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- PDB-1vkl: RABBIT MUSCLE PHOSPHOGLUCOMUTASE -

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Basic information

Entry
Database: PDB / ID: 1vkl
TitleRABBIT MUSCLE PHOSPHOGLUCOMUTASE
ComponentsPHOSPHOGLUCOMUTASE
KeywordsPHOSPHOTRANSFERASE / PHOSPHOGLUCOMUTASE
Function / homology
Function and homology information


phosphoglucomutase (alpha-D-glucose-1,6-bisphosphate-dependent) / phosphoglucomutase activity / sarcoplasmic reticulum / glucose metabolic process / magnesium ion binding / cytosol
Similarity search - Function
Phosphoglucomutase-1, C-terminal domain / 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, conserved site / Phosphoglucomutase and phosphomannomutase phosphoserine signature. / Alpha-D-phosphohexomutase, alpha/beta/alpha domain II ...Phosphoglucomutase-1, C-terminal domain / 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, conserved site / Phosphoglucomutase and phosphomannomutase phosphoserine signature. / 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, 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
NICKEL (II) ION / Phosphoglucomutase-1
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / Resolution: 2.7 Å
AuthorsRay Junior, W.J. / Baranidharan, S. / Liu, Y.
Citation
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.
#1: Journal: J.Biol.Chem. / Year: 1992
Title: The Crystal Structure of Muscle Phosphoglucomutase Refined at 2.7-Angstrom Resolution
Authors: Dai, J.B. / Liu, Y. / Ray Junior, W.J. / Konno, M.
#2: Journal: J.Biol.Chem. / Year: 1986
Title: The Catalytic Activity of Muscle Phosphoglucomutase in the Crystalline Phase
Authors: Ray Junior, W.J.
#3: Journal: J.Biol.Chem. / Year: 1986
Title: The Structure of Rabbit Muscle Phosphoglucomutase at Intermediate Resolution
Authors: Lin, Z. / Konno, M. / Abad-Zapatero, C. / Wierenga, R. / Murthy, M.R. / Ray Junior, W.J. / Rossmann, M.G.
History
DepositionJul 3, 1996Processing site: BNL
Revision 1.0Jan 11, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _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.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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 9, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Remark 650HELIX THE MONOMER CAN BE SUBDIVIDED INTO FOUR SEQUENCE DOMAINS: THE FINAL COLUMN OF THE HELIX ...HELIX THE MONOMER CAN BE SUBDIVIDED INTO FOUR SEQUENCE DOMAINS: THE FINAL COLUMN OF THE HELIX IDENTIFIER, 1-4, DESIGNATES THE DOMAINS; FOR STRANDS, THE DOMAINS ARE DESIGNATED BY THE NUMBERS IN THE SECOND COLUMN, 1-4, FOLLOWED BY EITHER B OR A SPATIAL RELATIONSHIP EXISTS BETWEEN GROUPS OF HELICES/STR IN DOMAINS 1-3. IN ORDER TO EMPHASIZE THIS RELATIONSHIP, AS 4S-1S. THUS, A SPATIAL DOMAIN-DOMAIN RELATIONSHIP EXIST AMONG STANDS/HELICES WHOSE DESIGNATOR CONTAINS 1S-4S IN THE SECOND COLUMN OR ENDS WITH 1-4, RESPECTIVELY. DOMAINS 1, 2, 3 IN MONOMER 1 AND MONOMER 2 ARE RELATED BY A ROTATION MATRIX GIVEN AS MTRIX1. DOMAIN 4 IN MONOMER 1 AND MONOMER 2 ARE RELATED BY A DIFFERENT ROTATION MATRIX GIVEN AS MTRIX2.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PHOSPHOGLUCOMUTASE
B: PHOSPHOGLUCOMUTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,2774
Polymers123,1602
Non-polymers1172
Water6,323351
1
A: PHOSPHOGLUCOMUTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,6392
Polymers61,5801
Non-polymers591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: PHOSPHOGLUCOMUTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,6392
Polymers61,5801
Non-polymers591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)174.420, 174.420, 101.120
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.263, -0.9648, 0.0087), (-0.964, -0.2631, -0.0393), (0.0402, 0.002, -0.9992)83.8643, 111.698, 84.7083
2given(0.2645, -0.9641, -0.0223), (-0.9638, -0.2635, -0.0411), (0.0337, 0.0323, -0.9989)83.8308, 111.554, 83.626
DetailsTHERE ARE TWO MONOMER COPIES PER ASYMMETRIC UNIT ALONG THE 4(1) SCREW AXIS. MONOMER A IS THE FIRST ENCOUNTERED IN AN ASYMMETRIC UNIT AS ONE MOVES CLOCKWISE ALONG A SCREW AXIS. AMINO ACID RESIDUES IN MONOMERS A AND B ARE DISTINGUISHED BY THE CHAIN IDENTIFIERS *A* AND *B*, RESPECTIVELY.

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Components

#1: Protein PHOSPHOGLUCOMUTASE


Mass: 61579.902 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Tissue: MUSCLE
References: UniProt: P00949, phosphoglucomutase (alpha-D-glucose-1,6-bisphosphate-dependent)
#2: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 351 / 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

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Sample preparation

CrystalDensity Matthews: 3.12 Å3/Da / Density % sol: 61 %
Crystal growpH: 6.4 / Details: pH 6.4
Crystal
*PLUS
Crystal grow
*PLUS
Method: unknown / Details: Lin, Z., (1986) J.Biol.Chem., 261, 264.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
147 %satammonium salfate11
23-4 %PEG40011

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Data collection

DiffractionMean temperature: 289 K
Diffraction sourceWavelength: 1.5418
DetectorType: XUONG-HAMLIN MULTIWIRE / Detector: AREA DETECTOR / Date: Oct 1, 1993
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→20 Å / Num. obs: 46280 / % possible obs: 97 % / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.15

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
XDSdata reduction
X-PLORphasing
RefinementStarting model: PDB ENTRY 3PMG

3pmg


Resolution: 2.7→6 Å / σ(F): 2
Details: MOSTLY X-PLOR DEFAULT VALUES THE MODEL CONTAINS TEN RESIDUES, OUT OF 1122, THAT FALL IN THE GENEROUSLY ALLOWED REGION OF A RAMACHANDRAN PLOT AS DEFINED IN PROCHECK AND TWO RESIDUES IN THE ...Details: MOSTLY X-PLOR DEFAULT VALUES THE MODEL CONTAINS TEN RESIDUES, OUT OF 1122, THAT FALL IN THE GENEROUSLY ALLOWED REGION OF A RAMACHANDRAN PLOT AS DEFINED IN PROCHECK AND TWO RESIDUES IN THE DISALLOWED REGION. THE TWO RESIDUES IN THE DISALLOWED REGION ARE SEP B 116 AND ASN B 461.
RfactorNum. reflection% reflection
Rfree0.21 -10 %
Rwork0.17 --
obs0.17 36032 92.1 %
Displacement parametersBiso mean: 34 Å2
Refinement stepCycle: LAST / Resolution: 2.7→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8666 0 2 351 9019
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.013
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_deg3
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.54
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.369
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
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARAM19XTOPH19
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.17 / Rfactor Rfree: 0.21 / Rfactor Rwork: 0.17
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.543
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.369

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