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- PDB-5ck7: Mouse ADP-dependent Glucokinase; AMP bound -

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Basic information

Entry
Database: PDB / ID: 5ck7
TitleMouse ADP-dependent Glucokinase; AMP bound
ComponentsADP-dependent glucokinase
KeywordsTRANSFERASE / ADPGK / ribokinase / kinase / AMP
Function / homology
Function and homology information


ADP-specific glucose/glucosamine kinase / ADP-specific glucokinase activity / Glycolysis / glycolytic process / glucose metabolic process / extracellular region / metal ion binding
Similarity search - Function
ADP-specific phosphofructokinase/glucokinase / ADP-specific Phosphofructokinase/Glucokinase conserved region / ADP-dependent kinase (ADPK) domain profile. / Ribokinase-like
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / ADP-dependent glucokinase
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.99 Å
AuthorsRichter, J.P. / Ronimus, R.S. / Sutherland-Smith, A.J.
CitationJournal: J.Biol.Chem. / Year: 2016
Title: The Structural and Functional Characterization of Mammalian ADP-dependent Glucokinase.
Authors: Richter, J.P. / Goroncy, A.K. / Ronimus, R.S. / Sutherland-Smith, A.J.
History
DepositionJul 15, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 18, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2019Group: Data collection / Database references / Derived calculations
Category: citation / pdbx_struct_oper_list
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _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.year / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Sep 27, 2023Group: 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 1.3Oct 16, 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: ADP-dependent glucokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,4152
Polymers53,0681
Non-polymers3471
Water48627
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.681, 58.492, 161.708
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein ADP-dependent glucokinase / ADPGK


Mass: 53067.738 Da / Num. of mol.: 1 / Fragment: UNP residues 51-495
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Adpgk / Plasmid: pBAD-TOPO / Production host: Escherichia coli (E. coli)
References: UniProt: Q8VDL4, ADP-specific glucose/glucosamine kinase
#2: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / 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: 2.04 Å3/Da / Density % sol: 39.59 %
Crystal growTemperature: 294 K / Method: vapor diffusion
Details: Seeding of preequilibrated drops of 0.2 M NH4Cl, 20% w/v PEG 3350

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Apr 9, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.99→39.64 Å / Num. all: 9031 / Num. obs: 9031 / % possible obs: 97.1 % / Redundancy: 5.9 % / Rmerge(I) obs: 0.091 / Rsym value: 0.091 / Net I/σ(I): 10.1
Reflection shellResolution: 2.99→3.1 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 2.6 / % possible all: 80.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0124refinement
XDSdata reduction
Aimlessdata scaling
Cootmodel building
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 5CCF

5ccf


Resolution: 2.99→39.64 Å / Cor.coef. Fo:Fc: 0.903 / Cor.coef. Fo:Fc free: 0.897 / SU B: 44.368 / SU ML: 0.383 / Cross valid method: THROUGHOUT / ESU R Free: 0.479 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24315 449 5 %RANDOM
Rwork0.22737 ---
obs0.22817 8542 96.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: MASK
Displacement parametersBiso mean: 63.723 Å2
Baniso -1Baniso -2Baniso -3
1--2.2 Å20 Å20 Å2
2---2.78 Å20 Å2
3---4.98 Å2
Refinement stepCycle: LAST / Resolution: 2.99→39.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3447 0 23 27 3497
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0193555
X-RAY DIFFRACTIONr_bond_other_d0.0020.023354
X-RAY DIFFRACTIONr_angle_refined_deg1.6961.9574839
X-RAY DIFFRACTIONr_angle_other_deg1.04337708
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2695447
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.01823.836159
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.55915562
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.2831522
X-RAY DIFFRACTIONr_chiral_restr0.110.2545
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0214046
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02827
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_it2.0453.6381791
X-RAY DIFFRACTIONr_mcbond_other2.0453.6361790
X-RAY DIFFRACTIONr_mcangle_it3.4155.4572237
X-RAY DIFFRACTIONr_mcangle_other3.4145.4592238
X-RAY DIFFRACTIONr_scbond_it2.0483.8461764
X-RAY DIFFRACTIONr_scbond_other2.0473.8471765
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.3865.7022603
X-RAY DIFFRACTIONr_long_range_B_refined8.15335.37215509
X-RAY DIFFRACTIONr_long_range_B_other8.15335.37515509
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.99→3.067 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.312 25 -
Rwork0.328 484 -
obs--75.07 %
Refinement TLS params.Method: refined / Origin x: -9.2534 Å / Origin y: -1.0758 Å / Origin z: 20.7389 Å
111213212223313233
T0.2952 Å2-0.0842 Å20.0391 Å2-0.1672 Å2-0.0084 Å2--0.0276 Å2
L0.8859 °20.123 °20.3332 °2-2.9887 °2-0.658 °2--1.6974 °2
S0.1611 Å °-0.3603 Å °0.0445 Å °0.7162 Å °-0.0308 Å °0.2444 Å °0.2209 Å °-0.2897 Å °-0.1303 Å °

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