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- PDB-5vin: Crystal Structure of the R515Q missense variant of human PGM1 -

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Basic information

Entry
Database: PDB / ID: 5vin
TitleCrystal Structure of the R515Q missense variant of human PGM1
ComponentsPhosphoglucomutase-1
KeywordsISOMERASE / phosphoglucomutase-1 / PGM1 / phosphoryl transfer
Function / homology
Function and homology information


Defective PGM1 causes PGM1-CDG / Galactose catabolism / phosphoglucomutase (alpha-D-glucose-1,6-bisphosphate-dependent) / phosphoglucomutase activity / galactose catabolic process via UDP-galactose / Glycogen breakdown (glycogenolysis) / Glycogen synthesis / gluconeogenesis / glycolytic process / glucose metabolic process ...Defective PGM1 causes PGM1-CDG / Galactose catabolism / phosphoglucomutase (alpha-D-glucose-1,6-bisphosphate-dependent) / phosphoglucomutase activity / galactose catabolic process via UDP-galactose / 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: 2.60004291837 Å
AuthorsStiers, K.M. / Beamer, L.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)MCB-1409898 United States
CitationJournal: Structure / Year: 2018
Title: A Hotspot for Disease-Associated Variants of Human PGM1 Is Associated with Impaired Ligand Binding and Loop Dynamics.
Authors: Stiers, K.M. / Beamer, L.J.
History
DepositionApr 17, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 27, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 5, 2018Group: Data collection / Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 17, 2018Group: Data collection / Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.3Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 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)130,24523
Polymers128,3252
Non-polymers1,91921
Water1,63991
1
A: Phosphoglucomutase-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,45515
Polymers64,1631
Non-polymers1,29214
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Phosphoglucomutase-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,7908
Polymers64,1631
Non-polymers6277
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)173.960, 173.960, 99.483
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

#1: Protein Phosphoglucomutase-1 / PGM 1 / Glucose phosphomutase 1


Mass: 64162.664 Da / Num. of mol.: 2 / Mutation: R515Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PGM1 / Production host: Escherichia coli (E. coli)
References: UniProt: P36871, phosphoglucomutase (alpha-D-glucose-1,6-bisphosphate-dependent)
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Co
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 91 / 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: 3.06 Å3/Da / Density % sol: 59.82 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.01 M Cobalt (II) chloride hexahydrate, O.1 M MES monohydrate pH 6.5, Ammonium Sulfate 1.8-2.1M

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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 1, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00003 Å / Relative weight: 1
ReflectionResolution: 2.6→61.51 Å / Num. obs: 47453 / % possible obs: 100 % / Redundancy: 13.9 % / Biso Wilson estimate: 50.495264229 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.185 / Rpim(I) all: 0.052 / Net I/σ(I): 15.2
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 13.6 % / Rmerge(I) obs: 1.846 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 4566 / CC1/2: 0.796 / Rpim(I) all: 0.518 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
PHENIX1.11.1_2575phasing
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5EPC

