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- PDB-1c47: BINDING DRIVEN STRUCTURAL CHANGES IN CRYSTALINE PHOSPHOGLUCOMUTAS... -

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Basic information

Entry
Database: PDB / ID: 1c47
TitleBINDING DRIVEN STRUCTURAL CHANGES IN CRYSTALINE PHOSPHOGLUCOMUTASE ASSOCIATED WITH CHEMICAL REACTION
ComponentsALPHA-D-GLUCOSE 1,6-BISPHOSPHATE PHOSPHOTRANSFERASE
KeywordsTRANSFERASE / PHOSPHOGLUCOMUTASE / PHOSPHOTRANSFERASE WITH BOUND REACTION INTERMEDIATE
Function / homology
Function and homology information


phosphoglucomutase (alpha-D-glucose-1,6-bisphosphate-dependent) / phosphoglucomutase activity / sarcoplasmic reticulum / glucose metabolic process / magnesium ion binding
Similarity search - Function
Phosphoglucomutase / Phosphoglucomutase/phosphomannomutase, C-terminal domain / Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 3 / Alpha-D-Glucose-1,6-Bisphosphate, subunit A, domain 3 / Alpha-D-phosphohexomutase, C-terminal domain / Alpha-D-phosphohexomutase superfamily / Alpha-D-phosphohexomutase, alpha/beta/alpha domain II / Alpha-D-phosphohexomutase, alpha/beta/alpha domain III / Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain II / Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain III ...Phosphoglucomutase / Phosphoglucomutase/phosphomannomutase, C-terminal domain / Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 3 / Alpha-D-Glucose-1,6-Bisphosphate, subunit A, domain 3 / Alpha-D-phosphohexomutase, C-terminal domain / Alpha-D-phosphohexomutase superfamily / Alpha-D-phosphohexomutase, alpha/beta/alpha domain II / Alpha-D-phosphohexomutase, alpha/beta/alpha domain III / Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain II / Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain III / Alpha-D-phosphohexomutase, conserved site / Phosphoglucomutase and phosphomannomutase phosphoserine signature. / Alpha-D-phosphohexomutase, alpha/beta/alpha domain I / Alpha-D-phosphohexomutase, alpha/beta/alpha I/II/III / Alpha-D-phosphohexomutase, C-terminal domain superfamily / Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain I / TATA-Binding Protein / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / 1,6-di-O-phosphono-alpha-D-glucopyranose / Phosphoglucomutase-1
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsBaranidharan, S. / Ray Jr., W.J.
Citation
Journal: To be Published
Title: Binding Driven Structural Changes in Crystaline Phosphoglucomutase Associated with Chemical Reaction
Authors: Baranidharan, S. / Ray Jr., W.J. / Liu, Y.
#1: Journal: Biochemistry / Year: 1993
Title: Structural Changes at the Metal Ion Binding Site During the Phosphoglucomutase Reaction
Authors: Ray Jr., W.J. / Post, C.B. / Liu, Y. / Rhyu, G.I.
#2: Journal: J.Biol.Chem. / Year: 1992
Title: The Crystal Structure of Phosphoglucomutase Refined at 2.7 A Resolution
Authors: Dai, J.B. / Liu, Y. / Ray, W.J. / Konno, M.
#3: Journal: J.Biol.Chem. / Year: 1986
Title: The Catalytic Activity of Muscle Phosphoglucomutase in the Crystalline Phase
Authors: Ray Jr., W.J.
#4: Journal: J.Biol.Chem. / Year: 1986
Title: The Structure of Rabbit Muscle Phosphoglucomutase at Intermediate Resolution
Authors: Lin, Z.-J. / Konno, M. / Abad-Zapatero, C. / Murthy, R.W.M.R.N. / Ray Jr., W.J. / Rossmann, M.G.
#5: Journal: Acta Crystallogr.,Sect.D / Year: 1997
Title: Structure of Rabbit Muscle Phosphoglucomutase at 2.4 A Resolution
Authors: Liu, Y.W. / Ray Jr., W.J. / Baranidharan, S.
#6: Journal: Acta Crystallogr.,Sect.D / Year: 1997
Title: ENHANCED DIFFRACTIVITY OF PHOSPHOGLUCOMUTASE CRYSTALS - USE OF AN ALTERNATE CRYOCRYSTALLOGRAPHIC PROCEDURE
Authors: Ray Jr., W.R. / Baranidharan, S. / Liu, Y.W.
History
DepositionAug 11, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 13, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 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_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _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.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
Revision 1.4Aug 9, 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: ALPHA-D-GLUCOSE 1,6-BISPHOSPHATE PHOSPHOTRANSFERASE
B: ALPHA-D-GLUCOSE 1,6-BISPHOSPHATE PHOSPHOTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,5645
Polymers123,0002
Non-polymers5643
Water2,666148
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)174.420, 174.420, 101.100
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein ALPHA-D-GLUCOSE 1,6-BISPHOSPHATE PHOSPHOTRANSFERASE / PHOSPHOGLUCOMUTASE


Mass: 61499.926 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Organ: MUSCLESkeletal muscle / References: UniProt: P00949, EC: 2.7.5.1
#2: Sugar ChemComp-G16 / 1,6-di-O-phosphono-alpha-D-glucopyranose / ALPHA-D-GLUCOSE 1,6-BISPHOSPHATE / 1,6-di-O-phosphono-alpha-D-glucose / 1,6-di-O-phosphono-D-glucose / 1,6-di-O-phosphono-glucose / Glucose 1,6-bisphosphate


Type: D-saccharide / Mass: 339.108 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H13O12P2
IdentifierTypeProgram
a-D-Glcp1PO36PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cd
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 148 / 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: 3.12 Å3/Da / Density % sol: 60.63 % / Description: PDB ENTRY 3PMG HAS RELATED INFORMATION

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Data collection

DiffractionMean temperature: 289 K
Diffraction sourceWavelength: 1.54
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Apr 1, 1996 / Details: NI FILTER
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.7→30 Å / Num. obs: 46085 / % possible obs: 96.5 % / Observed criterion σ(I): 1 / Redundancy: 2.2 % / Biso Wilson estimate: 24 Å2 / Rmerge(I) obs: 0.082

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Processing

Software
NameVersionClassification
Omodel building
X-PLORmodel building
X-PLOR3.8refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3PMG

3pmg


Resolution: 2.7→6 Å / σ(F): 1
RfactorNum. reflection% reflection
Rfree0.248 -10 %
Rwork0.183 --
obs0.183 37861 96.5 %
Displacement parametersBiso mean: 22.2 Å2
Refinement stepCycle: LAST / Resolution: 2.7→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8658 0 22 148 8828
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.029
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.36
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.33
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.23
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 2.7→2.7 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.34 -7.7 %
Rwork0.291 1230 -
obs--86 %
Xplor fileSerial no: 1 / Param file: PARAM19 / Topol file: TOPH19.PRO

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