PDB-6uiq: Crystal structure of wild-type human phosphoglucomutase 1 in comp...

ID or keywords:

Entry

Database: PDB / ID: 6uiq

Title

Crystal structure of wild-type human phosphoglucomutase 1 in complex with Glucose-6-Phosphate

Components

phosphoglucomutase-1

Keywords

ISOMERASE / phosphoglucomutase / G6P

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 ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.3 Å

Authors

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

Funding support

United States, 2items

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	Oct 1, 2019	Deposition site: RCSB / Processing site: RCSB
Supersession	Aug 12, 2020	ID: 6BJ0
Revision 1.0	Aug 12, 2020	Provider: repository / Type: Initial release
Revision 1.1	Oct 11, 2023	Group: 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

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	6uiq.cif.gz	548.2 KB	Display	PDBx/mmCIF format
PDB format	pdb6uiq.ent.gz	374.4 KB	Display	PDB format
PDBx/mmJSON format	6uiq.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	6uiq_validation.pdf.gz	375.3 KB	Display	wwPDB validaton report
Full document	6uiq_full_validation.pdf.gz	375.8 KB	Display
Data in XML	6uiq_validation.xml.gz	1.5 KB	Display
Data in CIF	6uiq_validation.cif.gz	15.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ui/6uiq ftp://data.pdbj.org/pub/pdb/validation_reports/ui/6uiq	HTTPS FTP

-
Related structure data

Related structure data	5vbiC 5vecC 5vg7C 5vinC 5epcS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	5hsh-2 1lxt-2 5jn5-1 6uo6-1 1vkl-1 1jdy-2 3pmg-1 5vin-1 2r0p-d 5epc-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

-
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

B: phosphoglucomutase-1

A: phosphoglucomutase-1

hetero molecules

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

1

B: phosphoglucomutase-1

hetero molecules

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

2

A: phosphoglucomutase-1

hetero molecules

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

Unit cell

Length a, b, c (Å)	171.874, 171.874, 99.447
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

#1: Protein

phosphoglucomutase-1

Mass: 64191.734 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Homo sapiens (human) / Production host:

Escherichia coli (E. coli)
References: UniProt: P36871, phosphoglucomutase (alpha-D-glucose-1,6-bisphosphate-dependent)

#2: Sugar

ChemComp-G6P / 6-O-phosphono-alpha-D-glucopyranose / ALPHA-D-GLUCOSE-6-PHOSPHATE / 6-O-phosphono-alpha-D-glucose / 6-O-phosphono-D-glucose / 6-O-phosphono-glucose

Type: D-saccharide, alpha linking / Mass: 260.136 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C₆H₁₃O₉P / Feature type: SUBJECT OF INVESTIGATION

#3: Chemical

ChemComp-MG / MAGNESIUM ION

Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg

#4: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 568 / Source method: isolated from a natural source / Formula: H₂O

Has ligand of interest

Y

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.86 Å³/Da / Density % sol: 57 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.3 Details: 0.2 M Sodium tartrate dibasic dihydrate, 20% w/v Polyethylene glycol 3,350

-
Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

ALS

/ Beamline: 4.2.2 / Wavelength: 1.00003 Å

Detector

Type: RDI CMOS_8M / Detector: CMOS / Date: Sep 23, 2017

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 1.00003 Å / Relative weight: 1

Reflection

Resolution: 2.3→60.82 Å / Num. obs: 64976 / % possible obs: 97.8 % / Redundancy: 13.5 % / B_iso Wilson estimate: 33.8431148121 Å² / CC_1/2: 0.998 / R_merge(I) obs: 0.16 / R_pim(I) all: 0.045 / R_rim(I) all: 0.167 / Net I/σ(I): 14.8 / Num. measured all: 878402 / Scaling rejects: 2

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. measured all	Num. unique obs	CC_1/2	R_pim(I) all	R_rim(I) all	Net I/σ(I) obs	% possible all
2.3-2.36	9.9	1.774	37536	3790	0.656	0.573	1.868	1.3	82.6
10.54-60.82	12.7	0.035	10241	809	0.999	0.01	0.036	51.5	99.4

