PDB-7f81: Structure of the bacterial cellulose synthase subunit Z from Ente...

ID or keywords:

Entry

Database: PDB / ID: 7f81

Title

Structure of the bacterial cellulose synthase subunit Z from Enterobacter sp. CJF-002

Components

Glucanase

Keywords

HYDROLASE /

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: 1.93 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 ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/f8/7f81 ftp://data.pdbj.org/pub/pdb/validation_reports/f8/7f81	HTTPS FTP

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Related structure data

Related structure data	7f82C 3qxfS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	7f81-3 3qxf-3 3qxf-4 7f82-2 3qxq-1 6hfd-d 4q88-1 7jvv-1 3qxf-1 1nnb-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

7f82C

3qxfS

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

160 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
39.7 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Glucanase

hetero molecules

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

3

C: Glucanase

hetero molecules

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

4

D: Glucanase

hetero molecules

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

Unit cell

Length a, b, c (Å)	89.267, 91.454, 89.931
Angle α, β, γ (deg.)	90.000, 98.154, 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

NCS domain segments:

Ens-ID: 1

Dom-ID	Component-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	CYS	CYS	PRO	PRO	(chain 'A' and (resid 22 through 44 or resid 46...	A	A	22 - 44	6 - 28
1	2	ASP	ASP	ILE	ILE	(chain 'A' and (resid 22 through 44 or resid 46...	A	A	46 - 244	30 - 228
1	3	VAL	VAL	GLU	GLU	(chain 'A' and (resid 22 through 44 or resid 46...	A	A	246 - 265	230 - 249
1	4	LEU	LEU	TRP	TRP	(chain 'A' and (resid 22 through 44 or resid 46...	A	A	267 - 359	251 - 343
1	5	GOL	GOL	GOL	GOL	(chain 'A' and (resid 22 through 44 or resid 46...	A	E - F	401 - 402
2	1	CYS	CYS	PRO	PRO	(chain 'B' and (resid 22 through 44 or resid 46...	B	B	22 - 44	6 - 28
2	2	ASP	ASP	ILE	ILE	(chain 'B' and (resid 22 through 44 or resid 46...	B	B	46 - 244	30 - 228
2	3	VAL	VAL	GLU	GLU	(chain 'B' and (resid 22 through 44 or resid 46...	B	B	246 - 265	230 - 249
2	4	LEU	LEU	TRP	TRP	(chain 'B' and (resid 22 through 44 or resid 46...	B	B	267 - 359	251 - 343
2	5	GOL	GOL	GOL	GOL	(chain 'B' and (resid 22 through 44 or resid 46...	B	G - H	401 - 402
3	1	CYS	CYS	PRO	PRO	(chain 'C' and (resid 22 through 44 or resid 46...	C	C	22 - 44	6 - 28
3	2	ASP	ASP	ILE	ILE	(chain 'C' and (resid 22 through 44 or resid 46...	C	C	46 - 244	30 - 228
3	3	VAL	VAL	GLU	GLU	(chain 'C' and (resid 22 through 44 or resid 46...	C	C	246 - 265	230 - 249
3	4	LEU	LEU	TRP	TRP	(chain 'C' and (resid 22 through 44 or resid 46...	C	C	267 - 359	251 - 343
3	5	GOL	GOL	GOL	GOL	(chain 'C' and (resid 22 through 44 or resid 46...	C	N - O	401 - 402
4	1	CYS	CYS	PRO	PRO	(chain 'D' and (resid 22 through 44 or resid 46...	D	D	22 - 44	6 - 28
4	2	ASP	ASP	ILE	ILE	(chain 'D' and (resid 22 through 44 or resid 46...	D	D	46 - 244	30 - 228
4	3	VAL	VAL	GLU	GLU	(chain 'D' and (resid 22 through 44 or resid 46...	D	D	246 - 265	230 - 249
4	4	LEU	LEU	TRP	TRP	(chain 'D' and (resid 22 through 44 or resid 46...	D	D	267 - 359	251 - 343
4	5	GOL	GOL	GOL	GOL	(chain 'D' and (resid 22 through 44 or resid 46...	D	T - U	401 - 402

