PDB-8csd: WbbB D232C Kdo adduct

ID or keywords:

Entry

Database: PDB / ID: 8csd

Title

WbbB D232C Kdo adduct

Components

N-acetyl glucosaminyl transferase

Keywords

TRANSFERASE / Glycsoyltransferase / retaining / donor adduct intermediate

Function / homology

Function and homology information

polysaccharide transport / polysaccharide biosynthetic process / transferase activity
Similarity search - Function

Biological species

Raoultella terrigena (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.95 Å

Authors

Forrester, T.J.B. / Kimber, M.S.

Funding support

Canada, 1items

Citation

Journal: Nat Commun / Year: 2022
Title: The retaining beta-Kdo glycosyltransferase WbbB uses a double-displacement mechanism with an intermediate adduct rearrangement step.
Authors: Forrester, T.J.B. / Ovchinnikova, O.G. / Li, Z. / Kitova, E.N. / Nothof, J.T. / Koizumi, A. / Klassen, J.S. / Lowary, T.L. / Whitfield, C. / Kimber, M.S.

History

Deposition	May 12, 2022	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 9, 2022	Provider: repository / Type: Initial release
Revision 1.1	Oct 18, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2	Nov 15, 2023	Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / struct_ref Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2 / _struct_ref.pdbx_seq_one_letter_code
Revision 1.3	Oct 9, 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	8csd.cif.gz	569.8 KB	Display	PDBx/mmCIF format
PDB format	pdb8csd.ent.gz	393.5 KB	Display	PDB format
PDBx/mmJSON format	8csd.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8csd_validation.pdf.gz	1.8 MB	Display	wwPDB validaton report
Full document	8csd_full_validation.pdf.gz	1.8 MB	Display
Data in XML	8csd_validation.xml.gz	33.5 KB	Display
Data in CIF	8csd_validation.cif.gz	48.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/cs/8csd ftp://data.pdbj.org/pub/pdb/validation_reports/cs/8csd	HTTPS FTP

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Related structure data

Related structure data	8csbC 8cscC 8cseC 8csfC 5fa1S S: Starting model for refinement C: citing same article (ref.)
Similar structure data	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

Deposited unit

A: N-acetyl glucosaminyl transferase

B: N-acetyl glucosaminyl transferase

hetero molecules

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

1

A: N-acetyl glucosaminyl transferase

hetero molecules

A: N-acetyl glucosaminyl transferase

hetero molecules

defined by author&software
Evidence: gel filtration
93.4 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: N-acetyl glucosaminyl transferase

hetero molecules

B: N-acetyl glucosaminyl transferase

hetero molecules

defined by author&software
Evidence: gel filtration
93.5 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	93.010, 156.730, 118.020
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	20
Space group name H-M	C222₁
Space group name Hall	C2c2
Symmetry operation	#1: x,y,z #2: x,-y,-z #3: -x,y,-z+1/2 #4: -x,-y,z+1/2 #5: x+1/2,y+1/2,z #6: x+1/2,-y+1/2,-z #7: -x+1/2,y+1/2,-z+1/2 #8: -x+1/2,-y+1/2,z+1/2

Components on special symmetry positions

ID	Model	Components
1	1	A-610- HOH

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Protein / Sugars , 2 types, 4 molecules AB

#1: Protein

N-acetyl glucosaminyl transferase / retaining Kdo transferase

Mass: 46100.824 Da / Num. of mol.: 2 / Mutation: D232C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Raoultella terrigena (bacteria) / Gene: wbbB / Plasmid: pET28a / Production host:

Escherichia coli (E. coli) / References: UniProt: Q6U8B0

#3: Sugar

ChemComp-KDO / 3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid / 3-deoxy-d-manno-oct-2-ulopyranosonic acid / 2-keto-3-deoxy-D-mannooctanoic acid / 3-deoxy-alpha-D-manno-oct-2-ulosonic acid / 3-deoxy-D-manno-oct-2-ulosonic acid / 3-deoxy-manno-oct-2-ulosonic acid

