PDB-5jmb: The Crystal structure of the N-terminal domain of a novel cellula...

ID or keywords:

Entry

Database: PDB / ID: 5jmb

Title

The Crystal structure of the N-terminal domain of a novel cellulases from Bacteroides coprocola

Components

Uncharacterized protein

Keywords

HYDROLASE / cellulases

Function / homology

Prokaryotic membrane lipoprotein lipid attachment site profile. / Uncharacterized protein

Function and homology information

Biological species

Bacteroides coprocola (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.05 Å

Authors

Tan, K. / Gu, M. / Jedrzejczak, R. / Joachimiak, A.

Funding support

United States, 1items

Citation

Journal: To Be Published
Title: The Crystal structure of the N-terminal domain of a novel cellulases from Bacteroides coprocola (CASP target)
Authors: Tan, K. / Gu, M. / Jedrzejczak, R. / Joachimiak, A.

History

Deposition	Apr 28, 2016	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jun 29, 2016	Provider: repository / Type: Initial release
Revision 1.1	Sep 27, 2017	Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2	Dec 4, 2019	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3	Nov 20, 2024	Group: Data collection / Database references / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5jmb.cif.gz	88 KB	Display	PDBx/mmCIF format
PDB format	pdb5jmb.ent.gz	67 KB	Display	PDB format
PDBx/mmJSON format	5jmb.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5jmb_validation.pdf.gz	404.4 KB	Display	wwPDB validaton report
Full document	5jmb_full_validation.pdf.gz	404.4 KB	Display
Data in XML	5jmb_validation.xml.gz	8.9 KB	Display
Data in CIF	5jmb_validation.cif.gz	11.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/jm/5jmb ftp://data.pdbj.org/pub/pdb/validation_reports/jm/5jmb	HTTPS FTP

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Related structure data

Similar structure data	5tvz-d 6dye-2 3g74-3 6dyh-1 3l1x-d 2lrs-d 2m7b-d 2vsd-d 2oo9-1 6dyj-3 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 - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#261 - Sep 2021 DNA-Sequencing Nanopores similarity (1) #22 - Oct 2001 Photosystem I similarity (1) #262 - Oct 2021 Fifty Years of Open Access to PDB Structures similarity (1) #29 - May 2002 Penicillin-binding Proteins similarity (1) #95 - Nov 2007 Multidrug Resistance Transporters similarity (1)

Deposited unit

A: Uncharacterized protein

B: Uncharacterized protein

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

1

A: Uncharacterized protein

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

2

B: Uncharacterized protein

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

Unit cell

Length a, b, c (Å)	47.860, 47.860, 292.850
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	179
Space group name H-M	P6₅22

Components on special symmetry positions

ID	Model	Components
1	1	A-206- HOH
2	1	B-205- HOH

#1: Protein	Uncharacterized protein Mass: 10581.402 Da / Num. of mol.: 2 / Fragment: N-terminal domain (UNP residues 43-133) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacteroides coprocola (bacteria) / Plasmid: pMCSG68 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Gold(DE3) / References: UniProt: B3JI28
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 77 / Source method: isolated from a natural source / Formula: H₂O
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: 2.31 Å³/Da / Density % sol: 46.71 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 1.8M Ammonium Citrate Tribasic pH7.0

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 22, 2016 / Details: Mirror
Radiation	Monochromator: Si 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97918 Å / Relative weight: 1
Reflection	Resolution: 2.05→41 Å / Num. obs: 13622 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 7.4 % / R_merge(I) obs: 0.113 / Net I/σ(I): 20.7
Reflection shell	Resolution: 2.05→2.09 Å / Redundancy: 4.2 % / R_merge(I) obs: 0.7 / Mean I/σ(I) obs: 2.4 / % possible all: 98.1

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Processing

Software

Name	Version	Classification
PHENIX	1.9_1692	refinement
HKL-3000		data scaling
HKL-3000		phasing
HKL-3000		data reduction
SBC-Collect		data collection

Refinement

Method to determine structure:

SAD / Resolution: 2.05→41 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.18

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2306	641	4.79 %	random
R_work	0.1871	-	-	-
obs	0.1892	13373	98.6 %	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Refinement step

Cycle: LAST / Resolution: 2.05→41 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1428	0	0	77	1505

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	1464
X-RAY DIFFRACTION	f_angle_d	1.096	1993
X-RAY DIFFRACTION	f_dihedral_angle_d	14.013	519
X-RAY DIFFRACTION	f_chiral_restr	0.044	220
X-RAY DIFFRACTION	f_plane_restr	0.007	261