#1: Protein	Glucanase / Mass: 39479.418 Da / Num. of mol.: 4 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
#2: Chemical	... ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol Mass: 92.094 Da / Num. of mol.: 21 / Source method: obtained synthetically / Formula: C₃H₈O₃
#3: Chemical	ChemComp-SRT / S,R MESO-TARTARIC ACID Mass: 150.087 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₄H₆O₆
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 957 / Source method: isolated from a natural source / Formula: H₂O
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: 2.3 Å³/Da / Density % sol: 46.55 %
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-NW12A / Wavelength: 1 Å
Detector	Type: ADSC QUANTUM 210r / Detector: CCD / Date: Feb 18, 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: 1.93→50 Å / Num. obs: 107156 / % possible obs: 99.7 % / Redundancy: 3.8 % / B_iso Wilson estimate: 25.33 Å² / CC_1/2: 0.999 / R_merge(I) obs: 0.063 / R_rim(I) all: 0.073 / Net I/σ(I): 18.26
Reflection shell	Resolution: 1.93→2.05 Å / Redundancy: 3.8 % / R_merge(I) obs: 0.597 / Mean I/σ(I) obs: 2.57 / Num. unique obs: 17297 / CC_1/2: 0.837 / R_rim(I) all: 0.696 / % possible all: 99.3

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Processing

Software

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

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3QXF

3qxf

Resolution: 1.93→38.34 Å / SU ML: 0.194 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.5141
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.1968	5341	4.99 %
R_work	0.1622	101767	-
obs	0.164	107108	99.72 %

Solvent computation

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

Displacement parameters

B_iso mean: 31.37 Å²

Refinement step

Cycle: LAST / Resolution: 1.93→38.34 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10832	0	146	957	11935

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0092	11341
X-RAY DIFFRACTION	f_angle_d	0.9521	15435
X-RAY DIFFRACTION	f_chiral_restr	0.0611	1594
X-RAY DIFFRACTION	f_plane_restr	0.0076	1992
X-RAY DIFFRACTION	f_dihedral_angle_d	19.4286	4100

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 (%)
1.93-1.95	0.3292	176	0.2629	3306	X-RAY DIFFRACTION	97.13
1.95-1.98	0.2683	188	0.2427	3372	X-RAY DIFFRACTION	99.92
1.98-2	0.2722	181	0.2246	3400	X-RAY DIFFRACTION	99.78
2-2.03	0.2631	174	0.2163	3365	X-RAY DIFFRACTION	99.92
2.03-2.05	0.269	194	0.2146	3364	X-RAY DIFFRACTION	99.86
2.05-2.08	0.2604	165	0.2104	3407	X-RAY DIFFRACTION	99.92
2.08-2.11	0.2343	185	0.1941	3325	X-RAY DIFFRACTION	99.8
2.11-2.14	0.2257	159	0.1831	3433	X-RAY DIFFRACTION	99.75
2.14-2.17	0.2471	177	0.1891	3407	X-RAY DIFFRACTION	99.69
2.17-2.21	0.2575	193	0.1805	3340	X-RAY DIFFRACTION	99.89
2.21-2.25	0.2361	155	0.1786	3426	X-RAY DIFFRACTION	99.83
2.25-2.29	0.2299	161	0.1788	3398	X-RAY DIFFRACTION	99.78
2.29-2.33	0.2305	176	0.1742	3381	X-RAY DIFFRACTION	99.92
2.33-2.38	0.2217	174	0.1698	3343	X-RAY DIFFRACTION	99.89
2.38-2.43	0.2074	186	0.1677	3412	X-RAY DIFFRACTION	99.78
2.43-2.49	0.2024	176	0.1619	3369	X-RAY DIFFRACTION	99.77
2.49-2.55	0.208	174	0.1593	3443	X-RAY DIFFRACTION	99.97
2.55-2.62	0.2205	187	0.1618	3370	X-RAY DIFFRACTION	99.89
2.62-2.7	0.2139	180	0.1616	3361	X-RAY DIFFRACTION	99.89
2.7-2.78	0.2049	161	0.1677	3420	X-RAY DIFFRACTION	99.83
2.78-2.88	0.1757	176	0.1659	3390	X-RAY DIFFRACTION	99.94
2.88-3	0.2243	161	0.1588	3414	X-RAY DIFFRACTION	99.89
3-3.14	0.1898	223	0.157	3366	X-RAY DIFFRACTION	99.89
3.14-3.3	0.2037	171	0.1547	3413	X-RAY DIFFRACTION	99.86
3.3-3.51	0.176	161	0.1482	3406	X-RAY DIFFRACTION	99.8
3.51-3.78	0.1714	174	0.1455	3426	X-RAY DIFFRACTION	99.83
3.78-4.16	0.1543	172	0.1394	3410	X-RAY DIFFRACTION	99.83
4.16-4.76	0.15	179	0.1244	3438	X-RAY DIFFRACTION	99.83
4.76-5.99	0.1761	189	0.1563	3421	X-RAY DIFFRACTION	99.72
5.99-38.34	0.1645	213	0.1594	3441	X-RAY DIFFRACTION	98.97

