PDB-4are: Crystal structure of the collagenase Unit of collagenase G from C...

ID or keywords:

Entry

Database: PDB / ID: 4are

Title

Crystal structure of the collagenase Unit of collagenase G from Clostridium histolyticum at 2.19 angstrom resolution.

Components

COLLAGENASE G

Keywords

HYDROLASE / COLLAGEN / PEPTIDASE / COLLAGENOLYSIS / 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 /

MOLECULAR REPLACEMENT / Resolution: 2.19 Å

Authors

Eckhard, U. / Brandstetter, H.

Citation

Journal: J.Biol.Chem. / Year: 2013
Title: Structural Basis for Activity Regulation and Substrate Preference of Clostridial Collagenases G, H, and T.
Authors: Eckhard, U. / Schonauer, E. / Brandstetter, H.

History

Deposition	Apr 23, 2012	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jun 5, 2013	Provider: repository / Type: Initial release
Revision 1.1	Jul 31, 2013	Group: Database references
Revision 1.2	Dec 20, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / 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 / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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	4are.cif.gz	301.5 KB	Display	PDBx/mmCIF format
PDB format	pdb4are.ent.gz	244.6 KB	Display	PDB format
PDBx/mmJSON format	4are.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4are_validation.pdf.gz	658.6 KB	Display	wwPDB validaton report
Full document	4are_full_validation.pdf.gz	666.9 KB	Display
Data in XML	4are_validation.xml.gz	28.6 KB	Display
Data in CIF	4are_validation.cif.gz	41.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ar/4are ftp://data.pdbj.org/pub/pdb/validation_reports/ar/4are	HTTPS FTP

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Related structure data

Related structure data	4aqoC 4ar1C 4ar8C 4ar9C 4arfC 2y3uS 2y50 2y6i 2y72 S: Starting model for refinement C: citing same article (ref.)
Similar structure data	2y6i-d 2y50-d 2y3u-d 2hro-d 3pu3-d 6ewx-d 5ve6-1 3lv4-d 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	#4 - Apr 2000 Collagen similarity (1) #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)

PDB pages

PDBj /

wwPDB /

NCBI

Related items in Molecule of the Month

#4 - Apr 2000
Collagen
similarity (1)
#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 G

hetero molecules

80.1 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)	55.290, 108.660, 181.000
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

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Protein , 1 types, 1 molecules A

#1: Protein	COLLAGENASE G Mass: 79477.461 Da / Num. of mol.: 1 / Fragment: COLLAGENASE UNIT, RESIDUES 119-790 Source method: isolated from a genetically manipulated source Source: (gene. exp.) CLOSTRIDIUM HISTOLYTICUM (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9X721, microbial collagenase

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Non-polymers , 5 types, 273 molecules

#2: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: 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
#4: Chemical	ChemComp-FLC / CITRATE ANION Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₆H₅O₇
#5: Chemical	ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₄H₁₂NO₃ / Comment: pH buffer*YM
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 269 / Source method: isolated from a natural source / Formula: H₂O

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Details

Sequence details	DIFFERENT STRAIN USED

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.98 Å³/Da / Density % sol: 58.78 % / Description: NONE
Crystal grow	pH: 8.25 / Details: 22.5% PEG 3350, 0.15M TRISODIUMCITRATE PH 8.2

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.8856
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 24, 2011
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.8856 Å / Relative weight: 1
Reflection	Resolution: 2.19→69.5 Å / Num. obs: 56974 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Redundancy: 4.8 % / B_iso Wilson estimate: 41.6 Å² / R_merge(I) obs: 0.07 / Net I/σ(I): 10.7
Reflection shell	Resolution: 2.19→2.31 Å / Redundancy: 4.7 % / R_merge(I) obs: 0.6 / Mean I/σ(I) obs: 2 / % possible all: 99.6

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Processing

Software

Name	Version	Classification
REFMAC	5.6.0117	refinement
MOSFLM		data reduction
SCALA		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2Y3U

2y3u

Resolution: 2.19→69.5 Å / Cor.coef. F_o:F_c: 0.964 / Cor.coef. F_o:F_c free: 0.944 / SU B: 17.625 / SU ML: 0.182 / Cross valid method: THROUGHOUT / ESU R: 0.615 / ESU R Free: 0.176 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.24297	2881	5.1 %	RANDOM
R_work	0.19321	-	-	-
obs	0.19567	54007	99.62 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 53.029 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	6.68 Å²	0 Å²	0 Å²
2-	-	-3.57 Å²	0 Å²
3-	-	-	-3.12 Å²

