PDB-8bn7: CjCel5C endo-glucanase

ID or keywords:

Entry

Database: PDB / ID: 8bn7

Title

CjCel5C endo-glucanase

Components

Cellulase, putative, cel5C

Keywords

HYDROLASE /

Carbohydrate /

inhibitor /

covalent /

cellulase

Function / homology

organic substance metabolic process /

Glycoside hydrolase, family 5 / Cellulase (glycosyl hydrolase family 5) /

cellulase /

cellulase activity / Glycoside hydrolase superfamily /

Cellulase, putative, cel5C

Function and homology information

Biological species

Cellvibrio japonicus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.182 Å

Authors

McGregor, N.G.S. / Davies, G.J.

Funding support

United Kingdom, European Union, 2items

Citation

Journal: To Be Published
Title: Dissection of a Native Bacterial Xyloglucan-degrading System using Activity-Based Probes
Authors: McGregor, N.G.S. / de Boer, C. / Foucart, Q. / Beenakker, T. / Willems, L. / Overkleeft, H.S. / Davies, G.J.

History

Deposition	Nov 13, 2022	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Nov 22, 2023	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	8bn7.cif.gz	396 KB	Display	PDBx/mmCIF format
PDB format	pdb8bn7.ent.gz		Display	PDB format
PDBx/mmJSON format	8bn7.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/bn/8bn7 ftp://data.pdbj.org/pub/pdb/validation_reports/bn/8bn7	HTTPS FTP

-
Related structure data

Related structure data	8bqaC 8bqbC 8bqcC 4htyS 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

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

CCC: Cellulase, putative, cel5C

AAA: Cellulase, putative, cel5C

BBB: Cellulase, putative, cel5C

121 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

CCC: Cellulase, putative, cel5C

defined by author
Evidence: gel filtration
40.2 kDa, 1 polymers

2

AAA: Cellulase, putative, cel5C

defined by author
40.2 kDa, 1 polymers

3

BBB: Cellulase, putative, cel5C

defined by author
40.2 kDa, 1 polymers

Unit cell

Length a, b, c (Å)	126.332, 175.709, 115.283
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	20
Space group name H-M	C222₁

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	CCC
2	1	AAA
3	2	CCC
4	2	BBB
5	3	AAA
6	3	BBB

NCS domain segments:

End auth comp-ID: ASN / End label comp-ID: ASN

Dom-ID	Component-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	1	THR	THR	CCC	A	8 - 337	8 - 337
2	1	1	THR	THR	AAA	B	8 - 337	8 - 337
3	2	2	GLN	GLN	CCC	A	6 - 337	6 - 337
4	2	2	GLN	GLN	BBB	C	6 - 337	6 - 337
5	3	3	THR	THR	AAA	B	8 - 337	8 - 337
6	3	3	THR	THR	BBB	C	8 - 337	8 - 337

NCS ensembles :

ID	Details
1	Local NCS retraints between domains: 1 2
2	Local NCS retraints between domains: 3 4
3	Local NCS retraints between domains: 5 6

#1: Protein	Cellulase, putative, cel5C / Mass: 40201.941 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Cellvibrio japonicus (bacteria) / Strain: Ueda107 / Gene: cel5C, CJA_3369 / Production host: Escherichia coli B (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: B3PF55, cellulase
#2: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 180 / Source method: isolated from a natural source / Formula: H₂O

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.65 Å³/Da / Density % sol: 53.62 % / Description: Plate clusters
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: PS: 12 mg/mL in 20 mM MOPS 7.5, 50 mM NaCl 1.5:1 with WS containing 30% MPD, 6% PEG4000, with seeding from higher [PEG] crystals. PH range: 7.5-8

-
Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
Detector	Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Mar 4, 2021
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9763 Å / Relative weight: 1
Reflection	Resolution: 2.18→102.57 Å / Num. obs: 60843 / % possible obs: 91 % / Observed criterion σ(I): 1 / Redundancy: 13.5 % / CC_1/2: 0.996 / R_merge(I) obs: 0.264 / R_pim(I) all: 0.074 / R_rim(I) all: 0.274 / Net I/σ(I): 8.3
Reflection shell	Resolution: 2.18→2.22 Å / Redundancy: 13.9 % / R_merge(I) obs: 3.784 / Num. unique obs: 3330 / CC_1/2: 0.351 / R_pim(I) all: 1.044 / R_rim(I) all: 3.926 / % possible all: 99.9

-
Processing

Software

Name	Version	Classification
REFMAC	5.8.0267	refinement
autoPROC		data reduction
autoPROC		data scaling
BUCCANEER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4HTY