-
Processing

Software

Name	Version	Classification
PHENIX	1.11.1_2575	refinement
Aimless	0.5.32	data scaling
PDB_EXTRACT	3.25	data extraction
XDS		data reduction
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5EPC

5epc

Resolution: 2.3→60.81 Å / SU ML: 0.249218060444 / Cross valid method: FREE R-VALUE / σ(F): 1.3503266864 / Phase error: 23.6345935342

	R_factor	Num. reflection	% reflection
R_free	0.222518346102	3287	5.06713530346 %
R_work	0.168233215946	-	-
obs	0.170935744974	64869	97.6016731114 %

Solvent computation

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

Displacement parameters

B_iso mean: 43.1234874366 Å²

Refinement step

Cycle: LAST / Resolution: 2.3→60.81 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8581	0	34	568	9183

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.00728842100076	8865
X-RAY DIFFRACTION	f_angle_d	0.892534842951	12025
X-RAY DIFFRACTION	f_chiral_restr	0.0548393087957	1359
X-RAY DIFFRACTION	f_plane_restr	0.00521783820272	1568
X-RAY DIFFRACTION	f_dihedral_angle_d	14.5754824728	5321

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 (%)
2.3-2.3343	0.259155238288	104	0.242999601592	2197	X-RAY DIFFRACTION	80.7935393258
2.3343-2.3708	0.293033319418	140	0.234626583338	2288	X-RAY DIFFRACTION	84.9545136459
2.3708-2.4097	0.2724409445	134	0.222227652338	2441	X-RAY DIFFRACTION	90.4143258427
2.4097-2.4512	0.291794398277	139	0.220346870794	2530	X-RAY DIFFRACTION	93.8797045375
2.4512-2.4958	0.267894455212	155	0.210668260529	2570	X-RAY DIFFRACTION	95.5469845722
2.4958-2.5438	0.310906071032	170	0.210943177724	2664	X-RAY DIFFRACTION	99.7536078845
2.5438-2.5957	0.286070159726	127	0.207194030297	2723	X-RAY DIFFRACTION	99.8948475289
2.5957-2.6522	0.238070641468	155	0.199418544704	2715	X-RAY DIFFRACTION	99.930362117
2.6522-2.7139	0.276550441952	150	0.197253107263	2690	X-RAY DIFFRACTION	99.9296270232
2.7139-2.7817	0.303555510546	130	0.197449013615	2728	X-RAY DIFFRACTION	99.8602375961
2.7817-2.857	0.2948508965	147	0.211833208146	2724	X-RAY DIFFRACTION	99.8956158664
2.857-2.941	0.275895633537	136	0.217637661653	2714	X-RAY DIFFRACTION	100
2.941-3.0359	0.250045018256	147	0.203161327187	2724	X-RAY DIFFRACTION	99.9303863557
3.0359-3.1444	0.254021183984	145	0.192773519056	2734	X-RAY DIFFRACTION	100
3.1444-3.2703	0.245018101216	142	0.194316709356	2739	X-RAY DIFFRACTION	100
3.2703-3.4192	0.213485890633	149	0.191076023895	2745	X-RAY DIFFRACTION	99.9654576857
3.4192-3.5994	0.235451380792	132	0.162589663716	2760	X-RAY DIFFRACTION	100
3.5994-3.8249	0.178934732749	139	0.139408179275	2767	X-RAY DIFFRACTION	100
3.8249-4.1202	0.168289282756	165	0.131377561145	2734	X-RAY DIFFRACTION	100
4.1202-4.5347	0.184659171135	153	0.120731340024	2776	X-RAY DIFFRACTION	99.9658703072
4.5347-5.1905	0.169306156122	144	0.116248763953	2787	X-RAY DIFFRACTION	100
5.1905-6.5383	0.242910361841	143	0.152052652739	2844	X-RAY DIFFRACTION	100
6.5383-60.81	0.157359230151	141	0.149147359179	2988	X-RAY DIFFRACTION	99.5545657016

