PDB-6wbt: 2.52 Angstrom Resolution Crystal Structure of 6-phospho-alpha-glu...

ID or keywords:

Entry

Database: PDB / ID: 6wbt

Title

2.52 Angstrom Resolution Crystal Structure of 6-phospho-alpha-glucosidase from Gut Microorganisms in Complex with NAD and Glucose-6-phosphate

Components

cellulase IBT99

Keywords

HYDROLASE / 6-phospho-alpha-glucosidase / Gut Microorganisms

Function / homology

6-O-phosphono-alpha-D-glucopyranose / : / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / PHOSPHATE ION

Function and homology information

Biological species

metagenomes (others)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.52 Å

Authors

Wu, R. / Kim, Y. / Endres, M. / Joachimiak, J.

Citation

Journal: To Be Published
Title: 2.52 Angstrom Resolution Crystal Structure of 6-phospho-alpha-glucosidase from Gut Microorganisms in Complex with NAD and Glucose-6-phosphate
Authors: Wu, R. / Kim, Y. / Endres, M. / Joachimiak, J.

History

Deposition	Mar 27, 2020	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 31, 2021	Provider: repository / Type: Initial release
Revision 1.1	Oct 18, 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
Revision 1.2	Nov 15, 2023	Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.3	Nov 20, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6wbt.cif.gz	742.8 KB	Display	PDBx/mmCIF format
PDB format	pdb6wbt.ent.gz	594 KB	Display	PDB format
PDBx/mmJSON format	6wbt.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	6wbt_validation.pdf.gz	2.3 MB	Display	wwPDB validaton report
Full document	6wbt_full_validation.pdf.gz	2.4 MB	Display
Data in XML	6wbt_validation.xml.gz	63.9 KB	Display
Data in CIF	6wbt_validation.cif.gz	84.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/wb/6wbt ftp://data.pdbj.org/pub/pdb/validation_reports/wb/6wbt	HTTPS FTP

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Related structure data

Related structure data	1u8xS S: Starting model for refinement
Similar structure data	5oie-1 6ck1-d 6vc6-d 5oju-1 7a17-d 5ohz-d 5oi0-1 5oiw-1 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: cellulase IBT99

B: cellulase IBT99

C: cellulase IBT99

D: cellulase IBT99

hetero molecules

209 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	102.797, 219.724, 97.978
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁
Space group name Hall	P2ac2ab
Symmetry operation	#1: x,y,z #2: x+1/2,-y+1/2,-z #3: -x,y+1/2,-z+1/2 #4: -x+1/2,-y,z+1/2

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Protein / Sugars , 2 types, 7 molecules ABCD

#1: Protein

cellulase IBT99

Mass: 51384.422 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) metagenomes (others) / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21DE3 / Variant (production host): gold

#3: 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.: 3
Source method: isolated from a genetically manipulated source
Formula: C₆H₁₃O₉P / Feature type: SUBJECT OF INVESTIGATION

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Non-polymers , 5 types, 196 molecules

#2: Chemical	ChemComp-MN / MANGANESE (II) ION Mass: 54.938 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: Mn
#4: Chemical	ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂₁H₂₇N₇O₁₄P₂ / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#5: Chemical	ChemComp-PO4 / PHOSPHATE ION Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO₄
#6: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₆O₂
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 185 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	Y
Has protein modification	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.74 Å³/Da / Density % sol: 55.13 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.2 Details: 0.2 M NaCl, 0.1 M Na/K phosphate pH 6.2, 20 %(w/v) PEG1000

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792 Å
Detector	Type: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Oct 19, 2019
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9792 Å / Relative weight: 1
Reflection	Resolution: 2.52→75.09 Å / Num. obs: 70393 / % possible obs: 92.7 % / Redundancy: 3.4 % / B_iso Wilson estimate: 54.48 Å² / CC_1/2: 0.981 / R_merge(I) obs: 0.121 / Net I/σ(I): 5
Reflection shell	Resolution: 2.52→2.56 Å / Redundancy: 3.4 % / R_merge(I) obs: 0.978 / Mean I/σ(I) obs: 1 / Num. unique obs: 3335 / CC_1/2: 0.402 / % possible all: 89.4