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	0.000228279681304	0.00116695523494	-0.00118940188304	0.000383956892486	-0.000722154187377	0.000925802337235	-0.0199346643656	0.0191761771844	0.0126517133208	-0.0120167166442	-0.0240056020665	-0.020991816928	0.00209908709367	-0.00711375135313	1.17844226653E-6	0.428580419061	0.0483723189939	0.0791730286421	0.335919571556	0.0586590945213	0.232436699056	-36.5508478449	-6.7244872556	31.441995836
2	0.0655154935907	-0.0479384968778	-0.00784059440636	0.0460955381213	0.00580834761633	0.0761309729166	-0.07089960922	0.0832148210795	-0.025240483487	-0.0532822473453	-0.0782880421757	-0.103590165788	0.00899317564208	0.0720736441465	-0.0734006621532	0.348975350864	0.0906147205569	0.157298534737	0.324580619385	0.0491708426074	0.245247107944	-23.8538642045	-14.6638391466	39.6771782552
3	0.00446732969365	-0.00439765645487	-0.0045983556596	0.00190997488513	0.00163991998452	0.0106893653587	-0.05243013036	-0.0111023830291	0.0219860790183	-0.0295679128728	-0.0555685917674	-0.0755837395811	0.0327841571054	0.0426919998953	-0.00034895689224	0.224257892557	0.0589939777909	0.0222656391645	0.170298432631	0.045625875931	0.194156361005	-30.4916086057	-13.5808243534	57.5353757291
4	0.0160126914204	0.0028961202928	-0.00728002102735	0.002051680944	-0.00391317289189	0.008765155732	-0.0640536920887	0.0119667696861	0.0496554365119	-0.0332504133499	-0.0439359980351	-0.0241590314869	-0.0413827889387	-0.0319368352386	-0.0384105027736	0.201980448759	0.0782927437501	-0.0101143821062	0.0970398686154	0.003573226496	0.087070233406	-45.3185566592	-10.3621473273	50.1098629142
5	0.00202837293733	-0.00221829375799	0.000633745833617	0.002518077183	-0.00228409766138	0.00332181754094	-0.010855182428	0.0205208043064	-0.0182126935082	-0.00866901551824	-0.0184665466298	0.0117314198205	0.0122919865057	-0.0323907226414	-4.08059695947E-6	0.440461423438	0.114255484062	-0.152604217704	0.419203244244	-0.0372078729009	0.267202886216	15.8512190711	-6.24005785279	31.5138737023
6	0.0500522292583	0.000273645347161	0.0290279030551	0.0100012374943	-0.00481087618837	0.0150958238977	-0.0919509786483	0.0788221762181	0.0658288119134	-0.032261133686	-0.0660945055054	0.0807645559664	-0.0853245486327	-0.130332103864	-0.0649254079593	0.239028305465	0.274806439688	-0.325672742012	0.543755456832	-0.156726746905	0.154744104659	3.0816312166	-9.56350562817	42.4021108449
7	0.00991893418591	-0.000310103698119	0.00314534979243	0.0140178226253	-0.00148336880081	0.0128961400043	-0.0944520678623	0.025250677173	-0.0197419889583	-0.014756604882	0.0123622621447	0.0182105435955	0.00467599958312	-0.117257387821	-0.0170986546486	0.223938715919	0.0637096539398	-0.031982983692	0.38963175447	-0.14765179689	0.187144645061	9.53242041662	-25.6136857368	50.2557498138
8	0.042314017459	-0.00685372498824	0.00281131673332	0.00671920080906	0.00736990672491	0.0609834798342	-0.0985065741197	0.0666657658883	-0.00395495617755	-0.0245126589982	-0.0513101715276	0.0202262647043	0.00641267137258	-0.0797928321165	-0.0509552393562	0.278604450268	0.0775246270277	-0.0184444789393	0.27821025142	-0.0949351557659	0.164848817782	24.6451774973	-20.5184391428	43.8004833888
