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- PDB-5vg7: Crystal Structure of the R503Q missense variant of human PGM1 -

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Basic information

Entry
Database: PDB / ID: 5vg7
TitleCrystal Structure of the R503Q missense variant of human PGM1
Components(Phosphoglucomutase- ...) x 2
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, Leloir pathway / Glycogen breakdown (glycogenolysis) / Glycogen synthesis / glycolytic process / gluconeogenesis / 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, Leloir pathway / Glycogen breakdown (glycogenolysis) / Glycogen synthesis / glycolytic process / gluconeogenesis / glucose metabolic process / tertiary granule lumen / ficolin-1-rich granule lumen / carbohydrate metabolic process / Neutrophil degranulation / magnesium ion binding / extracellular exosome / extracellular region / cytoplasm / cytosol
Similarity search - Function
Phosphoglucomutase-1, C-terminal domain / 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, conserved site / Phosphoglucomutase and phosphomannomutase phosphoserine signature. / Alpha-D-phosphohexomutase, alpha/beta/alpha domain II / Alpha-D-phosphohexomutase, alpha/beta/alpha domain III ...Phosphoglucomutase-1, C-terminal domain / 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, 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
Phosphoglucomutase-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95000322932 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 10, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 20, 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _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_asym_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
Revision 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)125,70027
Polymers123,4622
Non-polymers2,23825
Water17,096949
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A: Phosphoglucomutase-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,12816
Polymers61,7711
Non-polymers1,35715
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Phosphoglucomutase-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,57211
Polymers61,6911
Non-polymers88110
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)172.131, 172.131, 99.805
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
Components on special symmetry positions
IDModelComponents
11A-1290-

HOH

21B-908-

HOH

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Components

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Phosphoglucomutase- ... , 2 types, 2 molecules AB

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


Mass: 61770.980 Da / Num. of mol.: 1 / Mutation: R503Q
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: Protein Phosphoglucomutase-1 / PGM 1 / Glucose phosphomutase 1


Mass: 61691.004 Da / Num. of mol.: 1 / Mutation: R503Q
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)

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Non-polymers , 4 types, 974 molecules

#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 949 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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 Å3/Da / Density % sol: 58.97 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M Tris/HCl pH:7.5, 1.8 M Ammonium Sulfate, 16mg/mL

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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: Feb 2, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00003 Å / Relative weight: 1
ReflectionResolution: 1.95→60.95 Å / Num. obs: 108994 / % possible obs: 100 % / Redundancy: 14.3 % / Biso Wilson estimate: 27.988268727 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.14 / Rpim(I) all: 0.038 / Net I/σ(I): 15.1
Reflection shellResolution: 1.95→1.98 Å / Redundancy: 14 % / Rmerge(I) obs: 1.902 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 5314 / CC1/2: 0.709 / Rpim(I) all: 0.526 / % possible all: 99.9