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Processing

Software

Name	Version	Classification
PHENIX	1.13_2998	refinement
HKL-3000		data reduction
HKL-3000		data scaling
HKL-3000		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1U8X

1u8x

Resolution: 2.52→70.92 Å / Cross valid method: FREE R-VALUE

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.266	3582	5 %	random
R_work	0.227	-	-	-
obs	0.229	66728	92.87 %	-

Displacement parameters

B_iso mean: 63.73 Å²

Refinement step

Cycle: LAST / Resolution: 2.52→70.92 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	14066	0	181	185	14432

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0017	14539
X-RAY DIFFRACTION	f_angle_d	0.4893	19691
X-RAY DIFFRACTION	f_chiral_restr	0.0417	2196
X-RAY DIFFRACTION	f_plane_restr	0.0033	2487
X-RAY DIFFRACTION	f_dihedral_angle_d	20.8524	5593

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 (%)
2.52-2.55	0.3423	106	0.3364	2619	X-RAY DIFFRACTION	95.38
2.55-2.59	0.3635	133	0.3533	2617	X-RAY DIFFRACTION	94.86
2.59-2.63	0.3891	127	0.3388	2596	X-RAY DIFFRACTION	95.54
2.63-2.66	0.4455	126	0.326	2621	X-RAY DIFFRACTION	95.08
2.66-2.71	0.3384	150	0.3282	2572	X-RAY DIFFRACTION	94.81
2.71-2.75	0.3378	133	0.2977	2579	X-RAY DIFFRACTION	94.86
2.75-2.8	0.3502	132	0.3053	2598	X-RAY DIFFRACTION	94.2
2.8-2.85	0.3329	138	0.2907	2602	X-RAY DIFFRACTION	95.14
2.85-2.9	0.3286	124	0.2889	2504	X-RAY DIFFRACTION	91.41
2.9-2.96	0.2992	124	0.2926	2589	X-RAY DIFFRACTION	93.49
2.96-3.03	0.3153	127	0.2771	2596	X-RAY DIFFRACTION	94.58
3.03-3.1	0.3463	145	0.2819	2568	X-RAY DIFFRACTION	94.04
3.1-3.17	0.2918	152	0.2902	2541	X-RAY DIFFRACTION	93.25
3.17-3.26	0.3497	161	0.29	2543	X-RAY DIFFRACTION	93.34
3.26-3.36	0.3119	132	0.2687	2552	X-RAY DIFFRACTION	93.1
3.36-3.47	0.3215	149	0.2467	2590	X-RAY DIFFRACTION	93.58
3.47-3.59	0.2736	145	0.2315	2465	X-RAY DIFFRACTION	90.47
3.59-3.73	0.2727	149	0.2158	2570	X-RAY DIFFRACTION	93.37
3.73-3.9	0.2456	146	0.2053	2563	X-RAY DIFFRACTION	92.87
3.9-4.11	0.2515	132	0.1883	2539	X-RAY DIFFRACTION	91.57
4.11-4.37	0.2424	155	0.1742	2506	X-RAY DIFFRACTION	91.44
4.37-4.7	0.2194	123	0.1738	2551	X-RAY DIFFRACTION	90.43
4.7-5.18	0.2116	151	0.1708	2580	X-RAY DIFFRACTION	92.7
5.18-5.92	0.226	156	0.2035	2535	X-RAY DIFFRACTION	90.61
5.92-7.46	0.2635	135	0.2112	2506	X-RAY DIFFRACTION	87.86
7.46-70.92	0.1656	131	0.1656	2626	X-RAY DIFFRACTION	87.58