Type: D-saccharide, alpha linking / Mass: 238.192 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₈H₁₄O₈ / Feature type: SUBJECT OF INVESTIGATION

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Non-polymers , 4 types, 364 molecules

#2: Chemical	ChemComp-C5P / CYTIDINE-5'-MONOPHOSPHATE Mass: 323.197 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₉H₁₄N₃O₈P / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 357 / 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: 2.42 Å³/Da / Density % sol: 49.1 % / Description: prisms
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 200 mM ammonium sulfate, 100 mM Bis-Tris, 25% (w/v) PEG 3350

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.9795 Å
Detector	Type: RAYONIX MX300HE / Detector: CCD / Date: Aug 30, 2016
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9795 Å / Relative weight: 1
Reflection	Resolution: 1.95→47.5 Å / Num. obs: 62946 / % possible obs: 99.9 % / Redundancy: 5.7 % / B_iso Wilson estimate: 35.24 Å² / R_sym value: 0.069 / Net I/σ(I): 13.8
Reflection shell	Resolution: 1.95→2 Å / Mean I/σ(I) obs: 2.05 / Num. unique obs: 4594 / CC_1/2: 0.817 / R_sym value: 0.877

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Processing

Software

Name	Version	Classification
PHENIX	1.19_4092	refinement
XDS		data reduction
XSCALE		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5FA1

5fa1

Resolution: 1.95→47.49 Å / SU ML: 0.2027 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.5005
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.1988	3147	5 %
R_work	0.1617	59781	-
obs	0.1636	62928	99.86 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 45.46 Å²

Refinement step

Cycle: LAST / Resolution: 1.95→47.49 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6264	0	77	357	6698

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0142	6541
X-RAY DIFFRACTION	f_angle_d	1.0321	8904
X-RAY DIFFRACTION	f_chiral_restr	0.0681	991
X-RAY DIFFRACTION	f_plane_restr	0.0104	1147
X-RAY DIFFRACTION	f_dihedral_angle_d	15.5975	2312

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 (%)
1.95-1.98	0.3304	143	0.2727	2705	X-RAY DIFFRACTION	99.86
1.98-2.01	0.2837	140	0.2484	2657	X-RAY DIFFRACTION	99.86
2.01-2.05	0.2456	142	0.2106	2698	X-RAY DIFFRACTION	99.96
2.05-2.08	0.2447	141	0.198	2678	X-RAY DIFFRACTION	99.93
2.08-2.12	0.2341	143	0.1893	2710	X-RAY DIFFRACTION	99.79
2.12-2.17	0.231	140	0.184	2684	X-RAY DIFFRACTION	99.86
2.17-2.22	0.247	143	0.1775	2710	X-RAY DIFFRACTION	100
2.22-2.27	0.2244	141	0.174	2686	X-RAY DIFFRACTION	100
2.27-2.32	0.2016	142	0.1652	2699	X-RAY DIFFRACTION	99.96
2.32-2.39	0.2208	143	0.1528	2715	X-RAY DIFFRACTION	100
2.39-2.46	0.1856	143	0.1594	2708	X-RAY DIFFRACTION	99.93
2.46-2.54	0.2135	141	0.1575	2685	X-RAY DIFFRACTION	99.86
2.54-2.63	0.2103	142	0.1629	2697	X-RAY DIFFRACTION	99.89
2.63-2.73	0.2319	143	0.1765	2716	X-RAY DIFFRACTION	99.79
2.73-2.86	0.227	143	0.1864	2718	X-RAY DIFFRACTION	99.9
2.86-3.01	0.2055	143	0.1695	2711	X-RAY DIFFRACTION	99.89
3.01-3.2	0.2254	143	0.1765	2725	X-RAY DIFFRACTION	99.86
3.2-3.44	0.2146	143	0.1596	2721	X-RAY DIFFRACTION	99.69
3.44-3.79	0.1941	144	0.1449	2734	X-RAY DIFFRACTION	99.79
3.79-4.34	0.1549	146	0.1274	2763	X-RAY DIFFRACTION	99.86
4.34-5.46	0.1317	146	0.1318	2779	X-RAY DIFFRACTION	99.86
5.46-47.49	0.2093	152	0.1753	2882	X-RAY DIFFRACTION	99.44