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Processing

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

5epc


Resolution: 1.95000322932→60.8574986762 Å / SU ML: 0.196794435473 / Cross valid method: FREE R-VALUE / σ(F): 1.34841398363 / Phase error: 21.7167895447
RfactorNum. reflection% reflection
Rfree0.212939082377 5485 5.0369622113 %
Rwork0.16934233003 --
obs0.171520290168 108895 99.9770473742 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 41.8156901318 Å2
Refinement stepCycle: LAST / Resolution: 1.95000322932→60.8574986762 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8552 0 122 949 9623
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007285517341378938
X-RAY DIFFRACTIONf_angle_d0.8118310094812142
X-RAY DIFFRACTIONf_chiral_restr0.05470471144821356
X-RAY DIFFRACTIONf_plane_restr0.00549573249711574
X-RAY DIFFRACTIONf_dihedral_angle_d4.487038625138181
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-1.97220.3191191050641680.2625245616393390X-RAY DIFFRACTION99.9157540017
1.9722-1.99540.2758088959571690.2556326381953433X-RAY DIFFRACTION99.9445061043
1.9954-2.01970.276990477061750.2322088731473393X-RAY DIFFRACTION100
2.0197-2.04530.2523617467651590.2406366719383448X-RAY DIFFRACTION100
2.0453-2.07220.2726063696281750.2411693505733414X-RAY DIFFRACTION100
2.0722-2.10060.2908518358772160.230662214773348X-RAY DIFFRACTION100
2.1006-2.13060.2535348689261770.2253324934453410X-RAY DIFFRACTION99.97212932
2.1306-2.16240.263943505041790.2125990613223430X-RAY DIFFRACTION100
2.1624-2.19620.2371662496691730.1994441436653414X-RAY DIFFRACTION99.97212932
2.1962-2.23220.2513903103131970.1904684685383398X-RAY DIFFRACTION100
2.2322-2.27070.2505565495961770.1894863042323416X-RAY DIFFRACTION99.9443671766
2.2707-2.3120.2438767635962040.1841748449233411X-RAY DIFFRACTION100
2.312-2.35640.241676074091780.1868819857993392X-RAY DIFFRACTION100
2.3564-2.40450.2257084354691530.1803018146373442X-RAY DIFFRACTION100
2.4045-2.45680.2288081055851970.1695769746693423X-RAY DIFFRACTION99.9723833195
2.4568-2.5140.2082704145281870.1686955026343411X-RAY DIFFRACTION100
2.514-2.57680.2217577957821740.1766446523663458X-RAY DIFFRACTION99.9724745389
2.5768-2.64650.2274405716821890.1819276873183409X-RAY DIFFRACTION99.972214504
2.6465-2.72440.2469196959412090.1806329539853412X-RAY DIFFRACTION100
2.7244-2.81230.2316157378521730.1807965262613446X-RAY DIFFRACTION100
2.8123-2.91280.2322089951161770.1876042671973451X-RAY DIFFRACTION100
2.9128-3.02950.2218675193791970.179156192463458X-RAY DIFFRACTION100
3.0295-3.16730.2167182837291690.1665521374863462X-RAY DIFFRACTION100
3.1673-3.33430.2085072768721840.1607777991693462X-RAY DIFFRACTION99.9725802029
3.3343-3.54320.1972941654671920.1524748020243451X-RAY DIFFRACTION100
3.5432-3.81670.1678945927681850.1341048986013507X-RAY DIFFRACTION100
3.8167-4.20070.1856296914411730.1319345989613506X-RAY DIFFRACTION100
4.2007-4.80840.1737764809811970.1254957559693504X-RAY DIFFRACTION100
4.8084-6.05720.1835334942161800.1523037828013577X-RAY DIFFRACTION100
6.0572-60.88710.192892956352020.1746000146193734X-RAY DIFFRACTION99.7718631179
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)
11.05445451550.1249117297950.2217495091992.246331990180.2771333793061.22818070082-0.00868451479789-0.131822453846-0.1166005623110.5092384634070.110881774787-0.1070232595130.5951111764630.127410527786-0.06298739710790.5688192100670.082736699107-0.008632361465030.2272146040170.004274105053830.28028276373537.8311168361-74.08785479768.48417176574
21.45968606364-0.659277906124-0.05478647090662.165292600120.7630315670641.81173212304-0.0438131526893-0.00412819068971-0.2132374108030.263045751140.133815099563-0.04547967555260.5314444859870.137186185093-0.06883178264340.354414342323-0.014963595201-0.01268483757590.130937467886-0.01037823635640.20316607333.8534085587-70.14915241360.359502056771
30.880055401389-0.4901045310150.3508818468461.612353952230.7204414662641.733448351290.009238153262020.132356645030.108106727651-0.4034533569390.0185301839488-0.142461198592-0.21149465984-0.01216751678640.003010035394780.254445654005-0.06442187097610.04161483992860.1884888516330.02318051484290.17693754449328.1986390774-48.5503977436-10.7303792006
