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

ID or keywords:

Entry

Database: PDB / ID: 5vg7

Title

Crystal Structure of the R503Q missense variant of human PGM1

Components

(Phosphoglucomutase- ...) x 2

Keywords

ISOMERASE /

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 / Glycogen breakdown (glycogenolysis) /

Glycogen synthesis /

gluconeogenesis / glycolytic process / glucose metabolic process / tertiary granule lumen ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.95000322932 Å

Authors

Stiers, K.M. / Beamer, L.J.

Funding support

United States, 1items

Citation

Journal: 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

Deposition	Apr 10, 2017	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jun 20, 2018	Provider: repository / Type: Initial release
Revision 1.1	Sep 5, 2018	Group: 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 1.2	Oct 17, 2018	Group: Data collection / Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.3	Nov 27, 2019	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4	Oct 4, 2023	Group: 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

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5vg7.cif.gz	567.8 KB	Display	PDBx/mmCIF format
PDB format	pdb5vg7.ent.gz	386.8 KB	Display	PDB format
PDBx/mmJSON format	5vg7.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/vg/5vg7 ftp://data.pdbj.org/pub/pdb/validation_reports/vg/5vg7	HTTPS FTP

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Related structure data

Related structure data	5vbiC 5vecC 5vinC 6uiqC 5epcS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6y8x-d 6uo6-1 5jn5-2 2b7s-d 4qyr-d 5vec-1 1ksu-1 5vbi-2 5f9c-2 6uiq-2 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#44 - Aug 2003 Calmodulin similarity (1) #60 - Dec 2004 Ubiquitin similarity (1) #196 - Apr 2016 Lead Poisoning similarity (1) #28 - Apr 2002 Anthrax Toxin similarity (1) #234 - Jun 2019 MDM2 and Cancer similarity (1)

Deposited unit

A: Phosphoglucomutase-1

B: Phosphoglucomutase-1

hetero molecules

126 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Phosphoglucomutase-1

hetero molecules

defined by author&software
Evidence: light scattering, Dynamic Light Scattering
63.1 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Phosphoglucomutase-1

hetero molecules

defined by author&software
62.6 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

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 number	92
Space group name H-M	P4₁2₁2
Space group name Hall	P4abw2nw
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

ID	Model	Components
1	1	A-1290- HOH
2	1	B-908- HOH

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

#1: Protein	Phosphoglucomutase-1 / PGM1 / 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 / PGM1 / 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)

#1: Protein

Phosphoglucomutase-1 /

PGM1 / 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 /

PGM1 / 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 / Sulfate 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 / Glycerol Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₃H₈O₃
#6: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 949 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 3 Å³/Da / Density % sol: 58.97 %
Crystal grow	Temperature: 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

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1.00003 Å
Detector	Type: RDI CMOS_8M / Detector: CMOS / Date: Feb 2, 2016
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.00003 Å / Relative weight: 1
Reflection	Resolution: 1.95→60.95 Å / Num. obs: 108994 / % possible obs: 100 % / Redundancy: 14.3 % / B_iso Wilson estimate: 27.988268727 Å² / CC_1/2: 0.999 / R_merge(I) obs: 0.14 / R_pim(I) all: 0.038 / Net I/σ(I): 15.1
Reflection shell	Resolution: 1.95→1.98 Å / Redundancy: 14 % / R_merge(I) obs: 1.902 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 5314 / CC_1/2: 0.709 / R_pim(I) all: 0.526 / % possible all: 99.9

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Processing

Software

Name	Version	Classification
PHENIX	1.11.1_2575	refinement
PHENIX	1.11.1_2575	phasing
SCALA		data scaling
XDS		data reduction

Refinement

Method 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

	R_factor	Num. reflection	% reflection
R_free	0.212939082377	5485	5.0369622113 %
R_work	0.16934233003	-	-
obs	0.171520290168	108895	99.9770473742 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Displacement parameters

B_iso mean: 41.8156901318 Å²

Refinement step

Cycle: LAST / Resolution: 1.95000322932→60.8574986762 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8552	0	122	949	9623

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.00728551734137	8938
X-RAY DIFFRACTION	f_angle_d	0.81183100948	12142
X-RAY DIFFRACTION	f_chiral_restr	0.0547047114482	1356
X-RAY DIFFRACTION	f_plane_restr	0.0054957324971	1574
X-RAY DIFFRACTION	f_dihedral_angle_d	4.48703862513	8181