5epc


Resolution: 2.60004291837→61.5041478276 Å / SU ML: 0.453748262717 / Cross valid method: FREE R-VALUE / σ(F): 1.34691743164 / Phase error: 34.5518017215
RfactorNum. reflection% reflection
Rfree0.295418439253 2385 5.08952006999 %
Rwork0.238582434806 --
obs0.241435170817 46861 98.850356495 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 71.2698705059 Å2
Refinement stepCycle: LAST / Resolution: 2.60004291837→61.5041478276 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8044 0 103 91 8238
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009816689642048340
X-RAY DIFFRACTIONf_angle_d1.3835314434111362
X-RAY DIFFRACTIONf_chiral_restr0.08201619230741274
X-RAY DIFFRACTIONf_plane_restr0.01053871753941505
X-RAY DIFFRACTIONf_dihedral_angle_d5.206343968846454
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.65310.4049171033231370.3308736012352577X-RAY DIFFRACTION99.7427416391
2.6531-2.71080.3804550940991700.3205103675782574X-RAY DIFFRACTION99.7455470738
2.7108-2.77390.3687984068561520.3066137894622571X-RAY DIFFRACTION99.7435897436
2.7739-2.84320.4328167196331140.3059344921012632X-RAY DIFFRACTION99.4207096307
2.8432-2.92010.355744950111340.3022282944962616X-RAY DIFFRACTION99.8185117967
2.9201-3.0060.4048642941381420.2893370048752612X-RAY DIFFRACTION99.8549673677
3.006-3.10310.33187499021460.2703922385272601X-RAY DIFFRACTION99.8183139535
3.1031-3.2140.3294202720371240.266345740652630X-RAY DIFFRACTION99.7103548154
3.214-3.34260.3311904133241500.2818420764882615X-RAY DIFFRACTION99.7834716709
3.3426-3.49470.2577801951511330.2435939352552622X-RAY DIFFRACTION100
3.4947-3.6790.3927400620971300.3076176693092430X-RAY DIFFRACTION91.6249105225
3.679-3.90940.2946920881621530.2326189936892384X-RAY DIFFRACTION91.7872648336
3.9094-4.21120.2190913122931200.2025308352782676X-RAY DIFFRACTION99.679144385
4.2112-4.63490.2329664912041420.1772670519452660X-RAY DIFFRACTION99.857448325
4.6349-5.30520.272583065361500.1859618615652684X-RAY DIFFRACTION100
5.3052-6.68270.2845092831121330.2378218060992736X-RAY DIFFRACTION100
6.6827-61.52130.2374039007871550.2092734525162856X-RAY DIFFRACTION99.8342175066
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)
10.143307716913-0.00278899760946-0.08144678121920.264681546107-0.1017450277250.0870406736160.102948057603-0.353039050124-0.03796416038990.185884365392-0.04179145193750.079628952944-0.06927587925610.5784490783670.02999382198150.165071773999-0.0314458076184-0.003362601269750.522813353156-0.04505711430760.24573322544571.14961188435.13997859-20.9499367958
20.0396877615168-0.0188531542208-0.04656284116840.02439501258620.0766364824460.181532619262-0.186505847450.1776681512720.1166204239920.008771568786360.01539919766720.017373991150.1161928560010.328664539129-0.2892473870280.1447896186870.2714357745580.0319135108218-0.255335832550.01388296354880.33053459973447.046369719925.219277367-24.2413622954
30.1183346335920.00864347531653-0.01213369457760.08618744256030.0612766782250.0486837837295-0.112947259194-0.27763320218-0.04013053960810.3122700231610.02513305713530.1211623234550.2428200948780.1012264254380.0008011349506450.4698058866220.09137925861530.003438921247550.2640927111870.00288281494920.32758439300142.485740234520.99045341092.29668815091
40.03527749642480.0257019140761-0.01446290222240.033242544686-0.02018538454130.01781758378330.105222161605-0.0533231390570.04536399111320.1672923264770.03684354317280.1302763068810.156871245728-0.160026309675-0.0008208304136261.22536217373-0.401942696986-0.1279120144541.093601512880.1833907017890.48899050609520.584999715655.5953547363-31.8418990381
50.38388645227-0.140443424889-0.2477785081520.2187328495820.05081992390490.2087822426550.325663192898-0.032510776558-0.01194108952880.25932270277-0.102032494717-0.2148909100770.121201805695-0.342021819670.1177365997330.667121937489-0.100561705872-0.06758331321840.334853433690.03568473031830.24602948972426.137871759260.0707662406-41.200318731
60.01172421181-0.03346564851340.02283242189650.145130997777-0.1281368039910.3673222130650.3221868776340.0435709663248-0.07205141826160.1125855697930.203218756191-0.08140759106480.05409895466250.1220824292040.2316644539140.5651249412210.19721213189-0.1322429395810.222578672306-0.1283297229790.54388499012550.580084496465.6272109988-43.986674037
70.0597302425165-0.0490443828165-0.04983942206110.1667973215950.01052072242340.1564579344070.111941100349-0.1241134989280.1456467094130.4271996846010.06009972320920.054878099037-0.1255989183950.03990299083870.2457762622990.9389926692540.02187701807270.03373020644570.254051951062-0.01510726855110.34061381672444.391921137981.2884191476-27.4742158451
80.0386171270776-0.03827556978160.04464433268510.0452913029963-0.04773561597870.05503638279910.067258922284-0.0413466382202-0.09488727760610.03017347792230.2249670862290.0984762646473-0.049302122290.1146962414890.002768302953761.05892053772-0.0571752645051-0.08861603526730.385410685225-0.02996692454350.41030493041352.013154678375.76831646-14.833118761
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid -1 through 170 )
2X-RAY DIFFRACTION2chain 'A' and (resid 171 through 434 )
3X-RAY DIFFRACTION3chain 'A' and (resid 435 through 562 )
4X-RAY DIFFRACTION4chain 'B' and (resid 1 through 56 )
5X-RAY DIFFRACTION5chain 'B' and (resid 57 through 202 )
6X-RAY DIFFRACTION6chain 'B' and (resid 203 through 293 )
7X-RAY DIFFRACTION7chain 'B' and (resid 294 through 494 )
8X-RAY DIFFRACTION8chain 'B' and (resid 495 through 562 )

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