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	2.99900053296	0.0258484790583	0.396622748517	3.18123087564	0.553287999991	2.7772083207	0.0196659471738	-0.11300401773	-0.000999861581986	0.216565972629	0.0156504600792	-0.245502706163	0.476466438184	0.194646054763	-0.0336247884048	0.478894208232	0.0591892866222	-0.00373366912206	0.249220989739	0.00949139608988	0.299746070476	39.3441897281	-73.5186255531	9.68316996175
2	1.26084083681	-0.315674131327	0.166336241437	2.14081038307	0.200464117544	2.6149413185	-0.0075324738635	-0.00761854096608	-0.118532413491	0.183273254019	0.0667747089956	0.0261261024832	0.574977425354	0.04848517513	-0.0506959837945	0.314517068785	-0.035337871255	0.00206016043832	0.177731784115	-0.0130419228978	0.230892366605	33.3179999682	-70.678494641	0.505776955642
3	0.496160130998	-0.557377492788	0.209074859885	1.26891934968	0.54345851144	1.64726682132	-0.0175633432071	0.0624514176217	0.112908933136	-0.1338181076	0.0445173640136	-0.260673550606	-0.304301117335	0.122380835877	-0.0260572886512	0.274100280897	-0.101657514609	0.0262118178883	0.251166668876	0.0245851770748	0.302204004384	32.9269342803	-45.5321099537	-5.40468153798
4	0.897566032651	0.01826214887	0.285964164304	0.97642270562	0.0315857769193	2.36093997621	-0.0911562536777	-0.0181409459342	0.0738902935989	-0.0881671647812	0.0217666199738	0.0868455787265	-0.0732360026858	-0.278632803294	0.0480904491088	0.183786836812	-0.0124745182987	-0.0194488455826	0.231543471774	-0.0128794011939	0.298153938142	18.1994620695	-43.3531614054	6.30467618304
5	2.06733943264	-0.218259347313	0.380757168993	1.79440228992	0.789955750373	2.37432334605	0.035110933629	-0.451289395879	0.151357036824	0.236876635014	-0.0710432981894	0.0629657012768	0.0914914404867	-0.44810869713	0.0260092259261	0.253288010701	-0.0134568236243	0.00707399040978	0.475620045393	-0.00837094183507	0.288956631578	15.8560131954	-45.4127754021	30.5068321356
6	2.61841634704	1.34390938791	0.338348240193	3.51612869781	-0.63876624844	3.9579538732	0.0117225800553	-0.199949152801	-0.0657317235141	-0.0259957195391	0.0300497679966	-0.129379400502	0.223150721204	-0.136817001055	-0.0150984398117	0.159125541917	-0.0126503466697	-0.0344877425824	0.201788476702	-0.0225214332967	0.192876407561	20.6808162573	-45.7621913491	24.2488275989
7	3.06195848727	-0.748916913633	0.0986547597483	3.48932003902	-0.834626521241	2.93436180163	-0.0096294129408	-0.0827801573153	0.281593802122	0.0541341584644	-0.0334010148554	0.059041591296	-0.33803647649	-0.183892499291	0.0369765627063	0.218148022787	-0.0116033023479	-0.0450786736645	0.237419711922	-0.0733846371197	0.260061983494	26.1564226706	-34.0869023123	25.4487159415
8	2.50585232719	0.559499545484	0.0848178505942	3.08199920715	-0.600800629451	2.49543148022	-0.381417735157	0.529278137689	0.334351737549	-0.542054709626	0.515621613959	0.259435417146	0.435539447247	-0.468570455337	-0.157725142506	0.460532859193	-0.158992754013	-0.084991755552	0.524171183007	0.0779798419914	0.316443167844	-34.1321157772	-63.9866515432	-19.429552585
9	1.64937863453	0.990655476054	-0.45948308772	2.04080303486	-0.23220218466	2.7268191878	-0.133886138361	0.255140889395	0.014717765436	-0.254629474571	0.232254078932	0.152905222695	0.364158902989	-0.510683739418	-0.0980327013862	0.288295870656	-0.0322443549649	-0.0424497844806	0.356107386588	0.0427457328407	0.217369108461	-27.8932096246	-62.4591371538	-10.3712760575