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.95-1.9722	0.319119105064	168	0.262524561639	3390	X-RAY DIFFRACTION	99.9157540017
1.9722-1.9954	0.275808895957	169	0.255632638195	3433	X-RAY DIFFRACTION	99.9445061043
1.9954-2.0197	0.27699047706	175	0.232208873147	3393	X-RAY DIFFRACTION	100
2.0197-2.0453	0.252361746765	159	0.240636671938	3448	X-RAY DIFFRACTION	100
2.0453-2.0722	0.272606369628	175	0.241169350573	3414	X-RAY DIFFRACTION	100
2.0722-2.1006	0.290851835877	216	0.23066221477	3348	X-RAY DIFFRACTION	100
2.1006-2.1306	0.253534868926	177	0.225332493445	3410	X-RAY DIFFRACTION	99.97212932
2.1306-2.1624	0.26394350504	179	0.212599061322	3430	X-RAY DIFFRACTION	100
2.1624-2.1962	0.237166249669	173	0.199444143665	3414	X-RAY DIFFRACTION	99.97212932
2.1962-2.2322	0.251390310313	197	0.190468468538	3398	X-RAY DIFFRACTION	100
2.2322-2.2707	0.250556549596	177	0.189486304232	3416	X-RAY DIFFRACTION	99.9443671766
2.2707-2.312	0.243876763596	204	0.184174844923	3411	X-RAY DIFFRACTION	100
2.312-2.3564	0.24167607409	178	0.186881985799	3392	X-RAY DIFFRACTION	100
2.3564-2.4045	0.225708435469	153	0.180301814637	3442	X-RAY DIFFRACTION	100
2.4045-2.4568	0.228808105585	197	0.169576974669	3423	X-RAY DIFFRACTION	99.9723833195
2.4568-2.514	0.208270414528	187	0.168695502634	3411	X-RAY DIFFRACTION	100
2.514-2.5768	0.221757795782	174	0.176644652366	3458	X-RAY DIFFRACTION	99.9724745389
2.5768-2.6465	0.227440571682	189	0.181927687318	3409	X-RAY DIFFRACTION	99.972214504
2.6465-2.7244	0.246919695941	209	0.180632953985	3412	X-RAY DIFFRACTION	100
2.7244-2.8123	0.231615737852	173	0.180796526261	3446	X-RAY DIFFRACTION	100
2.8123-2.9128	0.232208995116	177	0.187604267197	3451	X-RAY DIFFRACTION	100
2.9128-3.0295	0.221867519379	197	0.17915619246	3458	X-RAY DIFFRACTION	100
3.0295-3.1673	0.216718283729	169	0.166552137486	3462	X-RAY DIFFRACTION	100
3.1673-3.3343	0.208507276872	184	0.160777799169	3462	X-RAY DIFFRACTION	99.9725802029
3.3343-3.5432	0.197294165467	192	0.152474802024	3451	X-RAY DIFFRACTION	100
3.5432-3.8167	0.167894592768	185	0.134104898601	3507	X-RAY DIFFRACTION	100
3.8167-4.2007	0.185629691441	173	0.131934598961	3506	X-RAY DIFFRACTION	100
4.2007-4.8084	0.173776480981	197	0.125495755969	3504	X-RAY DIFFRACTION	100
4.8084-6.0572	0.183533494216	180	0.152303782801	3577	X-RAY DIFFRACTION	100
6.0572-60.8871	0.19289295635	202	0.174600014619	3734	X-RAY DIFFRACTION	99.7718631179

Refinement TLS params.