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	0.806907179814	-0.428520585321	-0.376880914668	0.354233426016	-0.112775011012	0.339671645316	-0.0272891571787	0.510078409541	0.0273425626214	-0.084853370326	-0.0717185777295	0.380994113004	0.350545594132	-0.52782948857	0.156491901436	0.541721863606	-0.185257314836	-0.00715181894119	0.946600659449	-0.055202067011	0.857942679028	-29.1269377878	4.06022194962	21.462350467
2	1.44266697266	-0.321090190702	-0.848717255223	0.979937337026	0.765805518869	2.42756902611	-0.00491717940244	0.0664272203345	-0.269965826164	-0.0539794276113	-0.0285355034384	0.11114730479	-0.0425344727212	-0.445216221414	0.0664922400827	0.257596198083	0.0295216696321	-0.0503011022088	0.448955882957	0.0222973701011	0.370816104779	-14.0756326997	19.128793532	17.8140079586
3	0.941584110212	-0.512811811912	-0.483989491481	1.58746961503	0.715562950711	1.60247886001	-0.0533293327055	-0.0521179793662	-0.104670410479	-0.0299498803446	0.0764100351157	-0.0921539009325	0.130602642019	0.290780502543	-0.0458636821407	0.324995231265	0.0440756671615	-0.0145838324956	0.458190569885	-0.0192058185282	0.470363768473	27.7573711018	1.21703739686	9.88614487256
4	3.89195786732	0.676437052756	-0.277605822441	2.28716586153	0.212781351129	4.5040285771	-0.21776531396	0.533456453636	-0.437789087905	-0.570031757277	0.279213880443	-0.1035168647	0.343889730383	0.252890603882	-0.0745943502692	0.538561061793	0.0086535924258	-0.00797619030769	0.485072309813	-0.103890315028	0.484059210219	10.6983975281	11.5544032588	-8.48007003899
5	0.653684475808	-0.990875523956	-0.608457489635	0.640448530763	0.120733455934	0.717697669014	0.0221892058038	0.150302100031	-0.222489940676	-0.0562748978188	-0.0357165935192	0.00958679122184	0.146352877545	-0.0169265972297	0.013639504788	0.371352225425	0.00467586527973	-0.0234675775437	0.403484571871	-0.0309300219821	0.503496016904	12.9921576414	4.45290395997	8.17273155568
6	1.06352137626	0.368047048422	0.188676072416	1.65302685676	0.375799467844	0.601429142521	0.0186594731038	0.187482787841	0.0931867533802	-0.23012646493	0.0609355294367	-0.170632819103	-0.294885682354	0.24797215777	-0.0746450353651	0.605896100544	-0.149841711987	0.0301992297132	0.472510421769	0.0401194710884	0.345434659158	22.199920404	55.8012898292	-5.61063229945
7	0.740771894375	-0.334205037947	-0.304179463733	1.41142754357	-0.0631491097489	2.5974126704	0.036808163295	0.124054847744	-0.117775236541	-0.12944713417	0.0696504982111	-0.0594828754689	-0.368351714356	-0.145366174893	-0.102245642295	0.553777832116	-0.111796229295	0.0223326291249	0.393110984652	0.0130804589283	0.395919527074	12.4687480706	49.3433532279	5.12212461861
8	2.86361156879	-1.53404100257	0.323688798082	1.84202152608	-0.355812977924	2.93849159281	0.0705780167828	0.149965100622	-0.166951379888	-0.175049481759	-0.0856785886229	-0.499101451418	-0.295603266201	0.747829747025	0.00802279204179	0.512156387111	-0.173283531093	0.0190040723266	0.561449984846	-0.0394651721939	0.52069106286	35.6373348431	41.4199498461	15.9586426546
9	0.157080188941	-0.781004543054	0.449533138413	3.98062652967	-2.07486722678	1.07759404956	-0.159011013433	-0.00507358094267	0.115332788399	0.413862504911	0.139319872152	-0.198993685565	-0.625332358692	0.157825482635	0.0626060319502	0.753941088069	-0.229776166247	-0.00847204905919	0.712241332642	-0.0499180940026	0.569760406986	28.4214163578	54.1834598082	22.5192608798
10	0.852156880445	0.220352657394	-0.679515870726	1.19018291286	-1.10901435128	0.550327393496	0.0173507175345	0.0302076318003	0.0343654121515	0.0390997966185	-0.0134983478196	-0.0178560747769	-0.334604786205	0.170198833893	-0.0177400382844	0.507434932014	-0.105236526518	-0.014512035544	0.343037810222	-0.0131372983697	0.306554018014	17.0481458053	49.1172867566	11.1555124121
11	1.99695804974	0.672092902272	-0.765000319773	0.988977425192	0.109437916217	2.57262071169	0.100170082428	-0.516398340372	-0.16783837576	0.193600127647	-0.128850178423	-0.061032454958	-0.221562612032	0.213404281162	0.0214679297007	0.415732394128	0.00611994340791	-0.0448546247185	0.563964049283	0.0864573668762	0.303558361235	4.78355529336	33.4602229829	57.9907192751
