PDB-2y3u: Crystal structure of apo collagenase G from Clostridium histolyti...

ID or keywords:

Entry

Database: PDB / ID: 2y3u

Title

Crystal structure of apo collagenase G from Clostridium histolyticum at 2.55 Angstrom resolution

Components

COLLAGENASE

Keywords

HYDROLASE / GLUZINCIN / METALLOPROTEASE

Function / homology

Function and homology information

tripeptidase activity / microbial collagenase / collagen metabolic process / collagen binding / metalloendopeptidase activity / endopeptidase activity / calcium ion binding / proteolysis / extracellular region / zinc ion binding
Similarity search - Function

Biological species

CLOSTRIDIUM HISTOLYTICUM (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MAD / Resolution: 2.55 Å

Authors

Eckhard, U. / Brandstetter, H.

Citation

Journal: Nat.Struct.Mol.Biol. / Year: 2011
Title: Structure of Collagenase G Reveals a Chew-and -Digest Mechanism of Bacterial Collagenolysis
Authors: Eckhard, U. / Schoenauer, E. / Nuess, D. / Brandstetter, H.

History

Deposition	Dec 26, 2010	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Sep 28, 2011	Provider: repository / Type: Initial release
Revision 1.1	Oct 19, 2011	Group: Database references
Revision 1.2	Nov 20, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_entry_details.has_protein_modification / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	2y3u.cif.gz	294.5 KB	Display	PDBx/mmCIF format
PDB format	pdb2y3u.ent.gz	238.9 KB	Display	PDB format
PDBx/mmJSON format	2y3u.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/y3/2y3u ftp://data.pdbj.org/pub/pdb/validation_reports/y3/2y3u	HTTPS FTP

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Related structure data

Related structure data	2y50C 2y6iC 2y72C C: citing same article (ref.)
Similar structure data	2y50-d 4are-d 2y6i-d 6ewx-d 2hro-d 3lv4-d 6rmd-d 5ve6-1 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	#129 - Sep 2010 Isocitrate Dehydrogenase similarity (1) #154 - Oct 2012 Citric Acid Cycle similarity (1) #191 - Nov 2015 Glutamate-gated Chloride Receptors similarity (1) #215 - Nov 2017 Aspartate Transcarbamoylase similarity (1) #258 - Jun 2021 Glucocorticoid Receptor and Dexamethasone similarity (1) #89 - May 2007 Aconitase and Iron Regulatory Protein 1 similarity (1)

Deposited unit

A: COLLAGENASE

hetero molecules

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	56.960, 109.050, 182.460
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	COLLAGENASE / COLLAGENASE G Mass: 89594.695 Da / Num. of mol.: 1 / Fragment: RESIDUES 119-880 Source method: isolated from a genetically manipulated source Source: (gene. exp.) CLOSTRIDIUM HISTOLYTICUM (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834 / References: UniProt: Q9X721, microbial collagenase
#2: Chemical	ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400 Mass: 282.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₂H₂₆O₇ / Comment: precipitant*YM
#3: Chemical	ChemComp-FLC / CITRATE ANION Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₆H₅O₇
#4: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 86 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y
Nonpolymer details	CATALYTIC ZN BINDING SITE IS FORMED BY HIS523, HIS527 AND GLU555. ZN IS REPLACED BY WATER A2086 IN ...CATALYTIC ZN BINDING SITE IS FORMED BY HIS523, HIS527 AND GLU555. ZN IS REPLACED BY WATER A2086 IN THIS STRUCTURE
Sequence details	NATURAL VARIATION AT THESE THREE POSITIONS OWING TO ISOLATION FROM A DIFFERENT STRAIN.

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 3.15 Å³/Da / Density % sol: 61 % / Description: NONE
Crystal grow	pH: 8.3 / Details: 21.5% PEG 3350, 0.225 M TRISODIUM CITRATE PH 8.3.

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.98793
Detector	Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 12, 2010 / Details: MIRRORS
Radiation	Monochromator: DOUBLE CRYSTAL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.98793 Å / Relative weight: 1
Reflection	Resolution: 2.55→48.32 Å / Num. obs: 33182 / % possible obs: 88.1 % / Observed criterion σ(I): 1.8 / Redundancy: 5.4 % / B_iso Wilson estimate: 62.2 Å² / R_merge(I) obs: 0.1 / Net I/σ(I): 9.3
Reflection shell	Resolution: 2.55→2.69 Å / Redundancy: 5 % / R_merge(I) obs: 0.7 / Mean I/σ(I) obs: 1.8 / % possible all: 84.4

