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- PDB-1c4g: PHOSPHOGLUCOMUTASE VANADATE BASED TRANSITION STATE ANALOG COMPLEX -

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Basic information

Entry
Database: PDB / ID: 1c4g
TitlePHOSPHOGLUCOMUTASE VANADATE BASED TRANSITION STATE ANALOG COMPLEX
ComponentsPROTEIN (ALPHA-D-GLUCOSE 1-PHOSPHATE PHOSPHOGLUCOMUTASE)
KeywordsTRANSFERASE / PHOSPHOGLUCOMUTASE / PHOSPHOTRANSFERASE INHIBITOR SUBSTRATE COMPLEX
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 superfamily / Alpha-D-phosphohexomutase, C-terminal domain / 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 superfamily / Alpha-D-phosphohexomutase, C-terminal domain / 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
: / ALPHA-D-GLUCOSE-1-PHOSPHATE-6-VANADATE / 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: Structural Relationships at the Active Site of Phos in Analog Complexes
Authors: Baranidharan, S. / Ray Jr., W.J.
#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.J. / Baranidharan, S. / Liu, Y.W.
#7: Journal: Biochemistry / Year: 1990
Title: Characterization of a Vanadate-Based Transition-St 2 Analog Complex by Kinetic and Equilibrium Binding 3 Studies: Mechanistic Implications
Authors: Ray Jr., W.J. / Puvathingal, J.M.
History
DepositionAug 24, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 27, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Jul 29, 2020Group: Data collection / Derived calculations
Category: chem_comp / pdbx_struct_conn_angle ...chem_comp / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _pdbx_struct_conn_angle.ptnr1_auth_comp_id ..._chem_comp.mon_nstd_flag / _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.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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.ptnr2_label_seq_id / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Aug 9, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (ALPHA-D-GLUCOSE 1-PHOSPHATE PHOSPHOGLUCOMUTASE)
B: PROTEIN (ALPHA-D-GLUCOSE 1-PHOSPHATE PHOSPHOGLUCOMUTASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,4184
Polymers123,0002
Non-polymers4182
Water3,567198
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 PROTEIN (ALPHA-D-GLUCOSE 1-PHOSPHATE PHOSPHOGLUCOMUTASE) / 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: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Co
#3: Sugar ChemComp-VG1 / ALPHA-D-GLUCOSE-1-PHOSPHATE-6-VANADATE


Type: D-saccharide / Mass: 359.075 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13O12PV
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 198 / 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: 1.5418
DetectorType: XUONG-HAMLIN MULTIWIRE / Detector: AREA DETECTOR / Date: May 15, 1996 / Details: NI FILTER
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.7→30 Å / Num. obs: 36146 / % possible obs: 85.9 % / Observed criterion σ(I): 1 / Biso Wilson estimate: 23.4 Å2

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Processing

Software
NameVersionClassification
Omodel building
X-PLORmodel building
X-PLOR3.8refinement
XDSdata 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
Rfree0.29 -10 %
Rwork0.192 --
obs0.192 36132 85.9 %
Displacement parametersBiso mean: 19.3 Å2
Refinement stepCycle: LAST / Resolution: 2.7→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8658 0 21 198 8877
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.023
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_deg1.61
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25.56
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.331
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→2.81 Å / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.346 -10 %
Rwork0.239 180 -
obs--8.2 %
Xplor fileSerial no: 1 / Param file: PARAM19 / Topol file: TOPH19.PRO

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