PDB-7f82: Structure of the bacterial cellulose synthase subunit Z in comple...

ID or keywords:

Entry

Database: PDB / ID: 7f82

Title

Structure of the bacterial cellulose synthase subunit Z in complex with cellooligosaccharides from Enterobacter sp. CJF-002

Components

Glucanase

Keywords

HYDROLASE /

complex /

carbohydrate

Function / homology

Function and homology information

Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds /

cellulase activity / polysaccharide catabolic process
Similarity search - Function

Biological species

Enterobacter sp. CJF-002 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.3 Å

Authors

Fujiwara, T. / Fujishima, A. / Yao, M.

Citation

Journal: Acta Crystallogr.,Sect.D / Year: 2022
Title: Structural snapshot of a glycoside hydrolase family 8 endo-beta-1,4-glucanase capturing the state after cleavage of the scissile bond.
Authors: Fujiwara, T. / Fujishima, A. / Nakamura, Y. / Tajima, K. / Yao, M.

History

Deposition	Jun 30, 2021	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Feb 9, 2022	Provider: repository / Type: Initial release
Revision 1.1	Nov 29, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	7f82.cif.gz	691.1 KB	Display	PDBx/mmCIF format
PDB format	pdb7f82.ent.gz	473 KB	Display	PDB format
PDBx/mmJSON format	7f82.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/f8/7f82 ftp://data.pdbj.org/pub/pdb/validation_reports/f8/7f82	HTTPS FTP

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Related structure data

Related structure data	7f81SC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	7f82-3 7f81-3 3qxf-4 3qxf-3 1vd5-d 5tht-3 3otx-2 2fvl-2 2fv1-1 6ry6-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) 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

Related structure data

7f81SC

S: Starting model for refinement

C: citing same article (ref.)

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#74 - Feb 2006 alpha-Amylase similarity (2)

Deposited unit

A: Glucanase

B: Glucanase

C: Glucanase

D: Glucanase

hetero molecules

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

1

A: Glucanase

hetero molecules

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

2

B: Glucanase

hetero molecules

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

3

C: Glucanase

hetero molecules

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

4

D: Glucanase

hetero molecules

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

Unit cell

Length a, b, c (Å)	89.280, 92.860, 90.500
Angle α, β, γ (deg.)	90.000, 98.410, 90.000
Int Tables number	4
Space group name H-M	P12₁1
Space group name Hall	P2yb
Symmetry operation	#1: x,y,z #2: -x,y+1/2,-z

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID
1	1
2	1
3	1
4	1

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Protein , 1 types, 4 molecules ABCD

#1: Protein	Glucanase / Mass: 39435.410 Da / Num. of mol.: 4 / Mutation: D242A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterobacter sp. CJF-002 (bacteria) / Gene: bcsZ / Production host: Escherichia coli (E. coli) References: UniProt: K0IUV6, Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds

#1: Protein

Glucanase /

Mass: 39435.410 Da / Num. of mol.: 4 / Mutation: D242A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Enterobacter sp. CJF-002 (bacteria) / Gene: bcsZ / Production host:

Escherichia coli (E. coli)
References: UniProt: K0IUV6,

Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds

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Sugars , 3 types, 10 molecules

#2: Polysaccharide

beta-D-glucopyranose-(1-4)-beta-D-glucopyranose

Type: oligosaccharide

, Oligosaccharide

/ Class: Metabolism

/ Mass: 342.297 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: beta-cellobiose

#3: Polysaccharide

beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose

Type: oligosaccharide

, Oligosaccharide

/ Class: Metabolism

/ Mass: 504.438 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: beta-cellotriose

Descriptor	Type	Program
DGlcpb1-4DGlcpb1-4DGlcpb1-ROH	Glycam Condensed Sequence	GMML 1.0
WURCS=2.0/1,3,2/[a2122h-1b_1-5]/1-1-1/a4-b1_b4-c1	WURCS	PDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{}}}	LINUCS	PDB-CARE

#4: Polysaccharide

beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose

Type: oligosaccharide

, Oligosaccharide

/ Class: Metabolism

/ Mass: 666.578 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: beta-cellotetraose

Descriptor	Type	Program
DGlcpb1-4DGlcpb1-4DGlcpb1-4DGlcpb1-ROH	Glycam Condensed Sequence	GMML 1.0
WURCS=2.0/1,4,3/[a2122h-1b_1-5]/1-1-1-1/a4-b1_b4-c1_c4-d1	WURCS	PDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{}}}}	LINUCS	PDB-CARE

