PDB-2y50: Crystal Structure of Collagenase G from Clostridium histolyticum ...

ID or keywords:

Entry

Database: PDB / ID: 2y50

Title

Crystal Structure of Collagenase G from Clostridium histolyticum at 2. 80 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 /

MOLECULAR REPLACEMENT / Resolution: 2.8 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	Jan 11, 2011	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	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 / pdbx_struct_conn_angle / 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_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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	2y50.cif.gz	291.7 KB	Display	PDBx/mmCIF format
PDB format	pdb2y50.ent.gz	236.2 KB	Display	PDB format
PDBx/mmJSON format	2y50.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	2y50_validation.pdf.gz	633.2 KB	Display	wwPDB validaton report
Full document	2y50_full_validation.pdf.gz	640.2 KB	Display
Data in XML	2y50_validation.xml.gz	26.4 KB	Display
Data in CIF	2y50_validation.cif.gz	36.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/y5/2y50 ftp://data.pdbj.org/pub/pdb/validation_reports/y5/2y50	HTTPS FTP

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Related structure data

Related structure data	2y3uSC 2y6iC 2y72C S: Starting model for refinement C: citing same article (ref.)
Similar structure data	2y6i-d 4are-d 2y3u-d 6ewx-d 2hro-d 4jrv-1 4jq7-1 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

89.6 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)	57.260, 108.700, 181.520
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: 89031.945 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): BL21(DE3) / References: UniProt: Q9X721, microbial collagenase
#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: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 125 / Source method: isolated from a natural source / Formula: H₂O
Sequence details	SEQUENCE VARIATIONS ARISE AS THIS PROTEIN IS FROM A DIFFERENT STRAIN TO IN UNIPROT

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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: 23% PEG3350, 0.12M TRISODIUM CITRATE PH 8.3

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 1.282
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 27, 2007 / Details: TORODIAL FOCUSING MIRROR
Radiation	Monochromator: CHANNEL CUT ESRF MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.282 Å / Relative weight: 1
Reflection	Resolution: 2.8→35.56 Å / Num. obs: 28517 / % possible obs: 98.9 % / Observed criterion σ(I): 2.8 / Redundancy: 6.9 % / B_iso Wilson estimate: 72.6 Å² / R_merge(I) obs: 0.09 / Net I/σ(I): 12.4
Reflection shell	Resolution: 2.8→2.95 Å / Redundancy: 6.8 % / R_merge(I) obs: 0.59 / Mean I/σ(I) obs: 2.8 / % possible all: 98.1

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Processing

Software

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

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2Y3U

2y3u

Resolution: 2.8→34.83 Å / Cor.coef. F_o:F_c: 0.935 / Cor.coef. F_o:F_c free: 0.901 / SU B: 41.423 / SU ML: 0.358 / Cross valid method: THROUGHOUT / ESU R: 0.681 / ESU R Free: 0.362 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED. CATALYTIC ZN BINDING SITE IS FORMED BY HIS523, HIS527 AND GLU555

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.28159	1433	5 %	RANDOM
R_work	0.23204	-	-	-
obs	0.23452	27004	98.99 %	-

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: 70.962 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	13.09 Å²	0 Å²	0 Å²
2-	-	-5.15 Å²	0 Å²
3-	-	-	-7.94 Å²

Refinement step

Cycle: LAST / Resolution: 2.8→34.83 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5300	0	33	125	5458

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.006	0.022	5458
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	0.908	1.94	7401
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	4.619	5	670
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	34.086	24.704	270
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.217	15	852
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.571	15	20
X-RAY DIFFRACTION	r_chiral_restr	0.064	0.2	796
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.02	4225
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	0.242	1.5	3322
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	0.456	2	5327
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	0.926	3	2136
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	1.012	4.5	2074
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: 2.8→2.872 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.391	109	-
R_work	0.351	1942	-
obs	-	-	97.71 %

