PDB-2q1f: Crystal structure of chondroitin sulfate lyase abc from bacteroid...

ID or keywords:

Entry

Database: PDB / ID: 2q1f

Title

Crystal structure of chondroitin sulfate lyase abc from bacteroides thetaiotaomicron wal2926

Components

Chondroitinase

Keywords

LYASE / ALPHA PLUS BETA

Function / homology

Function and homology information

chondroitin-sulfate-ABC exolyase /

chondroitin-sulfate-ABC exolyase activity /

chondroitin B lyase activity /

chondroitin AC lyase activity /

chondroitin-sulfate-ABC endolyase activity / carbon-oxygen lyase activity, acting on polysaccharides / chondroitin sulfate catabolic process / dermatan sulfate catabolic process / glycosaminoglycan catabolic process /

hyaluronate lyase activity ...
Similarity search - Function

Biological species

Bacteroides thetaiotaomicron (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.85 Å

Authors

Shaya, D. / Cygler, M.

Citation

Journal: Glycobiology / Year: 2008
Title: Composite active site of chondroitin lyase ABC accepting both epimers of uronic acid.
Authors: Shaya, D. / Hahn, B.S. / Bjerkan, T.M. / Kim, W.S. / Park, N.Y. / Sim, J.S. / Kim, Y.S. / Cygler, M.

History

Deposition	May 24, 2007	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jan 29, 2008	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.2	Oct 18, 2017	Group: Refinement description / Category: software Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version

Remark 999

sequence THE SEQUENCE OF THIS PROTEIN IS NOT AVAILABLE IN UNP DATABASE AT THE TIME OF PROCESSING ...

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	2q1f.cif.gz	393.3 KB	Display	PDBx/mmCIF format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/q1/2q1f ftp://data.pdbj.org/pub/pdb/validation_reports/q1/2q1f	HTTPS FTP

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Related structure data

Similar structure data	1nlf-d 3cf6-d 1n15-d 5ech-2 4mh0-d 4mgi-d 1gjq-d 1nir-d 3ony-d 5guw-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 - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#198 - Jun 2016 Beta-galactosidase similarity (2) #156 - Dec 2012 ABO Blood Type Glycosyltransferases similarity (1) #39 - Mar 2003 lac Repressor similarity (2) #203 - Nov 2016 Aminopeptidase 1 and Autophagy similarity (1)

Deposited unit

A: Chondroitinase

B: Chondroitinase

hetero molecules

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

1

A: Chondroitinase

hetero molecules

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

2

B: Chondroitinase

hetero molecules

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

Unit cell

Length a, b, c (Å)	223.362, 223.362, 112.639
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	173
Space group name H-M	P6₃

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
1	2	A
2	2	B
1	3	A
2	3	B

NCS domain segments:

Component-ID: 1 / Refine code: 3

Dom-ID	Ens-ID	Beg label comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	ALA	HIS	A	A	14 - 190	14 - 190
2	1	ALA	HIS	B	B	14 - 190	14 - 190
1	2	TRP	GLN	A	A	191 - 595	191 - 595
2	2	TRP	GLN	B	B	191 - 595	191 - 595
1	3	GLY	LYS	A	A	596 - 1014	596 - 1014
2	3	GLY	LYS	B	B	596 - 1014	596 - 1014

NCS ensembles :

ID
1
2
3

#1: Protein	Chondroitinase / Chondroitin Sulfate Lyase ABC Mass: 117833.375 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacteroides thetaiotaomicron (bacteria) Strain: WAL2926 / Gene: cslABC / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): DL41(DE3) References: UniProt: Q8A2I1, UniProt: C5G6D7*PLUS, chondroitin-sulfate-ABC exolyase
#2: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical	ChemComp-PO4 / PHOSPHATE ION / Phosphate Mass: 94.971 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: PO₄
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 67 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 3.44 Å³/Da / Density % sol: 64.25 %
Crystal grow	Temperature: 282 K / pH: 6.5 Details: 17% PEG 3350, 0.2M ammonium sulfate, 100 mM HEPES , pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 282K, pH 6.50