Refinement step

Cycle: LAST / Resolution: 2.19→69.5 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5359	0	41	269	5669

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.02	5530
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	3607
X-RAY DIFFRACTION	r_angle_refined_deg	1.314	1.942	7496
X-RAY DIFFRACTION	r_angle_other_deg	0.811	3	8766
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.648	5	678
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	36.666	24.764	275
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.225	15	867
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	19.707	15	20
X-RAY DIFFRACTION	r_chiral_restr	0.113	0.2	803
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.02	6268
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1198
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
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it
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	2.57	3	9137
X-RAY DIFFRACTION	r_sphericity_free	43.203	5	142
X-RAY DIFFRACTION	r_sphericity_bonded	16.039	5	9155

LS refinement shell

Resolution: 2.19→2.247 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.4	200	-
R_work	0.353	3656	-
obs	-	-	98.92 %

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	31.935	22.5274	23.6793	18.4224	13.7108	21.0971	0.6478	-1.4137	1.0073	-0.2395	-1.101	1.0779	1.1142	-0.7641	0.4532	1.1814	-0.0849	0.1283	0.2415	-0.1829	0.5284	-9.216	44.8329	17.5919
2	2.0622	-1.074	7.9037	27.0812	-5.6092	30.4111	0.5856	0.0395	-0.2557	-0.2517	0.244	0.9913	1.3911	0.1777	-0.8296	0.8725	-0.1131	-0.1728	0.093	-0.0708	0.181	-10.0311	39.3791	11.0886
3	0.3706	0.3091	0.3184	2.5596	1.9283	2.5954	0.034	0.0701	-0.1676	0.284	-0.0966	0.0879	-0.0895	-0.0514	0.0626	0.511	-0.1275	0.0455	0.1081	-0.1232	0.183	-16.0795	44.1432	-0.2004
4	1.1771	0.3608	0.8884	1.9437	0.9245	1.7769	-0.0325	-0.1618	0.1175	-0.1708	0.0641	-0.0343	-0.3561	0.1158	-0.0316	0.4494	-0.0805	0.0392	0.0905	-0.0908	0.1717	-17.8396	39.4462	-20.026
5	1.0877	0.2381	0.6841	1.2934	0.3534	1.4956	-0.0508	-0.1202	0.0299	-0.2465	0.0905	0.0587	-0.1743	-0.0141	-0.0397	0.4279	-0.029	-0.0071	0.0483	-0.0111	0.1339	-27.4984	28.2563	-31.5077
6	0.4893	1.2658	0.1683	5.2129	0.768	1.8024	-0.0406	0.056	0.0243	-0.7004	0.091	0.5448	0.002	-0.0293	-0.0505	0.4695	-0.013	-0.0859	0.0797	0.0249	0.1739	-32.4002	10.6944	-35.9654
7	2.8726	0.5253	0.381	2.2428	-1.0814	0.992	-0.0497	-0.0579	-0.1324	-0.3686	-0.0058	-0.0294	-0.1286	0.0978	0.0555	0.4729	-0.0682	-0.0098	0.1114	-0.01	0.0899	-28.9457	-7.3321	-35.898
8	1.0406	0.9397	-0.1812	0.8931	0.0789	1.5116	-0.1367	-0.052	0.0533	-0.0922	-0.0459	0.0853	-0.0257	-0.0221	0.1827	0.3427	0.0317	0.0182	0.1069	0.0028	0.1232	-35.4773	-15.905	-23.497
9	3.4183	1.4424	-1.3514	2.4843	-0.7182	1.6068	0.0498	-0.0999	-0.1748	0.0545	-0.1117	-0.1498	-0.4081	0.0953	0.0619	0.4411	-0.029	-0.0299	0.1299	-0.0072	0.1091	-28.5645	3.3823	-25.296
10	0.0388	0.2454	0.0517	1.6746	0.2764	0.6335	-0.0628	-0.0008	-0.0186	-0.1654	0.028	-0.165	-0.0797	0.1933	0.0347	0.3865	-0.0002	-0.0002	0.1775	-0.0016	0.1495	-25.7801	-8.0838	-21.6491
11	3.0042	-4.4126	2.9236	6.506	-4.1483	9.0304	-0.0671	0.1967	0.0499	-0.0356	-0.3402	-0.0495	0.0824	0.0345	0.4073	0.5167	0.0094	0.0292	0.0902	-0.0671	0.1236	-40.8714	-5.1584	-5.9514
12	0.5906	-0.3656	-0.5332	0.3402	0.0922	0.9903	-0.1558	-0.1192	-0.1081	0.1724	0.0328	0.0435	-0.0305	0.1758	0.1229	0.3921	0.0206	0.0011	0.1068	0.0139	0.1034	-27.0947	-16.0962	-13.8392
13	2.7235	0.2979	-1.0772	1.823	1.0701	5.486	0.0018	-0.0454	-0.1041	0.3106	-0.05	-0.259	-0.1	0.5102	0.0482	0.4377	0.029	-0.0992	0.123	0.0403	0.0899	-17.6747	-11.1909	-3.5338
14	27.9892	31.0749	-35.5141	34.6817	-39.5877	45.201	1.8552	-1.2663	-0.7082	2.3161	-1.8292	-0.2049	-2.7162	1.6081	-0.026	0.985	0.119	-0.6219	0.2666	-0.0254	1.9288	-25.4456	0.1302	-0.5467
15	1.6969	-0.1302	0.1221	0.0164	0.0766	1.4488	-0.2195	0.0173	0.1038	0.0471	0.0371	-0.0032	0.0866	0.3238	0.1824	0.5174	0.0485	-0.0613	0.1241	0.0042	0.0797	-23.6424	-16.2296	-5.3451
16	1.381	1.3375	1.8824	1.7367	1.1486	3.8424	0.242	-0.2534	0.0461	0.3047	-0.2353	0.0968	0.7283	-0.3933	-0.0067	0.6631	0.0073	0.0885	0.0622	-0.004	0.0383	-38.0049	-17.2965	-1.4648
17	0.9267	0.4936	1.1553	2.8385	-1.2961	2.8674	0.12	0.0195	-0.2165	0.3858	-0.2643	-0.6847	-0.0115	0.2317	0.1443	0.6099	0.1033	-0.1131	0.1444	0.047	0.177	-17.673	-19.9699	-0.881
18	3.2737	1.4276	3.4521	2.079	2.3639	6.4197	-0.0516	0.0624	0.0007	0.0013	0.0282	-0.1227	0.3431	0.4828	0.0235	0.3489	0.0134	0.0732	0.0934	-0.0169	0.1301	-24.9763	-24.7246	-35.8774
19	0.755	0.2623	-1.1562	1.5077	-0.2968	1.8606	-0.0922	0.0142	-0.0173	-0.2022	0.0173	0.0996	0.0639	-0.0922	0.0749	0.4021	-0.0392	-0.0134	0.0877	-0.043	0.0842	-37.8821	-26.7357	-34.048
20	0.2959	0.396	-0.1982	0.8956	0.3154	1.0639	-0.1198	-0.0076	-0.0557	0.0506	0.0136	-0.0289	0.3726	0.0303	0.1063	0.4381	0.0084	0.0754	0.0868	0.0005	0.0843	-34.8654	-32.9722	-20.2625
21	7.2103	-0.1658	-9.0658	5.0977	-1.5737	12.0224	0.7001	0.6338	0.153	-0.8267	-0.3767	0.2046	-0.6679	-0.6912	-0.3234	0.4801	0.0676	0.0115	0.1216	-0.0205	0.0756	-34.3682	-24.9944	-42.6984

