PDB-5vec: Crystal Structure of the R515L missense variant of human PGM1

ID or keywords:

Entry

Database: PDB / ID: 5vec

Title

Crystal Structure of the R515L 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: 2.20001616144 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 4, 2017	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jun 27, 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: Advisory / Data collection ...Advisory / 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_unobs_or_zero_occ_atoms / struct_conn Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _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

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5vec.cif.gz	549.6 KB	Display	PDBx/mmCIF format
PDB format	pdb5vec.ent.gz	377.4 KB	Display	PDB format
PDBx/mmJSON format	5vec.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/ve/5vec ftp://data.pdbj.org/pub/pdb/validation_reports/ve/5vec	HTTPS FTP

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Related structure data

Related structure data	5vbiC 5vg7C 5vinC 6uiqC 5epcS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	4i1o-2 6uiq-2 5vg7-1 4i8c-3 4oev-1 3e3k-2 2grv-3 6y8x-d 5dlk-2 2qa2-d 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

129 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
64.8 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Phosphoglucomutase-1

hetero molecules

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

Unit cell

Length a, b, c (Å)	171.324, 171.324, 99.382
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-1095- HOH

#1: Protein	Phosphoglucomutase-1 / PGM1 / PGM 1 / Glucose phosphomutase 1 Mass: 64147.695 Da / Num. of mol.: 2 / Mutation: R515L 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.: 6 / 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.: 6 / Source method: obtained synthetically / Formula: C₃H₈O₃
#5: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 635 / 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: 2.96 Å³/Da / Density % sol: 58.39 %
Crystal grow	Temperature: 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 1.8-1.9M

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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: Oct 1, 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: 2.2→60.68 Å / Num. obs: 75286 / % possible obs: 100 % / Redundancy: 11.9 % / B_iso Wilson estimate: 33.0652578257 Å² / CC_1/2: 0.997 / R_merge(I) obs: 0.279 / R_pim(I) all: 0.084 / Net I/σ(I): 11.9
Reflection shell	Resolution: 2.2→2.25 Å / Redundancy: 9.8 % / R_merge(I) obs: 2.141 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 4379 / CC_1/2: 0.693 / R_pim(I) all: 0.72 / % possible all: 99.9

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Processing

Software

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

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5EPC

5epc

Resolution: 2.20001616144→60.6791870077 Å / SU ML: 0.294676044455 / Cross valid method: FREE R-VALUE / σ(F): 1.34865261235 / Phase error: 28.0591353504

	R_factor	Num. reflection	% reflection
R_free	0.250655699293	3814	5.07417015898 %
R_work	0.18972110479	-	-
obs	0.192775380156	75165	99.9096141321 %

Solvent computation

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

Displacement parameters

B_iso mean: 52.1669117066 Å²

Refinement step

Cycle: LAST / Resolution: 2.20001616144→60.6791870077 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8546	0	68	635	9249

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.00657718110399	8848
X-RAY DIFFRACTION	f_angle_d	0.852976312586	11997
X-RAY DIFFRACTION	f_chiral_restr	0.0547675145638	1351
X-RAY DIFFRACTION	f_plane_restr	0.00600463447509	1557
X-RAY DIFFRACTION	f_dihedral_angle_d	5.22008672908	7219

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 (%)
2.2-2.2279	0.369933448054	146	0.307417716824	2592	X-RAY DIFFRACTION	99.7086671522
2.2279-2.2572	0.398225847997	141	0.294027091375	2619	X-RAY DIFFRACTION	99.891422367
2.2572-2.2881	0.319495638301	153	0.287948483195	2559	X-RAY DIFFRACTION	100
2.2881-2.3208	0.351862130181	146	0.275416439056	2608	X-RAY DIFFRACTION	99.8549673677
2.3208-2.3554	0.354635619965	119	0.273344887194	2643	X-RAY DIFFRACTION	99.9638074557
2.3554-2.3922	0.32094804478	126	0.252531433126	2588	X-RAY DIFFRACTION	99.8528329654
2.3922-2.4315	0.326644580546	134	0.245236913596	2626	X-RAY DIFFRACTION	99.8552821997
2.4315-2.4734	0.312037788517	177	0.234408716632	2582	X-RAY DIFFRACTION	99.8191027496
2.4734-2.5184	0.306836500109	121	0.233807814748	2609	X-RAY DIFFRACTION	99.7807017544
2.5184-2.5668	0.302003390327	131	0.233854784329	2650	X-RAY DIFFRACTION	99.8563734291
2.5668-2.6192	0.295710544129	142	0.235370048024	2598	X-RAY DIFFRACTION	99.9635169646
2.6192-2.6762	0.315876649059	163	0.222594252423	2611	X-RAY DIFFRACTION	99.8919697515
2.6762-2.7384	0.296011277102	155	0.221504747639	2587	X-RAY DIFFRACTION	99.8543335761
2.7384-2.8069	0.293590654017	120	0.220062364243	2639	X-RAY DIFFRACTION	100
2.8069-2.8828	0.320277198507	138	0.225846553562	2635	X-RAY DIFFRACTION	99.8200143988
2.8828-2.9676	0.273119241136	137	0.228893434577	2624	X-RAY DIFFRACTION	100
2.9676-3.0634	0.306482142627	152	0.206886944609	2642	X-RAY DIFFRACTION	100
3.0634-3.1729	0.272097124365	125	0.202597414081	2647	X-RAY DIFFRACTION	99.9639379733
3.1729-3.2999	0.287157981371	148	0.194592247691	2653	X-RAY DIFFRACTION	99.9643112063
3.2999-3.4501	0.250785680674	138	0.188236897525	2636	X-RAY DIFFRACTION	99.9279538905
3.4501-3.6319	0.228732533243	140	0.161447483448	2653	X-RAY DIFFRACTION	100
3.6319-3.8595	0.207524949545	154	0.147723330991	2658	X-RAY DIFFRACTION	100
3.8595-4.1574	0.1944819217	125	0.141331499675	2687	X-RAY DIFFRACTION	99.9289267946
4.1574-4.5756	0.167290150005	138	0.125903074616	2679	X-RAY DIFFRACTION	99.8936170213
4.5756-5.2374	0.194197957491	158	0.132746096892	2700	X-RAY DIFFRACTION	100
5.2374-6.5973	0.215937683412	132	0.177668587101	2752	X-RAY DIFFRACTION	100
6.5973-60.7022	0.201230240011	155	0.180785301517	2874	X-RAY DIFFRACTION	99.8681173755