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Non-polymers , 2 types, 1181 molecules

#5: Chemical	ChemComp-SRT / S,R MESO-TARTARIC ACID Mass: 150.087 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₄H₆O₆
#6: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 1179 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	N

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.35 Å³/Da / Density % sol: 47.66 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.2 M di-sodium tartrate, 20%(v/v) PEG3350

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
Detector	Type: ADSC QUANTUM 270 / Detector: CCD / Date: Nov 10, 2013
Radiation	Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.3→50 Å / Num. obs: 355775 / % possible obs: 99.5 % / Redundancy: 4.2 % / B_iso Wilson estimate: 16.77 Å² / CC_1/2: 1 / R_merge(I) obs: 0.03 / R_rim(I) all: 0.033 / Net I/σ(I): 21.4
Reflection shell	Resolution: 1.3→1.38 Å / Redundancy: 3.5 % / R_merge(I) obs: 0.567 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 57751 / CC_1/2: 0.873 / R_rim(I) all: 0.669 / % possible all: 98.8

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Processing

Software

Name	Version	Classification
PHENIX	1.17.1_3660	refinement
PHENIX		phasing
XSCALE		data scaling
XDS		data reduction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 7F81

7f81

Resolution: 1.3→42.51 Å / SU ML: 0.1432 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.681
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.1866	17934	5.04 %
R_work	0.1689	337646	-
obs	0.1698	355580	99.47 %

Solvent computation

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

Displacement parameters

B_iso mean: 25.56 Å²

Refinement step

Cycle: LAST / Resolution: 1.3→42.51 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10820	0	349	1179	12348

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0139	11713
X-RAY DIFFRACTION	f_angle_d	1.5728	16034
X-RAY DIFFRACTION	f_chiral_restr	0.1779	1754
X-RAY DIFFRACTION	f_plane_restr	0.0105	2025
X-RAY DIFFRACTION	f_dihedral_angle_d	23.0347	1523

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 (%)
1.3-1.31	0.3518	541	0.3428	10842	X-RAY DIFFRACTION	95.48
1.31-1.33	0.3136	614	0.3085	11166	X-RAY DIFFRACTION	99.46
1.33-1.35	0.2909	572	0.2864	11250	X-RAY DIFFRACTION	99.55
1.35-1.36	0.2949	586	0.2794	11225	X-RAY DIFFRACTION	99.59
1.36-1.38	0.2861	578	0.2552	11242	X-RAY DIFFRACTION	99.5
1.38-1.4	0.2702	607	0.2507	11268	X-RAY DIFFRACTION	99.66
1.4-1.42	0.242	539	0.2316	11264	X-RAY DIFFRACTION	99.68
1.42-1.44	0.2382	645	0.2186	11225	X-RAY DIFFRACTION	99.76
1.44-1.46	0.2139	606	0.2073	11274	X-RAY DIFFRACTION	99.63
1.46-1.49	0.2172	594	0.2025	11207	X-RAY DIFFRACTION	99.65
1.49-1.51	0.2408	619	0.1943	11218	X-RAY DIFFRACTION	99.67
1.51-1.54	0.2041	585	0.1784	11319	X-RAY DIFFRACTION	99.79
1.54-1.57	0.1968	657	0.1767	11183	X-RAY DIFFRACTION	99.61
1.57-1.6	0.2051	610	0.1762	11222	X-RAY DIFFRACTION	99.73
1.6-1.64	0.1892	629	0.1693	11252	X-RAY DIFFRACTION	99.73
1.64-1.68	0.2022	626	0.1672	11230	X-RAY DIFFRACTION	99.61
1.68-1.72	0.2018	615	0.1728	11266	X-RAY DIFFRACTION	99.65
1.72-1.76	0.1948	602	0.1693	11215	X-RAY DIFFRACTION	99.71
1.76-1.82	0.1994	594	0.1661	11296	X-RAY DIFFRACTION	99.64
1.82-1.87	0.1856	588	0.1632	11250	X-RAY DIFFRACTION	99.41
1.87-1.94	0.1974	629	0.1633	11240	X-RAY DIFFRACTION	99.4
1.94-2.02	0.1768	556	0.166	11283	X-RAY DIFFRACTION	99.49
2.02-2.11	0.1766	573	0.1639	11317	X-RAY DIFFRACTION	99.64
2.11-2.22	0.1686	615	0.1566	11209	X-RAY DIFFRACTION	99.41
2.22-2.36	0.1885	581	0.1611	11267	X-RAY DIFFRACTION	99.36
2.36-2.54	0.1854	565	0.1628	11333	X-RAY DIFFRACTION	99.34
2.54-2.8	0.1844	558	0.174	11338	X-RAY DIFFRACTION	99.43
2.8-3.21	0.1821	604	0.1659	11333	X-RAY DIFFRACTION	99.74
3.21-4.04	0.1682	621	0.1553	11405	X-RAY DIFFRACTION	99.84
4.04-42.51	0.158	625	0.1454	11507	X-RAY DIFFRACTION	99.81