9	0.00170250663549	0.000147902020542	0.00308152882479	0.000390706782704	0.000713027847497	0.00183335952554	-0.016979269304	-0.0264275169817	-0.00418529711435	0.0126409346663	-0.0229649053936	0.00411405776888	-0.00940255743561	0.021290908646	1.41257260722E-6	0.242820094092	0.042730572476	0.000775457500801	0.204550829515	0.00548495757359	0.193195383739	35.5105369894	-13.8767046556	13.4191424826
10	0.0201500847497	0.001731306484	-0.0119968822834	0.0189873496553	-0.0114993450151	0.0311380840554	-0.0459235346272	0.0299480458663	-0.194742925658	0.0564311577563	-0.0647725162934	0.0655349876319	-0.0608994232655	-0.122925176879	-0.00188457142891	0.144905878333	0.025430208453	0.0335694612917	0.161155897811	-0.0140666463763	0.266927455325	22.2815290417	-19.5767873492	3.30881460228
11	0.0108715824103	0.0040172726861	-0.00322658899915	0.00864032074026	-0.00241867412721	0.0130521524882	0.00461323296776	0.103293899034	-0.0686985721855	-0.0593855581384	-0.0550853746289	0.0487311618506	-0.0506585308498	-0.111216003161	-0.0116573821285	0.161415209852	0.0570505725786	0.00119205037514	0.173181098305	-0.0752269512451	0.206034362638	29.2288321789	-14.7073148904	-13.8482353869
12	0.0324830683634	-0.00509613968269	0.0135346634367	0.0263713503023	0.00274716841795	0.0343706434806	-0.0203046547487	0.0210838088613	-0.0594811422261	-0.00305308950027	-0.0392783235239	0.0196956530368	-0.0846936981753	0.00667445183329	-0.0325325290833	0.114798559721	0.0320471731525	0.00460881044273	0.0927646506362	-0.0256400878246	0.148737966193	44.1425328641	-13.7088155528	-5.91921522331
13	0.00308392388982	0.0017125609113	-0.00145427898223	0.00146505431627	0.00121514632311	0.00316037470178	0.0086228801135	-0.0255968084492	-4.52880610862E-5	0.0171632253117	-0.00612563498328	0.0108457387695	0.00499439401644	0.0104512617858	-7.62537223349E-7	0.20736155247	0.0800910411006	-0.037332599624	0.266453796576	-0.0386702256348	0.201563834084	-16.8528152216	-15.0910281688	12.994100512
14	0.0209596053087	0.00914022417615	-0.00562801356575	0.0201253090457	0.00309179546712	0.00582075532874	-0.0405956266631	-0.0887275986539	0.0708837025331	0.0521994439327	-0.0131345587424	-0.118959259975	-0.0215090355553	0.0701320065331	-0.00015406362515	0.145050045053	0.0260172889655	-0.0341532721023	0.187392653938	-0.00765817768698	0.24081715135	-4.22566179744	-16.4368600895	1.49480153989
15	0.0114481646783	0.00312717927324	-0.00159568177708	0.00408853258872	0.00299390701703	0.00282817347042	0.00441818113177	0.0387132425186	-0.0320417370867	-0.00938670816235	0.0040627339313	-0.0374731252989	0.0164548201483	0.00447994756342	5.17477393367E-6	0.142117789679	0.0458604525093	0.00107369856535	0.138575921094	0.0123132114645	0.17008392924	-11.433786032	-30.1143248853	-9.63405246745
16	0.0294161756123	-0.00285051429993	-0.00187814644961	0.00691233678958	0.000737971334218	0.00226980690344	-0.00546211160841	-0.0252993670335	-0.0250952714587	-0.0225486601151	-0.0100987304307	0.0608241089403	0.00887673865391	-0.0203153693127	1.39555223614E-6	0.146225478265	0.0195246334358	0.000477566989378	0.146985143559	0.003055469735	0.187763330081	-26.2613896794	-25.8514320838	-2.14271678328

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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