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Processing

Software

Name	Version	Classification
REFMAC	5.5.0109	refinement
iMOSFLM		data reduction
SCALA		data scaling

Refinement

Method to determine structure:

MAD
Starting model: NONE

Resolution: 2.55→40 Å / Cor.coef. F_o:F_c: 0.949 / Cor.coef. F_o:F_c free: 0.919 / SU B: 25.2 / SU ML: 0.238 / Cross valid method: THROUGHOUT / ESU R: 0.429 / ESU R Free: 0.291 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.25645	1626	4.9 %	RANDOM
R_work	0.20806	-	-	-
obs	0.21043	31443	87.13 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 58.695 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	5.82 Å²	0 Å²	0 Å²
2-	-	-3.38 Å²	0 Å²
3-	-	-	-2.44 Å²

Refinement step

Cycle: LAST / Resolution: 2.55→40 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5490	0	39	86	5615

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.011	0.022	5524
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.152	1.94	7487
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.12	5	675
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	35.685	24.8	275
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.271	15	868
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	20.166	15	19
X-RAY DIFFRACTION	r_chiral_restr	0.075	0.2	801
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.02	4275
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
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	0.419	1.5	3351
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	0.828	2	5373
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	1.328	3	2173
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	2.226	4.5	2114
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined
X-RAY DIFFRACTION	r_long_range_B_other
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2.55→2.616 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.463	113	-
R_work	0.362	2081	-
obs	-	-	79.44 %