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 (%)
2.0506-2.2089	0.2955	104	0.2365	2339	X-RAY DIFFRACTION	94
2.2089-2.4312	0.2608	137	0.2117	2483	X-RAY DIFFRACTION	99
2.4312-2.783	0.2253	135	0.2026	2510	X-RAY DIFFRACTION	100
2.783-3.5059	0.2564	124	0.1853	2589	X-RAY DIFFRACTION	100
3.5-41	0.1974	141	0.166	2811	X-RAY DIFFRACTION	100

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	6.5061	-0.1624	-2.4772	5.5382	2.2467	2.4631	0.2543	0.0112	0.6592	0.3035	-0.4306	-0.2827	-1.1493	0.4849	0.188	0.3321	-0.0519	-0.0082	0.2292	0.0464	0.2908	-7.0012	27.1302	18.1672
2	2.6256	0.3307	0.6405	2.5892	-2.2003	7.6399	0.0493	-0.2376	0.3229	0.267	0.135	0.1321	-0.8789	-0.492	-0.2007	0.2418	0.0509	0.0303	0.1795	-0.0469	0.2222	-15.0052	20.4138	28.8578
3	6.4048	-1.9563	3.0489	4.1886	-2.9095	7.9306	-0.0009	-0.1599	-0.0129	-0.0505	0.0073	0.0946	-0.139	-0.088	-0.0485	0.1421	-0.0467	0.0174	0.139	-0.0267	0.1609	-11.638	12.107	27.2478
4	3.6222	-1.3147	1.9242	3.7955	-3.3999	3.1964	-0.1272	-0.054	0.3428	0.0515	-0.3253	-0.058	-0.7128	0.5313	0.3766	0.1808	-0.0183	-0.0116	0.1349	-0.0205	0.1719	-6.1356	17.0432	22.9958
5	2.3836	-0.3131	1.0528	2.9035	-2.1535	2.6645	0.2368	-0.2833	0.0937	0.1253	-0.0383	0.3221	-0.2364	0.4106	-0.2439	0.1848	-0.0392	-0.0187	0.1596	-0.0332	0.2758	-6.8728	14.8926	29.2995
6	9.1254	2.919	-3.5509	7.5951	4.4256	7.0793	0.1714	-0.226	1.8649	0.3669	0.4214	0.0184	-1.4564	0.788	-0.3246	0.5661	-0.108	0.0204	0.3553	-0.0706	0.4412	2.1922	23.3599	2.5972
7	2.0865	1.4447	2.0925	5.5618	2.3003	2.2736	0.1113	0.2956	0.0217	-0.9143	0.2909	-0.8628	-0.774	0.6061	-0.3889	0.3778	-0.1743	0.0914	0.3293	-0.0232	0.2271	5.4332	8.205	-11.0231
8	6.7542	1.0854	0.1282	3.562	1.1704	4.8732	-0.6711	-0.5965	0.0089	-0.048	0.0869	-0.6668	-0.4675	0.5281	-0.6062	0.0667	-0.1093	-0.1218	0.5418	-0.2819	0.5011	10.1603	13.7275	4.1206
9	3.4128	3.5358	2.7795	4.3507	1.1841	6.3399	-0.1361	-0.3365	0.3235	-0.0275	0.1092	0.2346	-0.1806	0.0092	0.1038	0.1993	0.0113	0.0021	0.1302	-0.0376	0.2406	-1.8951	5.6206	-0.5347
10	6.2846	-0.2982	4.3308	3.544	1.2956	9.7107	-0.0641	0.1067	0.1731	-0.0822	0.1026	-0.1706	0.1517	0.3989	-0.06	0.1416	-0.0353	0.0401	0.1136	-0.0058	0.1808	0.9992	1.5929	-7.44
11	4.035	2.0328	2.8045	3.8544	3.5703	3.5765	0.0229	-0.4247	0.2405	-0.3568	-0.1878	0.3265	-0.0006	-0.2353	0.1133	0.2453	-0.0388	-0.0251	0.1745	-0.0407	0.2162	-2.5923	11.3232	-3.0807
12	4.1862	-1.5751	-1.4124	5.8615	0.9435	1.2959	0.0713	-0.263	-0.106	0.4374	0.1808	0.1721	-0.4403	-0.2428	-0.0738	0.2813	-0.0579	-0.0675	0.1882	-0.0326	0.2428	-1.2588	16.4252	8.8042
13	1.5809	0.8722	1.4081	1.3611	2.6581	6.3747	-0.1083	0.3162	-0.0505	-0.6692	0.2667	-0.2982	-0.4255	0.4624	-0.0724	0.2507	-0.0337	-0.009	0.2183	0.059	0.249	-2.3591	3.1916	-15.0052

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 42 through 53 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 54 through 77 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 78 through 99 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 100 through 110 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 111 through 132 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 42 through 47 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 48 through 70 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 71 through 77 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 78 through 87 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 88 through 99 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 100 through 110 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 111 through 116 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 117 through 132 )

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