10	1.8675265125	1.60146688977	-0.000538585569998	1.38449315963	-0.157114386154	2.11396393148	0.0704226967243	-0.103698169024	0.224359581506	0.210623799906	0.0317179305857	0.171140936777	-0.475817305923	-0.0596670747882	-0.118399986999	0.364190938669	0.0990301210909	0.0329406403904	0.26901683966	-0.0234460044023	0.312510360733	-17.0340232219	-42.1358812011	0.736806694802
11	1.3210466403	0.44642116853	-0.172096421521	1.75279167958	-0.332941152103	3.27979856363	-0.0730110978177	0.14504451528	0.152937760263	0.047189930633	0.155498171198	0.125789375375	-0.424072873717	-0.0316993703974	-0.0781861573854	0.256886798492	0.0296229750293	-0.0202763540797	0.267726340503	0.0258271279079	0.25581107134	-12.105139494	-40.2688617263	-12.2160872344
12	1.52208945487	-0.623821660485	0.179931421157	1.59479580147	0.0161694156259	4.79218780996	0.0006047111255	0.25806992492	0.213022511166	-0.0349027362315	0.0744785928541	-0.128488409914	-0.939775879002	0.252917627446	-0.0184748096146	0.448738364632	-0.0609940821704	9.5195443743E-5	0.333273380395	0.0603764374985	0.350013523279	-7.90273247809	-30.815667028	-21.7706954885
13	3.87906637364	0.0559320905675	0.415900175728	1.94853483056	-0.0197176151661	2.60029980717	0.258442069242	0.654873977741	0.166513019402	-0.383354720291	-0.210594793507	-0.147661916357	-0.337720977627	0.230215532199	-0.0821467068939	0.522215963553	-0.0236274232896	-0.00226100698568	0.667849680147	0.070034441096	0.358427745225	-6.61247394855	-39.5446781165	-45.3228592351
14	1.9074331589	-0.99170532418	0.852943342143	2.82044973543	-0.252914304397	3.04492124445	-0.0124159392918	0.371358844526	-0.00661052034921	-0.19123220626	0.137325999139	0.0118200683312	0.215759646342	0.0852862829623	-0.138467490812	0.329957859504	-0.0346395377772	-0.0013767797359	0.489148760879	-0.00765329596374	0.238874780139	-5.83122834451	-45.8458015492	-34.5129950108
15	2.94658779068	-0.24502224498	-0.238366818582	1.75778179917	-0.0648576628358	2.25102251763	-0.0402085984974	0.43709660495	0.424941740407	-0.132301807601	-0.0051478323352	0.0600363343817	-0.934100865758	0.0803958094728	0.0436644821507	0.557412621328	-0.0222397541376	-0.0226909611329	0.402499082719	0.101636025011	0.318270688288	-11.302747391	-30.9817130846	-34.6903624977

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'B' and (resid -1 through 46 )
2	X-RAY DIFFRACTION	2	chain 'B' and (resid 47 through 183 )
3	X-RAY DIFFRACTION	3	chain 'B' and (resid 184 through 293 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 294 through 434 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 435 through 483 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 484 through 522 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 523 through 562 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid -1 through 46 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 47 through 183 )
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 184 through 227 )
11	X-RAY DIFFRACTION	11	chain 'A' and (resid 228 through 405 )
12	X-RAY DIFFRACTION	12	chain 'A' and (resid 406 through 434 )
13	X-RAY DIFFRACTION	13	chain 'A' and (resid 435 through 464 )
14	X-RAY DIFFRACTION	14	chain 'A' and (resid 465 through 511 )
15	X-RAY DIFFRACTION	15	chain 'A' and (resid 512 through 562 )

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
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

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi