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- PDB-4bb9: Crystal structure of glucokinase regulatory protein complexed to ... -

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Basic information

Entry
Database: PDB / ID: 4bb9
TitleCrystal structure of glucokinase regulatory protein complexed to fructose-1-phosphate
ComponentsGLUCOKINASE REGULATORY PROTEIN
KeywordsPROTEIN-BINDING PROTEIN / GLUCOSE METABOLISM
Function / homology
Function and homology information


negative regulation of glucokinase activity / fructose-6-phosphate binding / glucose sensor activity / urate metabolic process / kinase inhibitor activity / carbohydrate derivative metabolic process / response to fructose / Regulation of Glucokinase by Glucokinase Regulatory Protein / Defective TPR may confer susceptibility towards thyroid papillary carcinoma (TPC) / triglyceride homeostasis ...negative regulation of glucokinase activity / fructose-6-phosphate binding / glucose sensor activity / urate metabolic process / kinase inhibitor activity / carbohydrate derivative metabolic process / response to fructose / Regulation of Glucokinase by Glucokinase Regulatory Protein / Defective TPR may confer susceptibility towards thyroid papillary carcinoma (TPC) / triglyceride homeostasis / enzyme inhibitor activity / response to glucose / protein import into nucleus / glucose homeostasis / carbohydrate binding / carbohydrate metabolic process / enzyme binding / mitochondrion / nucleoplasm / cytosol / cytoplasm
Similarity search - Function
Helicase, Ruva Protein; domain 3 - #1080 / C-terminal lid domain of glucokinase regulatory protein / Glucokinase regulatory protein, conserved site / N-acetylmuramic acid 6-phosphate etherase/glucokinase regulatory protein / Glucokinase regulatory protein family signature. / SIS domain / SIS domain profile. / SIS domain superfamily / Glucose-6-phosphate isomerase like protein; domain 1 / Helicase, Ruva Protein; domain 3 ...Helicase, Ruva Protein; domain 3 - #1080 / C-terminal lid domain of glucokinase regulatory protein / Glucokinase regulatory protein, conserved site / N-acetylmuramic acid 6-phosphate etherase/glucokinase regulatory protein / Glucokinase regulatory protein family signature. / SIS domain / SIS domain profile. / SIS domain superfamily / Glucose-6-phosphate isomerase like protein; domain 1 / Helicase, Ruva Protein; domain 3 / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
1-O-phosphono-beta-D-fructopyranose / Glucokinase regulatory protein
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.47 Å
AuthorsPautsch, A. / Stadler, N. / Loehle, A. / Lenter, M. / Rist, W. / Berg, A. / Glocker, L. / Nar, H. / Reinert, D. / Heckel, A. ...Pautsch, A. / Stadler, N. / Loehle, A. / Lenter, M. / Rist, W. / Berg, A. / Glocker, L. / Nar, H. / Reinert, D. / Heckel, A. / Schnapp, G. / Kauschke, S.G.
CitationJournal: Biochemistry / Year: 2013
Title: Crystal Structure of Glucokinase Regulatory Protein.
Authors: Pautsch, A. / Stadler, N. / Loehle, A. / Rist, W. / Berg, A. / Glocker, L. / Nar, H. / Reinert, D. / Lenter, M. / Heckel, A. / Schnapp, G. / Kauschke, S.G.
History
DepositionSep 21, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 15, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 28, 2013Group: Database references
Revision 1.2Apr 3, 2019Group: Data collection / Other / Source and taxonomy
Category: entity_src_gen / pdbx_database_proc / pdbx_database_status
Item: _entity_src_gen.pdbx_host_org_cell_line / _pdbx_database_status.recvd_author_approval
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / pdbx_struct_conn_angle / 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.pdbx_synonyms / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _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.pdbx_dist_value / _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.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GLUCOKINASE REGULATORY PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,0753
Polymers69,7751
Non-polymers3002
Water12,611700
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)60.970, 72.300, 136.890
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 GLUCOKINASE REGULATORY PROTEIN / / GKRP / GLUCOKINASE REGULATOR


Mass: 69775.000 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PDEST8 / Cell line (production host): High Five / Production host: TRICHOPLUSIA NI (cabbage looper) / References: UniProt: Q14397
#2: Sugar ChemComp-F1P / 1-O-phosphono-beta-D-fructopyranose / BETA-D-FRUCTOPYRANOSE-1-PHOSPHATE / ((2R,3S,4R,5R)-TETRAHYDRO-2,3,4,5-TETRAHYDROXY-2H-PYRAN-2-YL)METHYL DIHYDROGEN PHOSPHATE


Type: D-saccharide / Mass: 260.136 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H13O9P
IdentifierTypeProgram
b-D-Frup1PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 700 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsSURFACE MUTATION K326T, K327T C-TERMINAL LEHHHHHH TAG

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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: 2.16 Å3/Da / Density % sol: 43.11 % / Description: NONE
Crystal growDetails: 12-16 MG/ML IN 25 MM HEPES PH 7.4, 50 MM KCL, 1 MM MGCL2, 2 MM DTT AND 5 MM FRUCTOSE-1-PHOSPHATE 14 % PEG 8000, 20% GLYCEROL, 0.16 M CALCIUM ACETATE AND 0.08 M CACODYLATE PH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.96
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96 Å / Relative weight: 1
ReflectionResolution: 1.47→72 Å / Num. obs: 102068 / % possible obs: 98.6 % / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Biso Wilson estimate: 15.5 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 14.7
Reflection shellResolution: 1.47→1.53 Å / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 3.9 / % possible all: 98.2

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Processing

Software
NameVersionClassification
BUSTER2.9.3refinement
XDSdata reduction
XSCALEdata scaling
autoSHARPphasing
RefinementMethod to determine structure: SIRAS
Starting model: NONE

Resolution: 1.47→21.52 Å / Cor.coef. Fo:Fc: 0.9644 / Cor.coef. Fo:Fc free: 0.9581 / SU R Cruickshank DPI: 0.061 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.065 / SU Rfree Blow DPI: 0.063 / SU Rfree Cruickshank DPI: 0.06
Details: NUMBER OF LIBRARIES USED: 7. IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=F1P CA. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE= 5340. NUMBER WITH ...Details: NUMBER OF LIBRARIES USED: 7. IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=F1P CA. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE= 5340. NUMBER WITH APPROX DEFAULT CCP4 ATOM TYPE=16. NUMBER TREATED BY BAD NON-BONDED CONTACTS=1.
RfactorNum. reflection% reflectionSelection details
Rfree0.1774 5102 5 %RANDOM
Rwork0.16 ---
obs0.1609 102029 98.58 %-
Displacement parametersBiso mean: 18.61 Å2
Baniso -1Baniso -2Baniso -3
1-0.9777 Å20 Å20 Å2
2--0.6609 Å20 Å2
3----1.6386 Å2
Refine analyzeLuzzati coordinate error obs: 0.145 Å
Refinement stepCycle: LAST / Resolution: 1.47→21.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4606 0 17 700 5323
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0084747HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.956441HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1670SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes114HARMONIC2
X-RAY DIFFRACTIONt_gen_planes688HARMONIC5
X-RAY DIFFRACTIONt_it4747HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.35
X-RAY DIFFRACTIONt_other_torsion14.05
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion644SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact6434SEMIHARMONIC4
LS refinement shellResolution: 1.47→1.51 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2253 370 5 %
Rwork0.2108 7032 -
all0.2115 7402 -
obs--98.58 %

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