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	0.0510847799	0.0313941026049	-0.076976076436	0.0961817836204	0.0608443574936	0.128730806975	-0.0501159973183	0.052416407018	0.0430487487649	0.0312766207421	0.00180493806737	0.056218748191	0.0445077860657	-0.25700837945	-0.000690255888788	0.196935429836	-0.0222926958565	0.0316723652501	0.193813781764	-0.0195847908244	0.218912240144	-8.57817396804	6.3930288072	-32.4700189795
2	0.518306097222	-0.0882053193276	-0.339033081701	0.483225908721	-0.0665049637404	0.940039080908	0.0350260338416	-0.168218046479	0.0492385552238	0.154724392705	-0.0488199324665	0.0870061358146	-0.0598470717346	-0.183080959358	0.0124692563152	0.228699644463	0.0104493337606	0.0474137180507	0.168367852478	-0.0365879389429	0.187001293263	-2.7179417492	14.4042630481	-18.5826344519
3	0.548119471388	-0.00575788145473	-0.103133126527	0.306750903701	0.18808413724	0.649647356825	0.00679170115509	-0.151084324696	0.0342583738076	0.107358902279	-0.00299412578251	-0.0293640956419	0.00467835926397	0.112620080813	0.00203669704774	0.217338613815	0.00117181318515	-0.000350638700276	0.132321095301	-0.0158265407866	0.164076257613	16.0269974315	13.8915585833	-22.1777189352
4	0.221785676721	-0.0424910157098	-0.21925331142	0.168590846103	-0.045271702775	1.05567144032	0.00956309436664	0.116738982231	-0.0174637094755	0.0455862844438	-0.036248799266	0.0200926953452	0.0184031578264	0.037056886408	-0.0285464677462	0.130669562564	0.0093798247404	0.0165422627879	-0.00380210141934	-0.0283635983751	0.11338005077	11.1783588238	10.7605539134	-38.2378897491
5	0.168872472998	0.0403848225497	-0.0999765497762	0.129609236062	0.154058249732	0.166195629304	0.0220056666917	0.157509985222	-0.0562049919147	-0.0555874384532	-0.0395229729481	0.116723764981	0.00853653642901	-0.300612742732	3.21338093248E-5	0.198770923458	0.00420198388439	-0.0411882285407	0.329051526107	-0.0740669573582	0.240667676698	-15.8904414808	6.50872640688	20.6902883374
6	0.383534530894	0.0244393595267	-0.0586795259092	0.59355420757	0.109605194261	0.527159598767	0.0869721697403	0.341372644579	-0.097451143055	-0.176826306832	-0.0523611122854	0.0200814021207	0.0513521174375	-0.0695881812321	0.0838311189672	0.216676401611	0.0724531174529	-0.0210050396743	0.301039556311	-0.0776901530005	0.169277255112	-3.003188826	9.85768359474	9.94749126833
7	0.166977051241	0.0895315101996	-0.0626962212453	0.408071420314	0.305074409078	0.451088362762	0.0688877406886	0.204634909526	-0.0105190923488	-0.080762006748	-0.00859880161455	-0.0269508266032	-0.0568427471526	-0.0135312285813	0.000237850660924	0.17095948473	0.0662014169592	0.0247580516472	0.216840557266	0.0141516422642	0.155246375162	3.81061750978	25.8132766448	17.6322252302
8	0.397104988683	-0.0346891241777	-0.265791052725	0.324269905709	-0.215580522137	0.746805612361	0.0784640870687	0.126137985935	-0.000356143821148	0.038667565824	-0.0210963549032	0.0148127631789	-0.0296756479476	-0.154115025272	0.0592976243124	0.103979675865	0.0505354597981	0.00864305311763	0.10223074206	-0.0160053061799	0.104484235687	-5.26255782891	20.933239053	31.5810431783
9	0.0608920936606	-0.0165051509487	-0.0643757018653	0.0707840605855	-0.0268580912034	0.0653710139943	0.00561192867863	-0.0441678792634	-0.0128011756768	0.0565215796104	0.113553565469	-0.185990510604	0.100965536763	0.284704687999	0.000166738238845	0.18320340724	0.022560177941	-0.0223619097359	0.322258358742	-0.0305626699586	0.341239276758	-36.7384014537	13.1372575585	39.2859044369