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	9.3287	-0.616	-0.3252	48.6247	-16.1908	17.813	0.7279	1.2491	-0.7817	-2.8924	-1.3933	2.9672	2.1595	-2.7234	0.6654	1.2756	0.1706	-0.2216	0.3037	-0.2353	-0.002	8.2598	40.6331	-13.8465
2	4.0552	0.691	1.3595	5.3249	-0.8371	4.6272	0.2179	0.3234	-0.4107	-0.9225	-0.0012	-0.0067	0.1682	-0.1533	-0.2167	0.528	0.195	0.0684	0.2075	0.1505	0.2141	13.9083	44.1395	-5.0834
3	6.2858	2.0086	-1.99	2.8964	-0.3319	9.0268	-0.0495	0.1295	-0.5558	0.1918	0.0547	0.9647	-0.4954	-1.0992	-0.0051	0.289	0.2393	0.1062	0.1826	0.2063	0.274	8.1589	44.2161	7.871
4	3.8566	-1.0937	-1.4387	3.2835	-0.0908	5.904	0.147	-0.0459	0.0412	-0.0745	-0.092	-0.4292	-0.253	0.5898	-0.0551	0.416	0.1204	0.0744	0.1686	0.2131	0.2827	22.1074	45.1794	6.5088
5	2.6133	-0.0228	0.0938	4.0537	-1.67	3.5573	-0.0138	0.2357	0.0451	0.4045	0.2103	0.2053	-0.4514	-0.2731	-0.1965	0.3498	0.1488	0.0508	0.1342	0.1374	0.1808	15.4594	36.669	19.7916
6	1.7124	-0.2844	1.1071	4.7949	-0.3479	2.8109	0.0131	0.0784	0.2156	0.6185	0.0711	-0.2675	-0.6118	0.1413	-0.0843	0.4437	0.0758	-0.009	0.1637	0.042	0.2034	24.1011	35.7507	28.0459
7	4.5017	0.3385	0.4146	2.8478	-2.2007	4.1346	-0.0991	-0.0284	0.3417	0.7647	0.0915	-0.1255	-0.5292	0.2433	0.0076	0.5551	0.0554	-0.0493	0.1642	0.006	0.1388	28.1058	30.1754	32.0626
8	2.374	3.4812	-6.2214	7.7678	-2.596	5.1348	0.1485	0.7685	0.0509	0.8603	0.2801	-1.5768	0.1645	0.0377	-0.4286	0.4597	-0.0478	-0.2377	0.2441	-0.0166	0.3019	35.0579	26.2307	31.1899
9	0.418	-0.924	-0.2844	7.212	-0.5325	1.5738	-0.1512	-0.151	0.0761	0.7257	0.1209	-0.2981	-0.2194	-0.0359	0.0302	0.3811	0.0684	-0.0792	0.1496	-0.0101	0.0696	31.653	1.4225	36.0943
10	0.9875	-0.6524	-0.6582	2.8341	0.215	3.1492	-0.1157	-0.0167	0.0892	0.1491	-0.0236	-0.332	-0.0647	0.1345	0.1394	0.2346	-0.0176	-0.0171	0.1562	0.0397	0.1544	36.54	-14.7251	24.1434
11	2.4891	-1.1703	-2.0916	6.1662	-0.0634	0.2943	0.0408	0.1951	0.2385	0.1442	-0.0626	0.2002	-0.2797	-0.2028	0.0217	0.4012	0.0717	-0.0841	0.1605	0.0088	0.0939	27.0244	5.7258	25.9398
12	2.5896	-2.038	1.3541	7.0957	1.8901	-0.1056	-0.3841	0.4992	-0.2065	0.0714	0.1579	-0.2722	-0.3141	0.0015	0.2262	0.3476	-0.002	-0.1036	0.2068	-0.037	0.1984	32.3453	-0.2712	24.465
13	4.8297	-1.3844	-2.0575	3.4454	0.6421	2.6559	-0.0488	0.1472	0.0994	0.0126	-0.0178	0.3669	-0.1512	-0.3787	0.0666	0.1834	-0.0175	-0.0442	0.1544	0.0154	0.1135	27.2216	-8.2544	21.2178
14	-1.9527	1.6538	0.0034	7.4494	-3.3261	10.5893	-0.151	-0.1522	0.1732	-0.4231	-0.2919	-0.1512	0.1279	-0.2043	0.4429	0.3149	-0.0258	0.0247	0.2426	0.0251	0.2826	41.7914	-4.3486	7.2927
15	1.2697	0.1496	-0.5856	2.6683	-0.4739	2.4653	-0.1132	0.2105	0.2305	-0.6899	0.1432	0.4997	-0.0873	-0.5017	-0.03	0.4498	-0.0929	-0.1	0.2659	0.0008	0.2055	22.8131	-13.6037	8.1409
16	1.6874	-0.9749	-4.3829	24.0771	-0.5152	0.4569	0.9717	0.777	2.0308	-0.1636	-0.8041	1.2829	-1.1486	0.4368	-0.1676	1.0184	-0.044	-0.2122	0.2841	0.1996	0.5997	24.0914	-4.2525	2.0554
17	1.6018	-0.4933	0.8337	3.2282	-0.096	2.0134	-0.2273	0.363	-0.1889	-0.8954	-0.0054	-0.0883	0.4401	-0.0237	0.2327	0.6302	-0.0798	0.0215	0.2137	0.004	0.1141	31.8143	-18.6803	1.3436
18	0.634	1.4787	-0.0414	0.4732	-1.8672	4.0714	-0.3773	-0.1615	0.1142	-0.2058	0.2369	0.5685	0.8838	-0.9873	0.1403	0.4437	-0.0534	-0.0621	0.2872	0.0259	0.4592	15.9787	-20.0641	14.8034
19	1.2869	-0.3653	-0.3426	2.5069	-0.1679	3.1251	-0.2047	-0.0641	-0.1066	0.1559	0.0314	-0.0605	0.2801	-0.0179	0.1732	0.3137	0.0016	0.051	0.1251	0.045	0.1341	36.6499	-29.7367	28.6316
20	2.6218	-1.1102	-1.634	3.5409	0.4288	4.1835	-0.1513	-0.0042	-0.0228	0.128	0.0559	-0.0018	0.3775	-0.0086	0.0954	0.3016	-0.0013	0.0135	0.1253	0.0388	0.1366	36.5159	-30.6825	26.5473

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	110 - 121
2	X-RAY DIFFRACTION	2	A	122 - 171
3	X-RAY DIFFRACTION	3	A	172 - 195
4	X-RAY DIFFRACTION	4	A	196 - 230
5	X-RAY DIFFRACTION	5	A	231 - 302
6	X-RAY DIFFRACTION	6	A	303 - 337
7	X-RAY DIFFRACTION	7	A	338 - 374
8	X-RAY DIFFRACTION	8	A	375 - 396
9	X-RAY DIFFRACTION	9	A	397 - 435
10	X-RAY DIFFRACTION	10	A	436 - 470
11	X-RAY DIFFRACTION	11	A	471 - 496
12	X-RAY DIFFRACTION	12	A	497 - 507
13	X-RAY DIFFRACTION	13	A	508 - 535
14	X-RAY DIFFRACTION	14	A	536 - 548
15	X-RAY DIFFRACTION	15	A	549 - 594
16	X-RAY DIFFRACTION	16	A	595 - 607
17	X-RAY DIFFRACTION	17	A	608 - 659
18	X-RAY DIFFRACTION	18	A	660 - 679
19	X-RAY DIFFRACTION	19	A	680 - 744
20	X-RAY DIFFRACTION	20	A	745 - 790

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