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- PDB-5hsh: Crystal structure of the G291R mutant of human phosphoglucomutase 1 -

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Basic information

Entry
Database: PDB / ID: 5hsh
TitleCrystal structure of the G291R mutant of human phosphoglucomutase 1
ComponentsPhosphoglucomutase-1PGM1
KeywordsISOMERASE / phosphoglucomutase / enzyme / missense mutant
Function / homology
Function and homology information


Defective PGM1 causes PGM1-CDG / Galactose catabolism / phosphoglucomutase (alpha-D-glucose-1,6-bisphosphate-dependent) / phosphoglucomutase activity / Glycogen breakdown (glycogenolysis) / Glycogen synthesis / gluconeogenesis / glycolytic process / glucose metabolic process / tertiary granule lumen ...Defective PGM1 causes PGM1-CDG / Galactose catabolism / phosphoglucomutase (alpha-D-glucose-1,6-bisphosphate-dependent) / phosphoglucomutase activity / Glycogen breakdown (glycogenolysis) / Glycogen synthesis / gluconeogenesis / glycolytic process / glucose metabolic process / tertiary granule lumen / ficolin-1-rich granule lumen / carbohydrate metabolic process / Neutrophil degranulation / magnesium ion binding / extracellular exosome / extracellular region / cytosol / cytoplasm
Similarity search - Function
Phosphoglucomutase / 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 / 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
Phosphoglucomutase-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsStiers, K.M. / Beamer, L.J.
Funding support United States, 2items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)MCB-0918389 United States
Patton Trust of the Kansas City Area Life Sciences Research Foundation United States
CitationJournal: J.Mol.Biol. / Year: 2016
Title: Induced Structural Disorder as a Molecular Mechanism for Enzyme Dysfunction in Phosphoglucomutase 1 Deficiency.
Authors: Stiers, K.M. / Kain, B.N. / Graham, A.C. / Beamer, L.J.
History
DepositionJan 25, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 27, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Sep 27, 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: Phosphoglucomutase-1
B: Phosphoglucomutase-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,7187
Polymers123,2382
Non-polymers4805
Water1,820101
1
A: Phosphoglucomutase-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,0035
Polymers61,6191
Non-polymers3844
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Phosphoglucomutase-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,7152
Polymers61,6191
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)170.780, 170.780, 99.287
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 Phosphoglucomutase-1 / PGM1 / PGM 1 / Glucose phosphomutase 1


Mass: 61619.035 Da / Num. of mol.: 2 / Mutation: G291R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PGM1 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P36871, phosphoglucomutase (alpha-D-glucose-1,6-bisphosphate-dependent)
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 101 / 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: 2.94 Å3/Da / Density % sol: 58.12 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 9.7 / Details: ~1.0M Sodium Citrate, 0.1M CHES Buffer pH 9.7.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1.00003 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: Oct 25, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00003 Å / Relative weight: 1
ReflectionResolution: 2.65→60.537 Å / Num. obs: 48369 / % possible obs: 100 % / Redundancy: 14 % / CC1/2: 0.999 / Rmerge(I) obs: 0.107 / Net I/σ(I): 18
Reflection shellResolution: 2.65→2.75 Å / Redundancy: 13.1 % / Rmerge(I) obs: 2.81 / Mean I/σ(I) obs: 0.9 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5EPC