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	0.970454291555	-0.1865031972	-0.0909323079245	0.502371857843	-0.467306191916	0.957507422457	0.0226085464578	-0.105504780058	-0.0306395606244	0.0364239350833	0.0192808046245	0.00344658121	-0.221316651902	0.532305792084	0.00861740966446	0.168092496338	-0.0292103062202	0.0307438587629	0.39847521605	-0.0416768885287	0.193919501366	69.576302096	35.4259137424	-21.5858911172
2	0.631498659764	0.0656534035938	-0.101272646399	0.297483699623	0.109348140863	0.27223259855	0.121346436713	-0.143188025768	-0.100735705932	0.0143450829079	0.045850909764	-0.0937780330789	-0.106950490786	0.465829304139	0.0175441437914	0.226976633506	-0.0413439059545	0.0470570030858	0.539938564947	-0.03356615602	0.244464119221	74.6701279777	33.6041523066	-23.160582506
3	0.553034554464	0.343344820332	-0.46003555411	-0.0172088434314	-0.102098922671	1.0081328957	0.0252340343074	0.296613255367	0.138932861114	-0.109556198749	0.0590532686911	0.0535995659357	0.0272785010001	-0.0653919939869	0.0177477379956	0.136648005823	0.072718887148	0.0185021526355	0.23727491456	0.0347725756392	0.23727498182	44.1159664197	30.6706399603	-28.8239551001
4	0.815367494547	-0.116585667513	-0.137591561719	0.575187608809	0.0115613920778	1.11939280311	0.0528747017653	0.1699789707	-0.0536789853954	-0.012794331268	-0.105130835874	0.00861571274672	0.314745115025	0.0626093566603	-0.0259140240006	0.169974646253	0.0282770612029	0.00696624935297	0.13975468005	-0.0357254805072	0.223612458067	44.5132367802	17.2407766921	-18.1327359522
5	0.365692783406	-0.13379936509	-0.12533659458	0.164284991076	0.270541907394	0.762608328665	-0.268074488579	-0.424483104085	0.0244115439119	0.539085089351	0.198560556684	0.0758003127082	0.793974870334	0.589091305426	0.00673848856069	0.512148485067	0.0477674980779	0.0192025835791	0.266059944082	-0.00385984043761	0.301587118512	45.743595864	15.4106108993	5.59146332491
6	0.198526969199	-0.737297619403	-0.329931977428	0.336969934826	0.297936458011	0.906258553464	-0.0800020932216	-0.000287847962499	0.0932518823526	0.337672264897	0.072784912247	-0.00887733498986	0.345406746099	0.00443256792649	-0.00460713268247	0.206037170948	-0.0440813896523	0.0379037366411	0.0591959597399	-0.0201972820159	0.241783520009	39.7966428772	23.4043301439	0.0439366494506
7	0.321136943981	0.180181653598	-0.273209343307	0.395518257369	0.0311577435218	0.367117655704	0.489423339312	-0.416431724693	-0.251331764133	0.108335102708	-0.151505926763	-0.0789297816468	0.699042669178	-0.285235201998	0.517510020282	0.713121228789	-0.277119467725	-0.189849124079	0.557593106651	0.117845580811	0.357148494794	22.2495203415	53.8145932579	-33.9609253283
8	1.05350439183	0.841308609835	1.19557302996	0.775531162867	0.481445320969	2.00123181514	0.284915616878	0.116397284374	-0.122155065008	0.193483151404	0.0099545864611	-0.177987934986	0.241145744787	0.00212251472244	0.0772086920299	0.309748016897	0.0526761475617	-0.0333823608013	0.170319377272	-0.0143811663057	0.237129203025	38.6584637564	68.6068037888	-39.593166555
9	0.827053993511	-0.4622421816	0.271239213831	0.41502918252	0.117679510726	1.20466921175	-0.100589440635	-0.212419490612	0.069709431347	0.592351249149	0.18897184146	-0.0901274977247	0.0676014785203	0.146872659087	0.000209808741526	0.625360094195	-0.0276696532438	-0.0895794827629	0.350433394204	0.00797021734499	0.332618501826	49.0401698492	78.170851806	-15.553442704

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid -1 through 125 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 126 through 183 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 184 through 319 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 320 through 434 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 435 through 483 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 484 through 562 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid -1 through 81 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 82 through 405 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 406 through 562 )

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