PDB-5vbi: Crystal Structure of the R515W missense variant of human PGM1

ID or keywords:

Entry

Database: PDB / ID: 5vbi

Title

Crystal Structure of the R515W missense variant of human PGM1

Components

Phosphoglucomutase-1

PGM1

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: 1.75000083769 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	Mar 29, 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 / struct_conn Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _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	5vbi.cif.gz	564.3 KB	Display	PDBx/mmCIF format
PDB format	pdb5vbi.ent.gz	384.5 KB	Display	PDB format
PDBx/mmJSON format	5vbi.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/vb/5vbi ftp://data.pdbj.org/pub/pdb/validation_reports/vb/5vbi	HTTPS FTP

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Related structure data

Related structure data	5vecC 5vg7C 5vinC 6uiqC 5epcS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	5jn5-1 5hsh-1 6uo6-1 3pmg-1 1lxt-2 1jdy-2 3ihg-3 1vkl-1 2efe-1 3mvw-1 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

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

1

A: Phosphoglucomutase-1

hetero molecules

defined by author
Evidence: light scattering
65.2 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Phosphoglucomutase-1

hetero molecules

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

Unit cell

Length a, b, c (Å)	172.330, 172.330, 99.370
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-1179- HOH
2	1	A-1374- HOH

#1: Protein	Phosphoglucomutase-1 / PGM1 / PGM 1 / Glucose phosphomutase 1 Mass: 64300.734 Da / Num. of mol.: 2 / Mutation: R515W 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 / Sulfate Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO₄
#3: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol Mass: 92.094 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C₃H₈O₃
#5: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 1180 / 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: 2.99 Å³/Da / Density % sol: 58.86 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1M HEPES 7.5, 0.1M Sodium Chloride, 1.5-1.7M Ammonium Sulfate

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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: Nov 3, 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: 1.75→60.93 Å / Num. obs: 150294 / % possible obs: 99.7 % / Redundancy: 13.6 % / B_iso Wilson estimate: 22.2163099368 Å² / CC_1/2: 0.999 / R_merge(I) obs: 0.093 / R_pim(I) all: 0.025 / Net I/σ(I): 20.1
Reflection shell	Resolution: 1.75→1.78 Å / Redundancy: 8.5 % / R_merge(I) obs: 1.58 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 6946 / CC_1/2: 0.595 / R_pim(I) all: 0.561 / % possible all: 93.6

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Processing

Software

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

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5EPC

5epc

Resolution: 1.75000083769→54.4955309177 Å / SU ML: 0.211417698887 / Cross valid method: FREE R-VALUE / σ(F): 0.028742346894 / Phase error: 18.6226333485

	R_factor	Num. reflection	% reflection
R_free	0.19087048899	7454	4.97786207035 %
R_work	0.16518324955	-	-
obs	0.166463873181	149743	99.9666206031 %

Solvent computation

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

Displacement parameters

B_iso mean: 32.065293762 Å²

Refinement step

Cycle: LAST / Resolution: 1.75000083769→54.4955309177 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8512	0	105	1180	9797

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.00604287594275	8890
X-RAY DIFFRACTION	f_angle_d	0.782577457852	12069
X-RAY DIFFRACTION	f_chiral_restr	0.0545048562095	1350
X-RAY DIFFRACTION	f_plane_restr	0.00526958626906	1569
X-RAY DIFFRACTION	f_dihedral_angle_d	4.42959414693	7178

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 (%)
1.75-1.7699	0.357791092427	233	0.326448675797	4709	X-RAY DIFFRACTION	99.9595469256
1.7699-1.7907	0.316230757108	248	0.305900203491	4709	X-RAY DIFFRACTION	99.9596692882
1.7907-1.8126	0.300709761268	243	0.290244326782	4684	X-RAY DIFFRACTION	99.939148073
1.8126-1.8355	0.297313618952	223	0.252614391814	4686	X-RAY DIFFRACTION	99.9592750967
1.8355-1.8596	0.29510161644	218	0.237343773678	4735	X-RAY DIFFRACTION	99.9798142915
1.8596-1.8851	0.274728788674	235	0.215389792	4683	X-RAY DIFFRACTION	99.9593495935
1.8851-1.9121	0.24531960263	264	0.202770667462	4697	X-RAY DIFFRACTION	99.9597017933
1.9121-1.9406	0.240299058726	243	0.20367532751	4691	X-RAY DIFFRACTION	100
1.9406-1.9709	0.222024786063	236	0.188361865567	4720	X-RAY DIFFRACTION	99.9596611537
1.9709-2.0032	0.193909326485	236	0.179737521923	4690	X-RAY DIFFRACTION	99.9797036736
2.0032-2.0378	0.199455135213	214	0.178720070941	4741	X-RAY DIFFRACTION	100
2.0378-2.0748	0.208557690413	249	0.193123510396	4713	X-RAY DIFFRACTION	100
2.0748-2.1147	0.220939891752	283	0.188046246114	4681	X-RAY DIFFRACTION	100
2.1147-2.1579	0.211224964623	248	0.17914010042	4700	X-RAY DIFFRACTION	100
2.1579-2.2048	0.201839762544	241	0.168346818508	4705	X-RAY DIFFRACTION	99.9797857287
2.2048-2.2561	0.209381965072	257	0.161283622062	4722	X-RAY DIFFRACTION	100
2.2561-2.3125	0.184925755597	273	0.15640756887	4711	X-RAY DIFFRACTION	100
2.3125-2.3751	0.200127868672	233	0.157805158865	4716	X-RAY DIFFRACTION	100
2.3751-2.445	0.180144944448	242	0.156302738101	4706	X-RAY DIFFRACTION	100
2.445-2.5239	0.177113739911	268	0.15446240683	4727	X-RAY DIFFRACTION	99.9799839872
2.5239-2.6141	0.185946324696	253	0.158624256872	4757	X-RAY DIFFRACTION	100
2.6141-2.7187	0.183908124492	275	0.157912473723	4689	X-RAY DIFFRACTION	100
2.7187-2.8425	0.19686633602	250	0.162307298994	4791	X-RAY DIFFRACTION	100
2.8425-2.9923	0.183080059448	243	0.165798708499	4775	X-RAY DIFFRACTION	100
2.9923-3.1798	0.197318549713	246	0.160009575422	4747	X-RAY DIFFRACTION	99.9799759712
3.1798-3.4253	0.194338376435	254	0.154114501808	4804	X-RAY DIFFRACTION	99.9802332477
3.4253-3.7699	0.165539613782	265	0.136933377036	4795	X-RAY DIFFRACTION	100
3.7699-4.3152	0.141214491651	239	0.130160200697	4868	X-RAY DIFFRACTION	100
4.3152-5.4359	0.155997541488	280	0.128895196742	4843	X-RAY DIFFRACTION	100
5.4359-54.5219	0.174147302644	262	0.177428373649	5094	X-RAY DIFFRACTION	99.4984209549