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 22-ID / Wavelength: 0.97233

Detector

Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: May 26, 2006
Details: DOUBLE-CRYSTAL FIXED-EXIT SI- 111 MONOCHROMATOR (E/E~10-4) AND A PLANAR PALLADIUM-COATED SILICON MIRROR

Radiation

Monochromator: FLAT DOUBLE CRYSTAL KOHZU / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.97233 Å / Relative weight: 1

Reflection

Redundancy: 3.1 % / Av σ(I) over netI: 14.6 / Number: 426753 / R_merge(I) obs: 0.063 / Χ²: 1.59 / D res high: 2.85 Å / D res low: 50 Å / Num. obs: 139387 / % possible obs: 94.7

Diffraction reflection shell

Highest resolution (Å)	Lowest resolution (Å)	% possible obs (%)	ID	R_merge(I) obs	Chi squared	Redundancy
7.02	50	99.7	1	0.029	2.087	3.2
5.58	7.02	100	1	0.043	2.261	3.3
4.87	5.58	99.9	1	0.049	2.454	3.3
4.43	4.87	100	1	0.045	2.07	3.3
4.11	4.43	100	1	0.051	1.94	3.3
3.87	4.11	100	1	0.063	1.759	3.3
3.67	3.87	100	1	0.078	1.582	3.3
3.51	3.67	100	1	0.091	1.328	3.3
3.38	3.51	100	1	0.115	1.151	3.3
3.26	3.38	100	1	0.159	1.072	3.2
3.16	3.26	99.8	1	0.195	1.02	3.1
3.07	3.16	98.2	1	0.262	0.999	2.9
2.99	3.07	91	1	0.32	0.952	2.5
2.92	2.99	75.4	1	0.382	0.979	2.1
2.85	2.92	56.7	1	0.4	0.887	1.7

Reflection

Resolution: 2.85→50 Å / Num. obs: 71079 / % possible obs: 94.7 % / Redundancy: 3.1 % / R_merge(I) obs: 0.063 / R_sym value: 0.05 / Net I/σ(I): 14.6

Reflection shell

Resolution: 2.85→2.92 Å / Redundancy: 1.7 % / R_merge(I) obs: 0.4 / Mean I/σ(I) obs: 1.6 / R_sym value: 0.326 / % possible all: 56.7

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Phasing

Phasing dm

FOM : 0.82 / FOM acentric: 0.82 / FOM centric: 0.8 / Reflection: 71085 / Reflection acentric: 68330 / Reflection centric: 2755

Phasing dm shell

Resolution (Å)	FOM	FOM acentric	FOM centric	Reflection	Reflection acentric	Reflection centric
8.1-44.617	0.96	0.96	0.91	3298	2967	331
5.1-8.1	0.93	0.94	0.85	10019	9488	531
4.1-5.1	0.94	0.94	0.92	12559	12068	491
3.6-4.1	0.91	0.91	0.88	12651	12232	419
3.1-3.6	0.85	0.85	0.82	22275	21627	648
2.8-3.1	0.35	0.35	0.32	10283	9948	335

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
RESOLVE	2.11	phasing
REFMAC	5.2.0019	refinement
PDB_EXTRACT	2	data extraction
HKL-2000		data reduction
SHARP		phasing

Refinement

Method to determine structure:

SAD / Resolution: 2.85→50 Å / Cor.coef. F_o:F_c: 0.921 / Cor.coef. F_o:F_c free: 0.89 / SU B: 34.325 / SU ML: 0.301 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 1.371 / ESU R Free: 0.376 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.262	3599	5.1 %	RANDOM
R_work	0.22	-	-	-
obs	0.222	67482	94.8 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK

Displacement parameters

B_iso mean: 59.33 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.88 Å²	-0.94 Å²	0 Å²
2-	-	-1.88 Å²	0 Å²
3-	-	-	2.82 Å²

Refinement step

Cycle: LAST / Resolution: 2.85→50 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	15824	0	82	67	15973