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	110 - 114
2	X-RAY DIFFRACTION	2	A	117 - 123
3	X-RAY DIFFRACTION	3	A	124 - 217
4	X-RAY DIFFRACTION	4	A	218 - 319
5	X-RAY DIFFRACTION	5	A	320 - 397
6	X-RAY DIFFRACTION	6	A	398 - 413
7	X-RAY DIFFRACTION	7	A	414 - 436
8	X-RAY DIFFRACTION	8	A	437 - 468
9	X-RAY DIFFRACTION	9	A	469 - 506
10	X-RAY DIFFRACTION	10	A	507 - 535
11	X-RAY DIFFRACTION	11	A	536 - 549
12	X-RAY DIFFRACTION	12	A	550 - 571
13	X-RAY DIFFRACTION	13	A	572 - 598
14	X-RAY DIFFRACTION	14	A	599 - 603
15	X-RAY DIFFRACTION	15	A	604 - 624
16	X-RAY DIFFRACTION	16	A	625 - 648
17	X-RAY DIFFRACTION	17	A	649 - 670
18	X-RAY DIFFRACTION	18	A	671 - 691
19	X-RAY DIFFRACTION	19	A	692 - 722
20	X-RAY DIFFRACTION	20	A	723 - 784
21	X-RAY DIFFRACTION	21	A	785 - 790

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Protein , 1 types, 1 molecules A

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Non-polymers , 5 types, 273 molecules

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