5epc


Resolution: 2.65→60.537 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2733 2162 5.03 %
Rwork0.23 --
obs0.2321 42988 99.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.65→60.537 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7373 0 25 101 7499
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.017561
X-RAY DIFFRACTIONf_angle_d1.21410308
X-RAY DIFFRACTIONf_dihedral_angle_d13.3974425
X-RAY DIFFRACTIONf_chiral_restr0.0651180
X-RAY DIFFRACTIONf_plane_restr0.0091375
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.65-2.71170.41031570.37262638X-RAY DIFFRACTION99
2.7117-2.77950.34081350.33012658X-RAY DIFFRACTION99
2.7795-2.85460.36181260.30042690X-RAY DIFFRACTION100
2.8546-2.93860.33221450.29572695X-RAY DIFFRACTION100
2.9386-3.03350.3241600.29242664X-RAY DIFFRACTION100
3.0335-3.14190.35471230.28642709X-RAY DIFFRACTION100
3.1419-3.26770.3141490.27912698X-RAY DIFFRACTION100
3.2677-3.41640.33261360.26272688X-RAY DIFFRACTION99
3.4164-3.59650.32671430.24032703X-RAY DIFFRACTION100
3.5965-3.82180.25771560.22132706X-RAY DIFFRACTION100
3.8218-4.11680.24521390.21742732X-RAY DIFFRACTION100
4.1168-4.53090.24521380.19082749X-RAY DIFFRACTION100
4.5309-5.18630.23881600.19882747X-RAY DIFFRACTION100
5.1863-6.53290.29291390.24552807X-RAY DIFFRACTION100
6.5329-60.55240.23091560.20092942X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.4853-0.57930.83713.86510.62782.8639-0.1199-0.51280.18370.48080.27290.2472-0.8869-0.6691-0.13150.94720.11160.20820.67620.15020.5966-33.73772.81111.8739
20.9451-0.81440.21222.0934-0.59864.0345-0.040.06090.0349-0.01540.12350.30750.025-0.0967-0.0830.3854-0.05060.04010.4770.07680.6195-24.292545.7433-1.3344
34.0461.3417-0.79751.3786-0.90875.52220.2685-0.87230.09470.3516-0.25950.24570.08990.403-0.02570.5457-0.00940.07440.64160.0410.5804-21.149940.315723.1204
42.82211.8984-0.00313.7551-1.71555.21350.11390.5359-0.2616-0.06010.1352-0.5644-0.70471.044-0.30220.6984-0.09570.10180.8831-0.19260.830730.026262.9439-14.8334
53.23472.61330.38762.8358-1.66565.7471-0.01151.0074-0.2316-0.19920.3330.0694-0.28810.0322-0.50050.64690.0686-0.01150.8107-0.09560.807619.359656.869-12.916
62.2770.89050.47821.79810.27314.6465-0.06340.54770.3248-0.56440.4731-0.5196-0.8810.7015-0.51190.9478-0.15030.18230.9167-0.13630.755729.811965.6995-16.1738
74.21551.7653-0.75512.58210.69422.53810.4745-0.1543-0.01880.5905-0.0111-0.22-0.46410.1226-0.40540.66110.0711-0.05480.66220.00470.772620.11854.10770.8531
82.45210.60330.43143.35360.88673.00540.3216-0.0735-0.84690.10230.0292-1.28050.68670.5928-0.5780.73530.2002-0.23310.754-0.13261.158220.142633.086-6.0776
92.50130.00991.15733.7128-0.14844.36010.09860.4551-0.1312-0.1770.2822-0.0320.328-0.2895-0.34120.3844-0.028-0.00790.82440.01940.6634.959739.2374-16.8837
101.6499-0.56171.15034.36150.48554.87260.51981.945-1.1735-1.9073-0.626-0.4482-0.3230.2873-0.35691.4193-0.1409-0.08111.60490.02280.99173.27738.8007-44.7228
111.5993-1.72140.57353.48521.10093.5745-0.02960.63520.3169-1.19110.3195-0.0087-0.4219-0.2082-0.27050.7656-0.10070.10091.23240.050.71954.758444.2343-33.2566
122.1554-0.86871.91014.00420.23514.50050.30440.5732-0.202-0.99120.5309-1.18711.0431.0501-0.7740.89110.06750.01791.0601-0.45671.183810.062928.1837-36.4664
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 183 )
2X-RAY DIFFRACTION2chain 'A' and (resid 184 through 405 )
3X-RAY DIFFRACTION3chain 'A' and (resid 406 through 562 )
4X-RAY DIFFRACTION4chain 'B' and (resid 1 through 95 )
5X-RAY DIFFRACTION5chain 'B' and (resid 96 through 140 )
6X-RAY DIFFRACTION6chain 'B' and (resid 141 through 170 )
7X-RAY DIFFRACTION7chain 'B' and (resid 171 through 212 )
8X-RAY DIFFRACTION8chain 'B' and (resid 213 through 293 )
9X-RAY DIFFRACTION9chain 'B' and (resid 294 through 434 )
10X-RAY DIFFRACTION10chain 'B' and (resid 435 through 473 )
11X-RAY DIFFRACTION11chain 'B' and (resid 474 through 522 )
12X-RAY DIFFRACTION12chain 'B' and (resid 523 through 562 )

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