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- PDB-4he2: Crystal structure of human muscle fructose-1,6-bisphosphatase Q32... -

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Basic information

Entry
Database: PDB / ID: 4he2
TitleCrystal structure of human muscle fructose-1,6-bisphosphatase Q32R mutant complex with AMP
ComponentsFructose-1,6-bisphosphatase isozyme 2
KeywordsHYDROLASE / allosteric enzyme
Function / homology
Function and homology information


sucrose biosynthetic process / fructose-bisphosphatase / fructose 1,6-bisphosphate 1-phosphatase activity / fructose 6-phosphate metabolic process / Gluconeogenesis / fructose metabolic process / fructose 1,6-bisphosphate metabolic process / anchoring junction / gluconeogenesis / Z disc ...sucrose biosynthetic process / fructose-bisphosphatase / fructose 1,6-bisphosphate 1-phosphatase activity / fructose 6-phosphate metabolic process / Gluconeogenesis / fructose metabolic process / fructose 1,6-bisphosphate metabolic process / anchoring junction / gluconeogenesis / Z disc / extracellular exosome / identical protein binding / metal ion binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Fructose-1,6-bisphosphatase / Fructose-1,6-bisphosphatase, active site / Fructose-1-6-bisphosphatase class 1, C-terminal / Fructose-1-6-bisphosphatase active site. / Fructose-1,6-bisphosphatase class 1 / Fructose-1-6-bisphosphatase class I, N-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 class 1, C-terminal / Fructose-1-6-bisphosphatase active site. / Fructose-1,6-bisphosphatase class 1 / Fructose-1-6-bisphosphatase class I, N-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 / PHOSPHITE ION / Fructose-1,6-bisphosphatase isozyme 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.6 Å
AuthorsShi, R. / Zhu, D.W. / Lin, S.X.
CitationJournal: Plos One / Year: 2013
Title: Crystal Structures of Human Muscle Fructose-1,6-Bisphosphatase: Novel Quaternary States, Enhanced AMP Affinity, and Allosteric Signal Transmission Pathway.
Authors: Shi, R. / Chen, Z.Y. / Zhu, D.W. / Li, C. / Shan, Y. / Xu, G. / Lin, S.X.
History
DepositionOct 3, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 9, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software
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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_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_alt_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.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_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_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_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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)37,2968
Polymers36,6961
Non-polymers6007
Water4,630257
1
A: Fructose-1,6-bisphosphatase isozyme 2
hetero molecules

A: Fructose-1,6-bisphosphatase isozyme 2
hetero molecules

A: Fructose-1,6-bisphosphatase isozyme 2
hetero molecules

A: Fructose-1,6-bisphosphatase isozyme 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,18432
Polymers146,7844
Non-polymers2,40028
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation7_555y,x,-z1
crystal symmetry operation8_555-y,-x,-z1
Buried area12320 Å2
ΔGint-66 kcal/mol
Surface area44010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.366, 73.366, 146.622
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number94
Space group name H-MP42212
Components on special symmetry positions
IDModelComponents
11A-407-

CL

21A-747-

HOH

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 36695.961 Da / Num. of mol.: 1 / Mutation: Q32R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: fbp2 / Plasmid: pKK223-3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O00757, fructose-bisphosphatase

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Non-polymers , 6 types, 264 molecules

#2: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE / Adenosine monophosphate


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#3: Chemical ChemComp-PO3 / PHOSPHITE ION / Phosphite ester


Mass: 78.972 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO3
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#6: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 257 / 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: 2.69 Å3/Da / Density % sol: 54.25 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M MgCl2, 15% PEG 4000, 0.1M Hepes pH 7.5, vapor diffusion, hanging drop, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 4r / Detector: CCD / Date: May 26, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 51809 / % possible obs: 96.5 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.051 / Χ2: 1.008 / Net I/σ(I): 13.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.6-1.666.70.49351841.024198.7
1.66-1.726.70.37251971.022198.5
1.72-1.86.80.26152231.016198.3
1.8-1.96.80.1851571.006198
1.9-2.026.80.11451981.007197.6
2.02-2.176.80.07751711.001197.2
2.17-2.396.80.05851531.006196.6
2.39-2.746.70.04851890.996195.9
2.74-3.456.60.03751511.001194.5
3.45-506.30.03351860.999190

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1EYI

1eyi


Resolution: 1.6→50 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.958 / WRfactor Rfree: 0.1961 / WRfactor Rwork: 0.182 / Occupancy max: 1 / Occupancy min: 0.25 / FOM work R set: 0.8894 / SU B: 2.639 / SU ML: 0.043 / SU R Cruickshank DPI: 0.0793 / SU Rfree: 0.0749 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.079 / ESU R Free: 0.075 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1937 2642 5.1 %RANDOM
Rwork0.181 ---
obs0.1816 51784 96.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 55.12 Å2 / Biso mean: 27.299 Å2 / Biso min: 10.69 Å2
Baniso -1Baniso -2Baniso -3
1-0.25 Å20 Å20 Å2
2--0.25 Å20 Å2
3----0.5 Å2
Refinement stepCycle: LAST / Resolution: 1.6→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2353 0 32 257 2642
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0222498
X-RAY DIFFRACTIONr_angle_refined_deg1.2662.0083402
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4565332
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.90724.78794
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.07615457
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.0411511
X-RAY DIFFRACTIONr_chiral_restr0.0820.2400
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211823
X-RAY DIFFRACTIONr_mcbond_it0.5871.51567
X-RAY DIFFRACTIONr_mcangle_it1.1522539
X-RAY DIFFRACTIONr_scbond_it2.0523931
X-RAY DIFFRACTIONr_scangle_it3.414.5849
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.255 217 -
Rwork0.237 3620 -
all-3837 -
obs--98.49 %
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)
11.80920.1234-0.82690.4698-0.24551.17590.1066-0.00680.01750.1122-0.05370.033-0.0138-0.077-0.0530.0878-0.04890.00260.05440.00590.0046-12.1505-13.148-6.1042
20.20240.08260.10190.77150.060.75720.0666-0.0604-0.02140.0593-0.018-0.02190.092-0.003-0.04870.0605-0.0309-0.01880.0283-0.00340.0444-8.3172-18.6496-14.7808
30.12940.142-0.14610.7953-0.30770.60850.03810.0312-0.0084-0.093-0.03390.03660.0511-0.0631-0.00420.05790.0122-0.02620.0316-0.0120.0459-9.8726-9.2474-35.2858
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A11 - 54
2X-RAY DIFFRACTION2A72 - 199
3X-RAY DIFFRACTION3A200 - 335

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