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	28.3908	-7.731	-10.3295	33.3125	9.4358	25.2814	0.8104	-1.6313	-1.3981	1.6681	-0.2765	0.7948	1.0036	0.7829	-0.5339	0.7143	-0.3466	-0.1277	0.4552	0.0073	0.2996	-9.6404	39.498	10.8406
2	5.0798	-0.3439	0.5847	7.4289	2.6832	10.2571	0.0051	0.0906	-0.4901	0.7474	0.3211	-0.4779	-0.5611	0.6253	-0.3262	0.6563	-0.2669	0.0115	0.2105	-0.1686	0.3696	-12.2284	44.7197	1.0945
3	0.1418	-0.8562	0.0109	8.4849	5.9695	14.1729	0.0731	0.0853	-0.052	0.1866	-0.6635	-0.1901	0.0644	-0.5257	0.5904	0.7241	-0.18	-0.0893	0.2427	-0.1423	0.8211	-17.2385	39.5269	-2.8461
4	3.5846	0.0794	0.0305	6.5481	2.4059	7.8908	0.2151	-0.3042	0.0002	-0.3209	-0.2133	0.297	-1.344	-0.3013	-0.0018	0.6319	-0.1283	-0.0026	0.2034	-0.174	0.3121	-19.5511	44.9671	-9.3242
5	6.52	-0.1627	-1.2942	7.8623	2.8373	7.7406	-0.0039	-0.3128	-0.2907	-1.0892	0.4646	-0.5441	-1.3044	1.0263	-0.4607	0.4596	-0.3208	0.1345	0.3342	-0.2105	0.331	-13.143	36.4902	-20.7333
6	8.4808	-1.0561	0.3335	4.0165	2.0688	5.9948	0.0177	-0.6204	0.5694	-0.7172	0.0532	0.4087	-1.2246	-0.7015	-0.0709	0.6696	-0.0402	-0.0448	0.2465	-0.1091	0.4613	-27.4031	39.1438	-22.2733
7	11.0399	-1.761	1.5093	6.3343	3.3779	6.6108	-0.193	-0.1561	0.1101	-0.7495	0.4518	-0.1998	-0.7812	0.0019	-0.2588	0.6856	-0.1711	0.0481	0.1938	-0.0465	0.2527	-23.7654	30.1322	-29.3089
8	1.0252	2.695	0.3506	7.7191	1.7052	1.8649	-0.314	0.0279	0.2921	-1.333	0.1103	1.0619	-0.5663	-0.0964	0.2037	0.6831	-0.0148	-0.213	0.2959	0.0751	0.4394	-32.5455	18.4247	-34.5218
9	1.7822	1.089	0.7233	6.2089	-2.4604	3.9893	-0.2312	0.0894	-0.3771	-0.6482	-0.0483	-0.2648	-0.5476	0.3129	0.2795	0.3493	-0.0355	0.0041	0.4096	-0.0782	0.4565	-30.3141	-12.789	-29.8627
10	1.155	2.0796	0.0206	7.4884	-0.5457	3.398	-0.3282	-0.1746	0.0798	-1.0246	0.0634	0.4373	-0.7403	-0.1702	0.2648	0.3483	0.0439	-0.0577	0.532	-0.0355	0.618	-34.3053	-1.1147	-25.2924
11	6.4858	-0.0619	-0.2053	6.848	-0.6975	3.7522	-0.1669	0.0554	-0.0793	-0.4956	0.0482	-0.4879	-0.414	0.4295	0.1187	0.1058	-0.0115	-0.004	0.656	-0.0555	0.7064	-25.665	-1.0547	-23.1695
12	6.3667	-3.6387	-0.346	5.4496	3.3781	3.0281	-0.485	-0.1635	0.3437	0.3389	0.3674	-0.0779	0.1381	0.2642	0.1176	0.4318	0.0502	0.0315	0.5008	0.1072	0.7249	-31.9775	-10.4822	-20.3575
13	0.8719	-3.2528	-1.7087	13.4738	2.9799	12.1557	-0.173	0.0655	-0.0941	1.1342	-0.2077	0.3971	-0.9265	-0.1614	0.3807	0.2229	0.0317	0.0461	0.4286	-0.0215	0.558	-41.9211	-5.4681	-7.3709
14	1.8556	0.7385	0.6632	7.766	-0.7554	0.4311	-0.4677	-0.1452	-0.1013	0.0144	0.4092	-0.5603	-0.2206	0.1093	0.0585	0.1411	-0.0279	-0.025	0.9396	-0.0046	0.5433	-26.936	-15.4744	-13.3197
15	1.8772	3.2654	-2.9086	7.8257	-2.0084	10.3489	0.4868	-0.3849	-0.0028	1.2658	-0.3889	-0.6351	-0.7561	1.0396	-0.0979	0.4444	0.028	-0.4209	0.4053	-0.0701	0.6132	-18.8543	-10.6655	-0.6979
16	9.4519	2.4068	-0.572	1.1036	1.0446	9.5362	-0.1163	-0.3804	0.5206	0.5244	0.0247	-0.0497	0.2924	0.2922	0.0915	0.8017	0.1797	-0.2612	0.1888	0.0311	0.2984	-26.365	-15.4676	-4.7788
17	1.3564	0.5502	0.236	3.8413	1.2981	3.4618	-0.1629	0.0042	-0.0984	0.3935	0.0822	-0.132	0.2701	0.2143	0.0807	0.2978	0.0851	0.024	0.4039	0.0288	0.4894	-30.9135	-22.9205	-15.9987
18	2.139	1.0344	-1.432	6.2446	-1.6371	6.1364	-0.2393	-0.0108	-0.178	-0.132	0.0425	-0.021	0.3453	0.0855	0.1968	0.1961	-0.0119	0.0562	0.3036	-0.0785	0.4237	-34.8768	-30.1548	-24.9944
19	2.5986	1.0977	-2.4214	4.1117	-1.6746	8.8384	-0.2999	0.1254	0.3269	-0.3272	0.1777	0.3669	0.7431	-0.7113	0.1221	0.3197	-0.0292	-0.0067	0.2851	-0.07	0.4446	-39.8815	-29.7809	-24.2507

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	117 - 124
2	X-RAY DIFFRACTION	2	A	125 - 185
3	X-RAY DIFFRACTION	3	A	186 - 200
4	X-RAY DIFFRACTION	4	A	201 - 236
5	X-RAY DIFFRACTION	5	A	237 - 285
6	X-RAY DIFFRACTION	6	A	286 - 326
7	X-RAY DIFFRACTION	7	A	327 - 357
8	X-RAY DIFFRACTION	8	A	358 - 418
9	X-RAY DIFFRACTION	9	A	419 - 452
10	X-RAY DIFFRACTION	10	A	453 - 489
11	X-RAY DIFFRACTION	11	A	490 - 517
12	X-RAY DIFFRACTION	12	A	518 - 533
13	X-RAY DIFFRACTION	13	A	534 - 548
14	X-RAY DIFFRACTION	14	A	549 - 575
15	X-RAY DIFFRACTION	15	A	576 - 597
16	X-RAY DIFFRACTION	16	A	600 - 627
17	X-RAY DIFFRACTION	17	A	628 - 709
18	X-RAY DIFFRACTION	18	A	710 - 757
19	X-RAY DIFFRACTION	19	A	758 - 790

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