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	1.06982273815	-0.127347480405	-0.566726271395	0.611479449681	0.886963512251	1.36359357742	-0.0734268868121	-0.372881811427	-0.529377160302	0.619302726228	0.0350979181781	-0.136468592167	0.630167576453	0.291538927299	8.85547751603E-6	0.637581088873	0.0816783851188	-0.0472640805596	0.471052423542	0.0595866433606	0.55269061218	26.3008708737	22.1197593065	36.5425605489
2	0.34545573669	0.457509465189	0.124260235478	0.63978804801	0.00307048182161	0.702421055176	0.151508395696	-0.568163690095	-0.329756702028	0.727322537922	-0.129364713088	-0.223884541782	0.641495544345	0.422576091486	0.000556916033955	0.682463546688	0.0757201695893	-0.0701971534807	0.600172200645	0.0197048882068	0.465301850915	25.774310716	28.5765532337	41.5399319019
3	0.324839669914	0.283582180479	0.200181037109	2.64288560562	1.21565893195	2.25245301824	0.0339483660475	-0.123106660755	0.0472911240671	0.438948070686	0.0463160561028	-0.153016572706	0.13079377673	0.209153141827	-0.000454748819634	0.284746136824	0.0168448596578	0.00792812289756	0.332571142788	-0.0205138675667	0.27372472816	23.4142176309	35.9620410289	31.8173661587
4	1.30382497574	-0.625051133044	-0.16335421613	1.48197558404	0.612258430525	2.06449622804	0.00334358247919	0.119323508541	-0.0014805219164	-0.443832508003	-0.0190227848665	0.0498905642657	-0.0333171971561	0.0692387844118	-4.23908393777E-5	0.355482610252	0.0322817882446	0.0194355022811	0.333096687941	-0.0238541973421	0.308527791708	20.6355635159	25.7103672218	8.62400021532
5	1.40757957024	-0.905067786685	-0.609943758256	1.07668838688	0.0398856052888	2.28019641029	-0.0535643018149	-0.0720657467001	-0.256193244607	0.081463743556	-0.0308643711419	0.443153811663	0.192608394104	-0.261670645271	-1.74033079536E-5	0.325041254294	-0.00620435373333	0.0674212379367	0.343164245881	-0.0312563537846	0.442414740721	1.60094325587	20.1046423222	20.7223458037
6	1.6508665153	0.18921078705	-0.855494292036	2.41129577635	0.848852049463	1.45215675803	0.00390752371647	0.0855024369335	0.0921107757943	-0.133971467549	0.0182112174706	0.0446727119685	0.0327387892472	-0.0139696533274	1.39113190627E-5	0.259824641958	0.0568029470219	0.0262448310134	0.2897980507	-0.019006765521	0.235850179848	18.7544463822	26.5482861917	12.2791769687
7	1.00163236871	-0.324572318623	0.556069755737	0.467964137307	-0.217246060545	1.27928966084	-0.0394910577164	0.406566922095	-0.0683602943158	-0.348306155706	0.363028605007	-0.774487431208	0.291437704413	0.879874628734	0.0116111772025	0.401037137406	0.0821731425887	0.0967024602461	0.589660432277	-0.0964099884061	0.523716926453	34.0048306731	22.5052099953	4.86503597536
8	1.63707687719	-0.565681120673	-0.110511405269	1.14837733396	0.279877311966	1.73887694436	0.138361531249	0.547352480428	0.353398878802	-1.00003222278	-0.0919980075774	0.0112970821286	-0.867838098854	0.0042431417696	-0.00243713623456	0.924350216384	-0.0220816519712	0.0944973439202	0.457999307779	0.0152568651345	0.444960705376	21.8785142842	67.2270320109	12.8092909419
9	0.686650080479	-0.160881994068	0.688531812402	3.07951030603	0.64634678031	2.47691717725	0.108121615243	0.0571626171474	-0.0897475094822	-0.770468984581	-0.0107850159153	-0.0669016684958	-0.263829727456	0.130843209854	0.00230443046276	0.415743114441	-0.00515598966444	0.0199871143505	0.278344384785	-0.0247180705589	0.254957355719	20.6904856844	52.2015747256	17.1371907036
10	0.968731403077	0.0666476324654	-0.596614787978	1.59001500392	0.907839552621	0.938129397198	0.00819671274656	-0.178994735745	0.0693747165462	0.222625804211	0.21545932206	-0.367797503877	-0.0995829208839	0.283211589043	-7.8704237532E-5	0.330246199932	-0.057804761585	-0.015633751952	0.367669135587	-0.061480653314	0.363792392811	27.64097205	63.8160464034	39.9939087688
11	2.67028871546	1.14479255579	0.332735473742	1.9779396439	0.242090323391	1.92996224334	0.102549564509	-0.13163730781	0.409103543939	-0.0438813382919	-0.109022885029	0.334309695863	-0.218568598109	-0.142468098653	3.22168531092E-5	0.319972310954	-0.00816239258089	-0.00749779357009	0.31210934822	-0.0424754492686	0.394323105055	8.32222948326	72.940997003	40.0548367656
12	0.651818614489	-0.108498653369	0.00182875978618	0.740995923105	-0.0793708492053	0.535382797944	0.00098525544237	-0.234906395074	0.00390935805668	0.206117920446	0.0615542620279	-0.020959345287	0.0469405800225	0.0881136032037	-4.35572839152E-5	0.304868306264	-0.0452484065753	-0.0371261841269	0.366611584168	-0.0319116561943	0.285056113426	20.7719761919	62.3352159243	45.5201645936
13	1.39030076775	-0.561822791574	-0.429188399248	1.60325511452	-0.382590044473	1.16425433816	-0.120413361672	-0.286781668831	-0.0454281144185	-0.0218014504546	0.39684312705	-1.13697406206	-0.399114392695	0.899812386386	0.0313214877453	0.305861828488	-0.138916430188	0.0652504542772	0.564034924203	-0.152921632475	0.621645451671	37.5641373787	63.738697837	35.5821528675

Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

ID	Refine TLS-ID	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	chain 'A' and (resid 1 through 64 )	A	A	1 - 64	1 - 64
2	2	chain 'A' and (resid 65 through 94 )	A	A	65 - 94	65 - 94
3	3	chain 'A' and (resid 95 through 170 )	A	A	95 - 170	95 - 170
4	4	chain 'A' and (resid 171 through 222 )	A	A	171 - 222	171 - 220
5	5	(chain 'A' and (resid 223 through 284 )) or (chain D and resid 1)	A - D	A - E	223 - 1	221
6	6	chain 'A' and (resid 285 through 365 )	A	A	285 - 365	283 - 363
7	7	chain 'A' and (resid 366 through 406 )	A	A	366 - 406	364 - 397
8	8	chain 'B' and (resid 1 through 94 )	B	B	1 - 94	1 - 94
9	9	chain 'B' and (resid 95 through 159 )	B	B	95 - 159	95 - 159
10	10	chain 'B' and (resid 160 through 208 )	B	B	160 - 208	160 - 208
11	11	(chain 'B' and (resid 209 through 309 )) or (chain D and resid 2)	B - D	B - F	209 - 2	209
12	12	chain 'B' and (resid 310 through 342 )	B	B	310 - 342	310 - 342
13	13	chain 'B' and (resid 343 through 403 )	B	B	343 - 403	343 - 393

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Non-polymers , 4 types, 364 molecules

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-Non-polymers , 4 types, 364 molecules

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Protein / Sugars , 2 types, 4 molecules AB

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Non-polymers , 4 types, 364 molecules

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Experimental details

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Yorodumi