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

ID	L11 (°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)
1	1.0544545155	0.124911729795	0.221749509199	2.24633199018	0.277133379306	1.22818070082	-0.00868451479789	-0.131822453846	-0.116600562311	0.509238463407	0.110881774787	-0.107023259513	0.595111176463	0.127410527786	-0.0629873971079	0.568819210067	0.082736699107	-0.00863236146503	0.227214604017	0.00427410505383	0.280282763735	37.8311168361	-74.0878547976	8.48417176574
2	1.45968606364	-0.659277906124	-0.0547864709066	2.16529260012	0.763031567064	1.81173212304	-0.0438131526893	-0.00412819068971	-0.213237410803	0.26304575114	0.133815099563	-0.0454796755526	0.531444485987	0.137186185093	-0.0688317826434	0.354414342323	-0.014963595201	-0.0126848375759	0.130937467886	-0.0103782363564	0.203166073	33.8534085587	-70.1491524136	0.359502056771
3	0.880055401389	-0.490104531015	0.350881846846	1.61235395223	0.720441466264	1.73344835129	0.00923815326202	0.13235664503	0.108106727651	-0.403453356939	0.0185301839488	-0.142461198592	-0.21149465984	-0.0121675167864	0.00301003539478	0.254445654005	-0.0644218709761	0.0416148399286	0.188488851633	0.0231805148429	0.176937544493	28.1986390774	-48.5503977436	-10.7303792006
4	1.13629802892	-0.17955232229	-0.203551584877	0.75781172947	0.390620771593	1.13686546673	-0.0455345252004	0.0463815780658	0.103115651992	-0.100477073649	0.0659766823466	-0.232122007837	-0.187007646435	0.223911695036	-0.0278786740788	0.231809760814	-0.0690895842755	0.0347557331325	0.175119583548	-0.00465726176569	0.270598850956	36.171036324	-43.4421933721	-1.80851668278
5	0.967668212961	0.323208470503	0.067723643246	1.18165525714	0.394863755597	1.92330899639	-0.0527561464622	0.00962582476065	0.0808847580942	-0.1457895738	0.013594776326	0.116121151516	-0.029292643084	-0.285811106001	0.0423709762599	0.110031845446	-0.00631272780771	-0.0249284157706	0.167009964175	-0.000120747687968	0.212000012035	18.1367028308	-43.4680214164	6.41139008756
6	2.10804305713	0.238900241545	0.5821702306	1.52332593579	0.359468623874	2.3724374359	0.050867472893	-0.60986296104	0.0581742307877	0.326619179574	-0.144774703828	0.0793924844228	0.223622213653	-0.54531306099	0.078913659501	0.210486620928	-0.0715372369732	0.0166562453162	0.433597061035	0.0140253424775	0.230491745491	15.9493605439	-45.7439722442	31.0236203546
7	2.01519194456	1.15922481719	0.249680342159	0.816881646038	0.400573013415	1.89506169786	0.0411050990798	-0.254964476544	0.0196069400445	0.0378450873833	-0.0899531037898	0.000417022868632	-0.0221463078843	-0.237719888685	0.0521360268677	0.123507656112	0.016157806873	-0.021675325569	0.211683940897	-0.0147252405685	0.202389751284	23.5401735865	-40.1240979616	25.2985586159
8	1.30379439104	0.242940732037	0.561492092736	1.43405966627	0.834073644055	1.59551067391	-0.366764775385	0.390765121591	0.0924302482706	-0.758675272366	0.588573714008	0.418724364019	0.392542848642	-0.679736056324	-0.197131495667	0.519877611299	-0.274228410992	-0.138459599427	0.668442812466	0.166753083925	0.336298510401	-32.1452008772	-63.556275758	-15.9027548371
9	2.05771098567	1.45147512124	-0.238071763933	2.52914982206	-0.496528955577	2.12819591285	-0.308855676345	0.498840982908	-0.00659237830799	-0.564504275856	0.607289345838	0.287159408743	0.395972306251	-0.614682209429	-0.174226926589	0.317453604329	-0.124442475639	-0.0732122719131	0.463476210672	0.0807440980215	0.200557934962	-26.9626529931	-62.0887317392	-10.9178766216
10	1.97124863505	0.833068331541	-0.480941617789	2.13452629718	-0.655550481991	1.99223686325	0.188226998016	-0.08238792768	0.488656436247	0.379061086213	0.0949942404159	0.233642096687	-0.427580210797	-0.090453930417	-0.23621152295	0.320966504698	0.0718507832131	0.0763629317306	0.32427601981	-0.0265098766064	0.276468717565	-17.125202092	-42.7379245329	0.372734092089
11	1.69639840472	0.169316681137	-0.815188640837	2.51177063865	-0.666986466953	2.44059859925	0.0852091784524	0.444175587073	0.316258955456	0.0366979875384	0.103629763245	0.254376078347	-0.281162038315	-0.327763204874	-0.0810121581659	0.170063715025	0.0766943280499	-0.00117217110138	0.335645282824	0.0366324032345	0.253220255795	-10.9415041365	-38.8816454188	-13.9322409808
12	1.99949654959	-0.636283920652	0.300019548717	2.32954277841	-0.136112675252	2.43591032013	0.442498709134	0.814626486707	0.277780346456	-0.943082357138	-0.286650728163	0.0278088504293	0.124819970162	0.040064852646	-0.159753764867	0.579990283547	0.111515404323	0.0736550744132	0.810758019558	0.0363746011549	0.349552556303	-4.35260082793	-43.4022966379	-40.9222268981
13	1.77605011335	-0.864019520683	0.238209940091	2.18280913092	0.0993169966963	1.90160240439	0.214356194393	0.700251530617	0.302977338603	-0.744793017178	-0.249754677281	0.207580150963	-0.407765682329	-0.34885252797	0.0265384330776	0.510127316846	0.129367409431	-0.0159949401822	0.7356406189	0.130176858493	0.38531544602	-9.91121194705	-35.2646770488	-35.1777237972

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid -1 through 52 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 53 through 183 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 184 through 229 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 230 through 293 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 294 through 434 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 435 through 483 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 484 through 562 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 0 through 80 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 81 through 183 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 184 through 228 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 229 through 434 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 435 through 483 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 484 through 562 )

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