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- PDB-5o7e: Crystal structure of the peptidase domain of collagenase H from C... -

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Basic information

Entry
Database: PDB / ID: 5o7e
TitleCrystal structure of the peptidase domain of collagenase H from Clostridium histolyticum in complex with N-aryl mercaptoacetamide-based inhibitor
ComponentsColH protein
KeywordsHYDROLASE / HYDROLASE-INHIBITOR COMPLEX / GLUZINCIN / METALLOPROTEASE / collagenase
Function / homology
Function and homology information


tripeptidase activity / microbial collagenase / collagen metabolic process / collagen binding / metalloendopeptidase activity / endopeptidase activity / calcium ion binding / proteolysis / zinc ion binding / extracellular region
Similarity search - Function
Neutral Protease; domain 2 - #20 / Collagenase ColT, N-terminal domain / Threonyl-tRNA Synthetase; Chain A, domain 2 - #50 / Collagenase ColG, catalytic helper subdomain / Collagenase G catalytic helper subdomain / Threonyl-tRNA Synthetase; Chain A, domain 2 / Peptidase M9A/M9B, collagenase, bacterial / Peptidase M9, collagenase, N-terminal domain / Collagenase / Peptidase family M9 N-terminal ...Neutral Protease; domain 2 - #20 / Collagenase ColT, N-terminal domain / Threonyl-tRNA Synthetase; Chain A, domain 2 - #50 / Collagenase ColG, catalytic helper subdomain / Collagenase G catalytic helper subdomain / Threonyl-tRNA Synthetase; Chain A, domain 2 / Peptidase M9A/M9B, collagenase, bacterial / Peptidase M9, collagenase, N-terminal domain / Collagenase / Peptidase family M9 N-terminal / PKD domain / Peptidase, C-terminal, archaeal/bacterial / Bacterial pre-peptidase C-terminal domain / Polycystic kidney disease (PKD) domain profile. / PKD domain / PKD domain superfamily / PKD/Chitinase domain / Repeats in polycystic kidney disease 1 (PKD1) and other proteins / Neutral Protease; domain 2 / Glutaredoxin / Neutral zinc metallopeptidases, zinc-binding region signature. / Concanavalin A-like lectin/glucanase domain superfamily / Immunoglobulin-like fold / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
~{N}-(4-ethanoylphenyl)-2-sulfanyl-ethanamide / Collagenase ColH
Similarity search - Component
Biological speciesHathewaya histolytica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.87 Å
AuthorsSchoenauer, E. / Brandstetter, H.
Funding support Austria, 1items
OrganizationGrant numberCountry
Austrian Science FundW_01213 Austria
CitationJournal: J. Am. Chem. Soc. / Year: 2017
Title: Discovery of a Potent Inhibitor Class with High Selectivity toward Clostridial Collagenases.
Authors: Schonauer, E. / Kany, A.M. / Haupenthal, J. / Husecken, K. / Hoppe, I.J. / Voos, K. / Yahiaoui, S. / Elsasser, B. / Ducho, C. / Brandstetter, H. / Hartmann, R.W.
History
DepositionJun 8, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 31, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2019Group: Data collection / Category: reflns_shell
Revision 1.2Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ColH protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,1354
Polymers45,8201
Non-polymers3153
Water2,036113
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area90 Å2
ΔGint-13 kcal/mol
Surface area16620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.304, 79.677, 56.959
Angle α, β, γ (deg.)90.00, 91.23, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein ColH protein / Collagenase


Mass: 45819.766 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Non-aligned residues at N-terminus were not ordered in crystal. GT = position 1-2, remainder of tag after cleavage LDK ... PNEG = position 3 -394, sequence of peptidase domain of ColH, ...Details: Non-aligned residues at N-terminus were not ordered in crystal. GT = position 1-2, remainder of tag after cleavage LDK ... PNEG = position 3 -394, sequence of peptidase domain of ColH, corresponding to L331-G721 of Uniprot entry Q46085
Source: (gene. exp.) Hathewaya histolytica (bacteria) / Gene: colH / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): NiCo21 (DE3) / References: UniProt: Q46085
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-9NB / ~{N}-(4-ethanoylphenyl)-2-sulfanyl-ethanamide


Mass: 209.265 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H11NO2S / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 113 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.54 Å3/Da / Density % sol: 52 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 6.4 / Details: polyethylene glycol methyl ether 2000, NaCl, MES

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.976 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 27, 2016 / Details: Toroidal mirror
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.87→46.33 Å / Num. obs: 37834 / % possible obs: 99.5 % / Redundancy: 1.6 % / Net I/σ(I): 8.8

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Processing

Software
NameVersionClassification
PHENIX1.8.3_1479refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4arf

4arf


Resolution: 1.87→46.33 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.55
RfactorNum. reflection% reflection
Rfree0.2264 1905 5.04 %
Rwork0.1903 --
obs0.1922 37777 99.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.87→46.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3129 0 16 113 3258
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043221
X-RAY DIFFRACTIONf_angle_d0.8184354
X-RAY DIFFRACTIONf_dihedral_angle_d12.31187
X-RAY DIFFRACTIONf_chiral_restr0.03443
X-RAY DIFFRACTIONf_plane_restr0.004566
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.87-1.91680.34911480.29272577X-RAY DIFFRACTION100
1.9168-1.96860.29131380.25782577X-RAY DIFFRACTION100
1.9686-2.02650.23461080.21712537X-RAY DIFFRACTION100
2.0265-2.0920.22771430.21192551X-RAY DIFFRACTION100
2.092-2.16670.27551330.20722570X-RAY DIFFRACTION100
2.1667-2.25350.24661290.24222539X-RAY DIFFRACTION99
2.2535-2.3560.26991370.20852541X-RAY DIFFRACTION99
2.356-2.48020.25271520.19712552X-RAY DIFFRACTION100
2.4802-2.63560.21431360.20232551X-RAY DIFFRACTION100
2.6356-2.83910.26161390.2072563X-RAY DIFFRACTION100
2.8391-3.12470.23231570.20672527X-RAY DIFFRACTION100
3.1247-3.57670.22231240.2022578X-RAY DIFFRACTION99
3.5767-4.50570.20621110.14972598X-RAY DIFFRACTION99
4.5057-46.34370.15621500.13142611X-RAY DIFFRACTION99

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