10	0.40538827825	-0.0404314441191	-0.269446465798	0.57925745975	0.163120220499	0.319348776767	0.122327788344	0.302594322382	0.0807396715099	-0.0842172323542	-0.0628688016706	-0.173846795953	-0.0239778822487	0.194100550061	0.000931865068117	0.17648743572	0.0159597072966	0.035831073848	0.329572429777	0.0302070753848	0.282984717383	-43.973484645	18.8181306215	24.881814374
11	0.595908151307	-0.0199866115145	0.327673554616	0.314276192637	0.0988458111376	0.454114117255	0.106286326998	0.254684121363	-0.0232322249723	-0.0553887465911	-0.0587769191049	-0.00351647071012	0.0369259941121	0.143202183297	4.9612350044E-5	0.174952225669	0.0540831143646	0.00354802662096	0.215388039906	-0.0154082232984	0.220853597936	-62.2214638406	14.800852658	28.6952024851
12	0.459413645852	-0.152259045955	0.12922862273	0.11991984078	0.0380750516451	0.762551675814	0.0743240656135	0.0114209200575	-0.0495844210959	0.0156986357167	-0.00433401665686	-0.0569882713506	0.0643720308797	0.124772529487	0.00886596837285	0.115267563606	0.0274058878711	-0.0191751000807	0.111548911239	-0.012932566136	0.165497940513	-56.9285731506	13.9233698244	44.8967870775
13	0.064322430523	0.0519682202174	-0.00848391281948	0.0727238253498	-0.0648596933505	0.0922841361727	-0.0155804082422	-0.137531168705	-0.0351327022201	0.00853645181436	0.0723358618307	-0.0471519690038	0.0527293947249	0.328469674353	0.000180157997998	0.225942472842	0.0553413756906	-0.0667090133753	0.387119844824	-0.0383050608207	0.250860133936	-29.4581178057	15.1161605842	-13.8501500444
14	0.356938178488	0.0402313045504	0.263177782204	0.483714475604	-0.236809088275	0.218080601776	-0.0139552226884	-0.401221386264	-0.0295027518558	0.133761916478	0.10908776957	-0.0780927147157	0.0354585847081	0.0271533820242	0.0077562895227	0.243103850187	0.0545259111352	-0.0550234204461	0.387521606884	-0.00694217564357	0.203606956671	-42.9101918453	16.3899298887	-3.36474737088
15	0.269960543455	-0.106718609078	-0.0213668704186	0.246342916979	-0.265590370109	0.421612187608	-0.0277297578004	-0.203453413814	0.0738034716784	0.0537139828376	0.0769621248534	-0.0148682754711	-0.0515588478031	0.000871724066859	3.67984011191E-5	0.204406849693	0.00138171085833	-0.0198063005374	0.251415465318	-0.0469471621873	0.220001383691	-52.6097079474	30.0225681163	-12.2511930356
16	0.409082929453	-0.125651067326	-0.0520770339	0.28679632584	0.203798864205	0.50418879074	0.0153446657408	-0.072430982597	0.0699785994261	-0.0132840014303	0.0585500911337	-0.0710670647513	-0.0203836112837	0.133275157441	0.000135782201211	0.113405735289	-0.0123384550432	-0.0247493672243	0.13534136581	-0.0190116781964	0.149818886412	-42.8884431127	26.0872217024	-25.7376235417

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 22 through 52 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 53 through 173 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 174 through 259 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 260 through 359 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 22 through 52 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 53 through 173 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 174 through 259 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 260 through 359 )
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 22 through 52 )
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 53 through 173 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 174 through 259 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 260 through 359 )
13	X-RAY DIFFRACTION	13	chain 'D' and (resid 22 through 52 )
14	X-RAY DIFFRACTION	14	chain 'D' and (resid 53 through 173 )
15	X-RAY DIFFRACTION	15	chain 'D' and (resid 174 through 259 )
16	X-RAY DIFFRACTION	16	chain 'D' and (resid 260 through 359 )

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