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.006	0.022	16276
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.007	1.959	22004
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.167	5	1978
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	34.854	23.603	766
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	17.472	15	2822
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	15.287	15	114
X-RAY DIFFRACTION	r_chiral_restr	0.07	0.2	2302
X-RAY DIFFRACTION	r_gen_planes_refined	0.002	0.02	12404
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined	0.189	0.2	7243
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined	0.3	0.2	10880
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.111	0.2	480
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined	0.073	0.2	7
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.179	0.2	27
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.176	0.2	3
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	0.826	4	10119
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	1.214	6	15822
X-RAY DIFFRACTION	r_scbond_it	1.195	5	7070
X-RAY DIFFRACTION	r_scangle_it	1.864	8	6182
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Refine-ID: X-RAY DIFFRACTION

Ens-ID	Number	Type	Rms dev position (Å)	Weight position
1	708	tight positional	0.01	0.05
2	1580	tight positional	0.02	0.05
3	1676	tight positional	0.02	0.05
1	713	loose positional	0.46	5
2	1598	loose positional	0.47	5
3	1637	loose positional	0.4	5
1	708	tight thermal	0.03	0.5
2	1580	tight thermal	0.03	0.5
3	1676	tight thermal	0.03	0.5
1	713	loose thermal	1.04	10
2	1598	loose thermal	1.34	10
3	1637	loose thermal	1.1	10

LS refinement shell

Resolution: 2.85→2.92 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.464	158	-
R_work	0.413	3102	-
obs	-	-	59.36 %

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	3.3712	0.2923	-0.6384	3.9015	-0.6574	1.8825	0.4459	0.1616	0.2081	-0.5624	-0.1967	0.4142	-0.4138	-0.4758	-0.2492	-0.0362	0.259	-0.1059	-0.1426	0.0707	-0.3621	4.648	49.641	-5.755
2	1.9906	-2.0517	-0.3124	2.1159	0.3469	0.5651	0.079	-0.1098	-0.2742	-0.1882	0.0502	0.2202	0.0197	-0.1388	-0.1291	-0.2126	-0.0841	-0.0983	-0.2734	0.0263	-0.2248	21.262	19.148	4.159
3	2.535	-0.1225	-0.9124	2.6268	0.8616	3.2224	0.209	-0.4486	0.8645	-0.3544	0.1644	-0.5527	-0.3989	0.738	-0.3734	-0.2009	-0.2486	0.2304	-0.1144	-0.2187	0.0637	60.644	20.866	-0.603
4	4.3217	-0.2754	-0.5932	4.8352	-0.3618	2.6882	-0.1232	-0.3555	0.6515	0.3222	0.2657	1.096	-0.4051	-0.9293	-0.1425	0.0956	0.0575	0.1074	0.2006	-0.2273	0.6196	60.371	60.87	-37.304
5	1.4616	0.0061	-0.0678	3.3698	0.2642	0.8526	-0.1711	-0.0198	0.3987	-0.1516	0.0826	-0.3065	-0.2112	0.1462	0.0885	-0.0898	-0.169	0.0901	-0.1501	-0.1424	0.0103	90.886	43.518	-45.755
6	2.8999	0.2018	0.2743	1.9082	-0.1536	2.4803	-0.0917	-0.0411	-0.7187	0.0597	0.0763	-0.5855	0.4204	0.2853	0.0154	-0.0988	-0.0749	0.2222	-0.2989	-0.0737	0.0338	86.367	4.254	-45.978

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	X-RAY DIFFRACTION	1	A	A	14 - 190	14 - 190
2	X-RAY DIFFRACTION	2	A	A	191 - 595	191 - 595
3	X-RAY DIFFRACTION	3	A	A	596 - 1014	596 - 1014
4	X-RAY DIFFRACTION	4	B	B	14 - 190	14 - 190
5	X-RAY DIFFRACTION	5	B	B	191 - 595	191 - 595
6	X-RAY DIFFRACTION	6	B	B	596 - 1014	596 - 1014

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