41.13629802892-0.17955232229-0.2035515848770.757811729470.3906207715931.13686546673-0.04553452520040.04638157806580.103115651992-0.1004770736490.0659766823466-0.232122007837-0.1870076464350.223911695036-0.02787867407880.231809760814-0.06908958427550.03475573313250.175119583548-0.004657261765690.27059885095636.171036324-43.4421933721-1.80851668278
50.9676682129610.3232084705030.0677236432461.181655257140.3948637555971.92330899639-0.05275614646220.009625824760650.0808847580942-0.14578957380.0135947763260.116121151516-0.029292643084-0.2858111060010.04237097625990.110031845446-0.00631272780771-0.02492841577060.167009964175-0.0001207476879680.21200001203518.1367028308-43.46802141646.41139008756
62.108043057130.2389002415450.58217023061.523325935790.3594686238742.37243743590.050867472893-0.609862961040.05817423078770.326619179574-0.1447747038280.07939248442280.223622213653-0.545313060990.0789136595010.210486620928-0.07153723697320.01665624531620.4335970610350.01402534247750.23049174549115.9493605439-45.743972244231.0236203546
72.015191944561.159224817190.2496803421590.8168816460380.4005730134151.895061697860.0411050990798-0.2549644765440.01960694004450.0378450873833-0.08995310378980.000417022868632-0.0221463078843-0.2377198886850.05213602686770.1235076561120.016157806873-0.0216753255690.211683940897-0.01472524056850.20238975128423.5401735865-40.124097961625.2985586159
81.303794391040.2429407320370.5614920927361.434059666270.8340736440551.59551067391-0.3667647753850.3907651215910.0924302482706-0.7586752723660.5885737140080.4187243640190.392542848642-0.679736056324-0.1971314956670.519877611299-0.274228410992-0.1384595994270.6684428124660.1667530839250.336298510401-32.1452008772-63.556275758-15.9027548371
92.057710985671.45147512124-0.2380717639332.52914982206-0.4965289555772.12819591285-0.3088556763450.498840982908-0.00659237830799-0.5645042758560.6072893458380.2871594087430.395972306251-0.614682209429-0.1742269265890.317453604329-0.124442475639-0.07321227191310.4634762106720.08074409802150.200557934962-26.9626529931-62.0887317392-10.9178766216
101.971248635050.833068331541-0.4809416177892.13452629718-0.6555504819911.992236863250.188226998016-0.082387927680.4886564362470.3790610862130.09499424041590.233642096687-0.427580210797-0.090453930417-0.236211522950.3209665046980.07185078321310.07636293173060.32427601981-0.02650987660640.276468717565-17.125202092-42.73792453290.372734092089
111.696398404720.169316681137-0.8151886408372.51177063865-0.6669864669532.440598599250.08520917845240.4441755870730.3162589554560.03669798753840.1036297632450.254376078347-0.281162038315-0.327763204874-0.08101215816590.1700637150250.0766943280499-0.001172171101380.3356452828240.03663240323450.253220255795-10.9415041365-38.8816454188-13.9322409808
121.99949654959-0.6362839206520.3000195487172.32954277841-0.1361126752522.435910320130.4424987091340.8146264867070.277780346456-0.943082357138-0.2866507281630.02780885042930.1248199701620.040064852646-0.1597537648670.5799902835470.1115154043230.07365507441320.8107580195580.03637460115490.349552556303-4.35260082793-43.4022966379-40.9222268981
131.77605011335-0.8640195206830.2382099400912.182809130920.09931699669631.901602404390.2143561943930.7002515306170.302977338603-0.744793017178-0.2497546772810.207580150963-0.407765682329-0.348852527970.02653843307760.5101273168460.129367409431-0.01599494018220.73564061890.1301768584930.38531544602-9.91121194705-35.2646770488-35.1777237972
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid -1 through 52 )
2X-RAY DIFFRACTION2chain 'A' and (resid 53 through 183 )
3X-RAY DIFFRACTION3chain 'A' and (resid 184 through 229 )
4X-RAY DIFFRACTION4chain 'A' and (resid 230 through 293 )
5X-RAY DIFFRACTION5chain 'A' and (resid 294 through 434 )
6X-RAY DIFFRACTION6chain 'A' and (resid 435 through 483 )
7X-RAY DIFFRACTION7chain 'A' and (resid 484 through 562 )
8X-RAY DIFFRACTION8chain 'B' and (resid 0 through 80 )
9X-RAY DIFFRACTION9chain 'B' and (resid 81 through 183 )
10X-RAY DIFFRACTION10chain 'B' and (resid 184 through 228 )
11X-RAY DIFFRACTION11chain 'B' and (resid 229 through 434 )
12X-RAY DIFFRACTION12chain 'B' and (resid 435 through 483 )
13X-RAY DIFFRACTION13chain 'B' and (resid 484 through 562 )

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Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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