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	1.62393070512	0.0677600439578	-0.158796828729	0.76818911586	0.054512220441	1.18869055005	0.0971347702245	-0.188574947382	0.0442795513168	0.118824324519	-0.0466495761826	-0.148847009293	-0.135390147212	0.527417828453	-0.0404993124173	0.166709283349	-0.0508981879672	-0.00634929195989	0.357015376579	-0.0129376829457	0.205192963358	72.9921247307	37.4942197852	-18.7923011875
2	1.6420730498	0.505358539451	-0.619427296402	1.19395497156	-0.125077751061	1.67196254257	0.107158754377	-0.19086837713	-0.00764695167972	0.0655300786561	-0.052377988171	-0.148383063004	-0.0808102460779	0.446139807166	-0.0530016580364	0.110785048426	0.00721662326289	-0.00528005577849	0.26911955643	-0.00996524337193	0.149789670327	70.3723733231	33.0059866595	-23.9023940208
3	1.22189964295	0.329858542245	-0.651846166742	0.826620761034	0.163581036166	1.33401031853	-0.00144121806521	0.312597541172	0.107725828899	-0.0892921692644	0.0203647885726	0.0874160885398	0.0497598889662	-0.186006069841	-0.0126002582228	0.155519330079	0.0342456088627	-0.0247494959322	0.219646439761	0.0221841619928	0.146387205197	48.2289983303	28.0738125565	-35.8374530798
4	0.847737759311	0.0477528193721	-0.154079999982	0.541021355468	-0.163437824032	1.61925818151	0.0156733556258	0.105956031264	0.0159765195706	-0.0131984598643	-0.00369477884909	0.0437685107826	0.119797910237	-0.0551138886403	-0.0129888015912	0.125311839583	0.0139549125417	-0.00495591234601	0.113622307389	-0.0160393002045	0.166934175218	45.5319279827	23.9279814881	-22.4846576805
5	1.00813059355	-0.289752641062	-0.130036975371	0.829681676563	0.233583381136	1.54229361921	-0.0148649258566	0.118190514498	-0.0915910137218	0.0204581482335	-0.0461349635792	0.138583862828	0.112047551391	-0.209715430028	0.0465074764492	0.113251441784	-0.0402697927076	0.0173234269717	0.128216195701	-0.0137036605845	0.200328273573	35.3626145235	22.6208258355	-12.8448615463
6	1.25406569542	-0.395198276417	-0.19153243165	1.65553967992	0.320872658708	1.66404169931	-0.0546126419205	-0.142655137655	-0.0482085871781	0.404940166927	0.0304726089392	-0.00498552804163	0.356587026843	0.129374634492	0.00973504433142	0.2872240187	0.0181287280611	-0.0113339547565	0.141377936558	-0.0134192371485	0.162268361047	46.1400169514	18.4013074292	3.03431484225
7	1.38517015564	-0.257720583845	-0.0358733280863	1.85370667999	0.229174725184	1.85159968535	-0.0131289541891	-0.018403770771	-0.140663437205	0.137552858187	0.00809707125176	0.122834965863	0.256083209004	-0.244552900526	0.00430314989888	0.189579327628	-0.0371324520606	0.0368805956546	0.134219399135	-0.0238682386139	0.175952545771	34.2858645436	26.2687547117	0.68964590462
8	2.91458661788	1.45263892095	1.26586988636	1.85632749098	0.748254473655	2.12864062319	0.486304163944	-0.339305995703	-0.406473772845	0.34599496472	-0.215257300659	-0.212875472718	0.50949046498	-0.285347115932	-0.0935465874496	0.301561498835	-0.035160607351	-0.0715374177566	0.14239812538	0.0546695763261	0.144067059745	32.9283478578	60.6262996337	-39.778622219
9	1.13019540119	-0.172042760327	-0.111013459747	0.86984010741	-0.0668134446429	2.4256937574	0.050189760975	-0.188495687342	0.017337743556	0.267437739743	-0.00548541327533	-0.10834530875	-0.144960893156	0.160190381203	-0.0371407191409	0.276624645843	-0.026632450269	-0.0120401573616	0.136876956194	0.00281035833121	0.196891741217	46.6414921931	79.6034788044	-23.7659591864

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 0 through 80 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 81 through 183 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 184 through 227 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 228 through 405 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 406 through 434 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 435 through 522 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 523 through 562 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 1 through 293 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 294 through 562 )

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