4hty

Resolution: 2.182→102.57 Å / Cor.coef. F_o:F_c: 0.955 / Cor.coef. F_o:F_c free: 0.939 / SU B: 7.002 / SU ML: 0.165 / Cross valid method: FREE R-VALUE / ESU R: 0.252 / ESU R Free: 0.197
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2262	2991	4.938 %	0.05
R_work	0.1874	57576	-	-
all	0.189	-	-	-
obs	-	60567	90.555 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 39.267 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.783 Å²	-0 Å²	-0 Å²
2-	-	1.5 Å²	-0 Å²
3-	-	-	-0.717 Å²

Refinement step

Cycle: LAST / Resolution: 2.182→102.57 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8122	0	0	180	8302

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.009	0.013	8410
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.018	7574
X-RAY DIFFRACTION	r_angle_refined_deg	1.627	1.636	11442
X-RAY DIFFRACTION	r_angle_other_deg	1.311	1.582	17364
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	8.417	5	1001
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	35.952	22.209	498
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.39	15	1310
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	15.423	15	55
X-RAY DIFFRACTION	r_chiral_restr	0.083	0.2	1033
X-RAY DIFFRACTION	r_gen_planes_refined	0.009	0.02	9728
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	2194
X-RAY DIFFRACTION	r_nbd_refined	0.203	0.2	1629
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.178	0.2	7108
X-RAY DIFFRACTION	r_nbtor_refined	0.174	0.2	4068
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.082	0.2	3841
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.136	0.2	233
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.148	0.2	22
X-RAY DIFFRACTION	r_nbd_other	0.191	0.2	66
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.214	0.2	10
X-RAY DIFFRACTION	r_mcbond_it	3.76	4.038	3995
X-RAY DIFFRACTION	r_mcbond_other	3.739	4.037	3994
X-RAY DIFFRACTION	r_mcangle_it	5.295	6.04	4990
X-RAY DIFFRACTION	r_mcangle_other	5.296	6.042	4991
X-RAY DIFFRACTION	r_scbond_it	4.057	4.26	4415
X-RAY DIFFRACTION	r_scbond_other	4.057	4.262	4416
X-RAY DIFFRACTION	r_scangle_it	5.798	6.257	6449
X-RAY DIFFRACTION	r_scangle_other	5.799	6.257	6449
X-RAY DIFFRACTION	r_lrange_it	7.252	44.6	9614
X-RAY DIFFRACTION	r_lrange_other	7.239	44.553	9593
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.06	0.05	11777
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.064	0.05	11769
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.056	0.05	11799

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)	Weight position
1	1	CCC	X-RAY DIFFRACTION	Local ncs	0.05999	0.05009
1	2	AAA	X-RAY DIFFRACTION	Local ncs	0.05999	0.05009
2	3	CCC	X-RAY DIFFRACTION	Local ncs	0.06351	0.05009
2	4	BBB	X-RAY DIFFRACTION	Local ncs	0.06351	0.05009
3	5	AAA	X-RAY DIFFRACTION	Local ncs	0.05552	0.05009
3	6	BBB	X-RAY DIFFRACTION	Local ncs	0.05552	0.05009

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 (%)
2.182-2.238	0.323	210	0.324	3999	X-RAY DIFFRACTION	85.8279
2.238-2.3	0.313	118	0.292	2392	X-RAY DIFFRACTION	52.368
2.3-2.366	0.288	238	0.277	4367	X-RAY DIFFRACTION	99.8482
2.366-2.439	0.278	231	0.261	4296	X-RAY DIFFRACTION	99.8897
2.439-2.519	0.301	196	0.247	4193	X-RAY DIFFRACTION	99.9772
2.519-2.608	0.279	198	0.219	4006	X-RAY DIFFRACTION	99.9762
2.608-2.706	0.271	160	0.217	2585	X-RAY DIFFRACTION	66.8046
2.706-2.816	0.233	187	0.193	3740	X-RAY DIFFRACTION	100
2.816-2.942	0.281	198	0.2	3594	X-RAY DIFFRACTION	100
2.942-3.085	0.248	169	0.188	3456	X-RAY DIFFRACTION	100
3.085-3.252	0.223	172	0.18	3251	X-RAY DIFFRACTION	100
3.252-3.449	0.236	125	0.197	2578	X-RAY DIFFRACTION	82.0832
3.449-3.687	0.266	118	0.198	2007	X-RAY DIFFRACTION	69.0159
3.687-3.982	0.211	133	0.173	2337	X-RAY DIFFRACTION	85.6449
3.982-4.361	0.167	150	0.138	2492	X-RAY DIFFRACTION	100
4.361-4.875	0.144	116	0.122	2306	X-RAY DIFFRACTION	100
4.875-5.628	0.154	96	0.134	2033	X-RAY DIFFRACTION	100
5.628-6.888	0.207	74	0.167	1760	X-RAY DIFFRACTION	100
6.888-9.724	0.184	61	0.146	1384	X-RAY DIFFRACTION	100
9.724-102.57	0.252	41	0.233	800	X-RAY DIFFRACTION	99.6445

-
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