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- PDB-3pmg: STRUCTURE OF RABBIT MUSCLE PHOSPHOGLUCOMUTASE AT 2.4 ANGSTROMS RE... -

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Basic information

Entry
Database: PDB / ID: 3pmg
TitleSTRUCTURE OF RABBIT MUSCLE PHOSPHOGLUCOMUTASE AT 2.4 ANGSTROMS RESOLUTION. USE OF FREEZING POINT DEPRESSANT AND REDUCED TEMPERATURE TO ENHANCE DIFFRACTIVITY
ComponentsPhosphoglucomutase-1PGM1
KeywordsISOMERASE / PHOSPHOTRANSFERASE
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
Phosphoglucomutase-1
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / Resolution: 2.4 Å
AuthorsRay Junior, W.J. / Liu, Y. / Baranidharan, S.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 1997
Title: Structure of rabbit muscle phosphoglucomutase refined at 2.4 A resolution.
Authors: Liu, Y. / Ray, W.J. / Baranidharan, S.
#1: Journal: Biochemistry / Year: 1993
Title: Structural Changes at the Metal Ion Binding Site During the Phosphoglucomutase Reaction
Authors: Ray Junior, 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 Angstroms 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 Junior, 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. / Wierenga, R. / Murthy, M.R.N. / Ray Junior, W.J. / Rossmann, M.G.
History
DepositionMar 2, 1995Processing site: BNL
SupersessionDec 7, 1995ID: 2PMG
Revision 1.0Dec 7, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 24, 2019Group: Data collection / Derived calculations / Structure summary
Category: entity / struct ...entity / struct / struct_biol / struct_conn / struct_keywords
Item: _entity.pdbx_description / _struct.pdbx_descriptor ..._entity.pdbx_description / _struct.pdbx_descriptor / _struct_conn.pdbx_leaving_atom_flag / _struct_keywords.pdbx_keywords / _struct_keywords.text
Revision 1.4Nov 20, 2019Group: Derived calculations
Category: pdbx_struct_conn_angle / struct_conn / struct_conn_type
Item: _struct_conn_type.id
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 S. A SPATIAL RELATIONSHIP EXISTS BETWEEN GROUPS OF HELICES/STRANDS IN DOMAINS 1 - 3. IN ORDER TO EMPHASIZE THIS RELATIONSHIP, A PORTION OF THE MAIN SHEET IN DOMAIN 1, 1 B - 7 B, IS REPEATED AS 4 S - 1 S. THUS, A SPATIAL DOMAIN-DOMAIN RELATIONSHIP EXISTS AMONG STRANDS/HELICES WHOSE DESIGNATOR CONTAINS 1 S - 4 S 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 MTRIX 1. DOMAIN 4 IN MONOMER 1 AND MONOMER 2 ARE RELATED BY A DIFFERENT ROTATION MATRIX GIVEN AS MTRIX 2.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phosphoglucomutase-1
B: Phosphoglucomutase-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,2084
Polymers123,1602
Non-polymers492
Water8,899494
1
B: Phosphoglucomutase-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,6042
Polymers61,5801
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Phosphoglucomutase-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,6042
Polymers61,5801
Non-polymers241
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)83.5455, 111.242, 84.6436
2given(0.2525, -0.9675, -0.0119), (-0.9658, -0.2513, -0.0043), (0.0592, 0.0278, -0.9979)84.1752, 111.433, 83.0535
DetailsMTRIX THE TRANSFORMATIONS PRESENTED ON MTRIX RECORDS BELOW DESCRIBE NON-CRYSTALLOGRAPHIC RELATIONSHIPS AMONG THE VARIOUS DOMAINS IN THIS ENTRY. APPLYING THE APPROPRIATE MTRIX TRANSFORMATION TO THE RESIDUES LISTED FIRST WILL YIELD APPROXIMATE COORDINATES FOR THE RESIDUES LISTED SECOND. APPLIED TO TRANSFORMED TO MTRIX RESIDUES RESIDUES RMSD M1 B 1 .. B 420 A 1 .. A 420 0.426 M2 B 421 .. B 561 A 421 .. A 561 1.117 M1 SUPERIMPOSES DOMAINS I - III OF MONOMER B ON THE CORRESPONDING DOMAINS OF MONOMER A, BASED ON A LEAST SQUARES PROCEDURE (HOMOLOGY, ROSSMANN AND ARGOS,1975) USING 301 SELECTED ALPHA-CARBON ATOMS IN THESE DOMAINS. M2 SUPERIMPOSES DOMAIN IV OF MONOMER B ON DOMAIN IV OF MONOMER A, USING 35 SELECTED ALPHA-CARBON ATOMS FROM THE CENTRAL PART OF THE BETA-SHEET IN THESE DOMAINS.

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Components

#1: Protein Phosphoglucomutase-1 / PGM1 / PHOSPHOGLUCOMUTASE


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


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 494 / Source method: isolated from a natural source / Formula: H2O

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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: 60.59 %
Crystal grow
*PLUS
pH: 6.5 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
155 %PEG6001reservoir
210 mMMES1reservoir
31 mM1reservoirMgCl2

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Data collection

Diffraction sourceWavelength: 1.5418 Å
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: 2.4→13.1 Å / Num. obs: 54770 / % possible obs: 90 % / Observed criterion σ(I): 1 / Redundancy: 4.1 % / Rmerge(I) obs: 0.054
Reflection
*PLUS
Highest resolution: 2.35 Å / Lowest resolution: 20 Å / Num. obs: 54817 / % possible obs: 84.2 % / Rmerge(I) obs: 0.054
Reflection shell
*PLUS
Highest resolution: 2.35 Å / Lowest resolution: 2.41 Å / % possible obs: 56.8 %

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
HOMOLOGYrefinement
FRODOmodel building
MAPMANrefinement
Omodel building
XTSdata reduction
X-PLOR3.1phasing
RefinementResolution: 2.4→6 Å / σ(F): 1
Details: THE MODEL CONTAINS FIVE RESIDUES OUT OF 1122 THAT FALL IN THE GENEROUSLY ALLOWED REGION OF A RAMACHANDRAN PLOT AS DEFINED IN PROCHECK AND ONE RESIDUE IN THE DISALLOWED REGION. TWO OF THE ...Details: THE MODEL CONTAINS FIVE RESIDUES OUT OF 1122 THAT FALL IN THE GENEROUSLY ALLOWED REGION OF A RAMACHANDRAN PLOT AS DEFINED IN PROCHECK AND ONE RESIDUE IN THE DISALLOWED REGION. TWO OF THE FIVE ARE ACTIVE SITE RESIDUES IN CHAIN A AND B AND THE OTHER FOUR ARE INVOLVED IN CRYSTALLOGRAPHIC CONTACTS. THE RESIDUES ARE ARG A 216, SER A 116, ASN A 461, SER B 116, AND ASN B 461.
RfactorNum. reflection% reflection
Rfree0.191 --
Rwork0.163 --
obs0.163 49694 87 %
Displacement parametersBiso mean: 28 Å2
Refinement stepCycle: LAST / Resolution: 2.4→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10600 0 10 1482 12092
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.018
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_deg3.23
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.1
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.94
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 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.1
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.94

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