12	3.89290294536	0.677342619204	-0.992413582079	2.64569482782	-0.233480119698	3.40417724052	0.355345762045	-0.660749106828	0.355313416089	0.41063638261	0.00768060719451	0.382858857184	-0.696837997811	0.0874426051886	-0.344452977875	0.815513406866	0.0540297546053	0.10378165518	0.501250116864	0.0172731493653	0.447043446485	-6.51472722385	51.5798844032	41.8819711817
13	1.15556679698	0.566734442364	-0.000781296260238	0.0533980186628	0.269485429177	2.5326182864	0.135999671342	-0.275259908744	0.0460577075462	0.190937802256	-0.0525555198367	-0.0241744501393	-0.494545235407	0.0775732755705	-0.0836256196483	0.498437659847	-0.0207778285613	0.00593164049159	0.359023059203	0.0219682000786	0.372048359726	6.67932021484	40.3342129959	46.9972462462
14	3.75916069014	-0.600962199875	-0.803595669976	4.80996187391	0.0942314227667	3.52843656394	0.106450077076	-0.183424433758	-0.610202707762	0.108620418746	-0.272293807411	0.62221585794	0.135798108144	-1.28142452137	0.17350193571	0.358385362162	0.101967811563	-0.0140352465475	1.0082318591	0.0641082751249	0.64949803633	-37.248719382	23.7786377255	28.1197740117
15	1.58606881073	0.118688641942	-0.240550695631	1.1457319475	-0.011488496208	1.98686543594	0.080844568292	0.321108083612	-0.216448303957	0.0175448911103	-0.0723706986819	0.332646100843	-0.133214450037	-1.00413528149	0.0134906553912	0.364902997084	0.0722420178479	-0.0404151529521	0.943496445538	0.0130225047601	0.501632549049	-30.9267764842	22.6356766638	18.6559590658
16	2.82708438545	0.398545249869	-0.569212103665	4.28762858154	-0.317009194795	3.9036509748	-0.133574294987	-0.0999449161349	-0.405159280358	0.38133222257	0.12151465249	0.0928877650822	0.531861316083	-0.296947597185	0.0443804399058	0.395457858087	-0.0236433184591	0.0368616283561	0.540122048423	0.0959303660107	0.561208252745	-16.8946148501	10.988295803	35.8906950828
17	3.62601670834	-1.04425125616	-2.58488540018	5.68895211708	0.8491294164	6.3535842296	-0.297994877985	-0.231726534166	-0.88909242759	0.118662317738	-0.272972131465	0.314420546907	0.587631603952	0.0391149753803	0.54199917997	0.56532486017	-0.0775959896834	0.0652046716892	0.471773994315	0.0720471526892	0.649859400254	-14.7556852092	0.665718516135	36.5890437037

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'D' and (resid 256 through 319 )
2	X-RAY DIFFRACTION	2	chain 'D' and (resid 320 through 443 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 2 through 174 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 175 through 256 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 257 through 443 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 2 through 104 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 105 through 174 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 175 through 243 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 244 through 293 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 294 through 443 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 3 through 174 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 175 through 278 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 279 through 443 )
14	X-RAY DIFFRACTION	14	chain 'D' and (resid 2 through 26 )
15	X-RAY DIFFRACTION	15	chain 'D' and (resid 27 through 174 )
16	X-RAY DIFFRACTION	16	chain 'D' and (resid 175 through 210 )
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 211 through 255 )

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Protein / Sugars , 2 types, 7 molecules ABCD

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Non-polymers , 5 types, 196 molecules

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-Non-polymers , 5 types, 196 molecules

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Protein / Sugars , 2 types, 7 molecules ABCD

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Non-polymers , 5 types, 196 molecules

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Details

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Experimental details

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Experiment

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Sample preparation

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Data collection

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Processing

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About Yorodumi

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

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Yorodumi