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- PDB-2ske: PYRIDOXAL PHOSPHORYLASE B IN COMPLEX WITH PHOSPHITE, GLUCOSE AND ... -

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Basic information

Entry
Database: PDB / ID: 2ske
TitlePYRIDOXAL PHOSPHORYLASE B IN COMPLEX WITH PHOSPHITE, GLUCOSE AND INOSINE-5'-MONOPHOSPHATE
ComponentsPYRIDOXAL PHOSPHORYLASE B
KeywordsTRANSFERASE / GLYCOGEN PHOSPHORYLASE / GLYCOGEN METABOLISM / ALLOSTERIC ENZYME / PYRIDOXAL PHOSPHATE
Function / homology
Function and homology information


glycogen phosphorylase / glycogen phosphorylase activity / glycogen catabolic process / skeletal muscle myofibril / pyridoxal phosphate binding / nucleotide binding
Similarity search - Function
Glycosyl transferase, family 35 / Glycogen/starch/alpha-glucan phosphorylase / Phosphorylase pyridoxal-phosphate attachment site / Carbohydrate phosphorylase / Phosphorylase pyridoxal-phosphate attachment site. / Glycogen Phosphorylase B; / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
alpha-D-glucopyranose / INOSINIC ACID / PYRIDOXAL-5'-PHOSPHATE / PHOSPHITE ION / Glycogen phosphorylase, muscle form
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.46 Å
AuthorsOikonomakos, N.G. / Zographos, S.E. / Tsitsanou, K.E. / Johnson, L.N. / Acharya, K.R.
CitationJournal: Protein Sci. / Year: 1996
Title: Activator anion binding site in pyridoxal phosphorylase b: the binding of phosphite, phosphate, and fluorophosphate in the crystal.
Authors: Oikonomakos, N.G. / Zographos, S.E. / Tsitsanou, K.E. / Johnson, L.N. / Acharya, K.R.
History
DepositionDec 11, 1998Deposition site: PDBE / Processing site: RCSB
SupersessionDec 16, 1998ID: 1ske
Revision 1.0Dec 16, 1998Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / 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 / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Aug 30, 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: PYRIDOXAL PHOSPHORYLASE B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,1465
Polymers97,2911
Non-polymers8544
Water4,720262
1
A: PYRIDOXAL PHOSPHORYLASE B
hetero molecules

A: PYRIDOXAL PHOSPHORYLASE B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)196,29110
Polymers194,5822
Non-polymers1,7098
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area8560 Å2
ΔGint-11 kcal/mol
Surface area58390 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)128.500, 128.500, 116.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Cell settingtetragonal
Space group name H-MP43212

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Components

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein PYRIDOXAL PHOSPHORYLASE B / E.C.2.4.1.1


Mass: 97291.203 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: IN COMPLEX WITH PHOSPHITE, GLUCOSE AND INOSINE-5'-MONOPHOSPHATE
Source: (natural) Oryctolagus cuniculus (rabbit) / Tissue: MUSCLE / References: UniProt: P00489, glycogen phosphorylase
#2: Sugar ChemComp-GLC / alpha-D-glucopyranose / alpha-D-glucose / D-glucose / glucose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-glucopyranoseCOMMON NAMEGMML 1.0
a-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 4 types, 265 molecules

#3: Chemical ChemComp-PO3 / PHOSPHITE ION


Mass: 78.972 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO3
#4: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10NO6P
#5: Chemical ChemComp-IMP / INOSINIC ACID


Mass: 348.206 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H13N4O8P
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 262 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.47 Å3/Da / Density % sol: 48 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.7
Details: T-STATE PYRIDOXAL PHOSPHORYLASE B, FROM RABBIT MUSCLE, WAS CO-CRYSTALLIZED WITH 8-10 MM FLUOROPHOSPHATE IN A MEDIUM CONSISTING OF 15-25 MG/ML ENZYME, 2 MM IMP, 2 MM SPERMINE, 50 MM GLUCOSE, ...Details: T-STATE PYRIDOXAL PHOSPHORYLASE B, FROM RABBIT MUSCLE, WAS CO-CRYSTALLIZED WITH 8-10 MM FLUOROPHOSPHATE IN A MEDIUM CONSISTING OF 15-25 MG/ML ENZYME, 2 MM IMP, 2 MM SPERMINE, 50 MM GLUCOSE, 10 MM BES, 0.1 MM EDTA, AND 0.02% SODIUM AZIDE, PH 6.7 (16 DEGREE C). JUST BEFORE DATA COLLECTION, THE CRYSTALS WERE TRANSFERRED TO A FRESH BUFFER SOLUTION, CONTAINING THE SAME CONSTITUENTS AS THEIR MOTHER LIQUOR WITH THE EXCEPTION OF THE PROTEIN., VAPOR DIFFUSION, HANGING DROP, temperature 289K
Components of the solutions
IDNameCrystal-IDSol-ID
1SPERMINE11
2BES11
3EDTA11
4NAN311
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 16 ℃ / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
18-10 mMphosphate1
28-10 mMphosphite1
315-25 mg/mlenzyme1
42 mMIMP1
52 mMspermine11
650 mMGlc11
710 mMBes11
80.1 mMEDTA11
90.02 %sodium azide11

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX7.2 / Wavelength: 1.488
DetectorDetector: FILM / Date: Oct 21, 1993
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.488 Å / Relative weight: 1
ReflectionResolution: 2.46→16.88 Å / Num. all: 30529 / Num. obs: 30529 / % possible obs: 84.89 % / Observed criterion σ(I): 0 / Redundancy: 3.039 % / Rmerge(I) obs: 0.074
Reflection shellResolution: 2.46→2.57 Å / % possible all: 65
Reflection
*PLUS
Num. measured all: 98321

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Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLOR3.851refinement
MOSCOdata reduction
CCP4data scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2PRJ

2prj


Resolution: 2.46→16.88 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.218 -5 %RANDOM
Rwork0.168 ---
obs0.168 30529 84.89 %-
all-30529 --
Refinement stepCycle: LAST / Resolution: 2.46→16.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6749 0 50 262 7061
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
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_deg1.4
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25.5
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.72
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
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_deg1.4
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25.5
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.72

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