1,6-bisphosphatase 1
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 Å
AuthorsGao, Y. / Honzatko, R.B.
CitationJournal: To be Published
Title: Fluorescent 2',3'-O-(2,4,6-trinitrophenyl) (TNP)-AMP Is an Active Site Inhibitor for Porcine Liver Fructose-1,6-bisphosphatase Rather Than Allosteric Inhibitor
Authors: Gao, Y. / Honzatko, R.B.
History
DepositionSep 16, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 18, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_conn_type / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_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 / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Sep 20, 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
Revision 1.3Oct 9, 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: Fructose-1,6-bisphosphatase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,5456
Polymers36,6911
Non-polymers8545
Water1,820101
1
A: Fructose-1,6-bisphosphatase 1
hetero molecules

A: Fructose-1,6-bisphosphatase 1
hetero molecules

A: Fructose-1,6-bisphosphatase 1
hetero molecules

A: Fructose-1,6-bisphosphatase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,18024
Polymers146,7654
Non-polymers3,41520
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,-y,z1
crystal symmetry operation3_455-x-1,y,-z1
crystal symmetry operation4_555x,-y,-z1
Buried area22970 Å2
ΔGint-152 kcal/mol
Surface area43670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.561, 78.673, 164.928
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

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Protein / Sugars , 2 types, 2 molecules A

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


Mass: 36691.207 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Gene: FBP, FBP1 / Plasmid: pET24B / Production host: Escherichia coli (E. coli) / Strain (production host): DF657 / References: UniProt: P00636, 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.: 1
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 , 5 types, 105 molecules

#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#6: Chemical ChemComp-NEN / 1-ETHYL-PYRROLIDINE-2,5-DIONE


Mass: 127.141 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H9NO2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 101 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.77 Å3/Da / Density % sol: 55.52 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG3350, t-butyl alcohol, 1,2-ethanediol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Nov 24, 2011
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→42.1 Å / Num. all: 14501 / Num. obs: 13863 / % possible obs: 95.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.73 % / Rmerge(I) obs: 0.111 / Net I/σ(I): 7.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2.5-2.593.620.3442.6198.4
2.59-2.693.660.313198
2.69-2.823.660.2633.7197.5
2.82-2.963.690.2124.1197.6
2.96-3.153.710.1874.8196.5
3.15-3.393.760.1257.2196.5
3.39-3.733.780.0998.8195.6
3.73-4.273.810.07611194.7
4.27-5.383.870.0613.9192.9
5.38-42.13.780.05612.7189.3

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.63 Å42.1 Å
Translation2.63 Å42.1 Å

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Processing

Software
NameVersionClassificationNB
d*TREK9.7Ldata scaling
d*TREK9.7Ldata reduction
MOLREPphasing
REFMAC5.5.0066refinement
PDB_EXTRACT3.11data extraction
CrystalCleardata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2F3D

2f3d


Resolution: 2.5→41.3 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.896 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / ESU R: 0.486 / ESU R Free: 0.294 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25644 694 5 %RANDOM
Rwork0.19449 ---
obs0.19745 13147 95.5 %-
all-14493 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.162 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2--0.02 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.5→41.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2439 0 54 101 2594
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0222534
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0522.0113433
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3595317
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.52724.37596
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.43815445
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.7381513
X-RAY DIFFRACTIONr_chiral_restr0.1360.2396
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0211838
X-RAY DIFFRACTIONr_gen_planes_other
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_it1.0531.51582
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.95622552
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.6363952
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.0074.5881
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.371 40 -
Rwork0.241 981 -
obs--98.27 %

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