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- PDB-7zbv: Crystal structure of the peptidase domain of collagenase G from C... -

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Basic information

Entry
Database: PDB / ID: 7zbv
TitleCrystal structure of the peptidase domain of collagenase G from Clostridium histolyticum in complex with a diphosphonate-based inhibitor
ComponentsCollagenase ColG
KeywordsHYDROLASE / collagenase / diphosphonate / ColG / inhibitor / complex
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
Collagenase ColG, catalytic helper subdomain / Collagenase G catalytic helper subdomain / Peptidase M9A/M9B, collagenase, bacterial / Peptidase M9, collagenase, N-terminal domain / Collagenase / Peptidase family M9 N-terminal / Peptidase, C-terminal, archaeal/bacterial / Bacterial pre-peptidase C-terminal domain / PKD domain / Polycystic kidney disease (PKD) domain profile. ...Collagenase ColG, catalytic helper subdomain / Collagenase G catalytic helper subdomain / Peptidase M9A/M9B, collagenase, bacterial / Peptidase M9, collagenase, N-terminal domain / Collagenase / Peptidase family M9 N-terminal / Peptidase, C-terminal, archaeal/bacterial / Bacterial pre-peptidase C-terminal domain / PKD 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 zinc metallopeptidases, zinc-binding region signature. / Immunoglobulin-like fold
Similarity search - Domain/homology
TRIS-HYDROXYMETHYL-METHYL-AMMONIUM / Chem-ITO / Collagenase ColG
Similarity search - Component
Biological speciesHathewaya histolytica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsSchoenauer, E. / Brandstetter, H.
Funding support Austria, 1items
OrganizationGrant numberCountry
Austrian Science FundP 31843 Austria
CitationJournal: J.Med.Chem. / Year: 2022
Title: Discovery and Characterization of Synthesized and FDA-Approved Inhibitors of Clostridial and Bacillary Collagenases.
Authors: Alhayek, A. / Abdelsamie, A.S. / Schonauer, E. / Camberlein, V. / Hutterer, E. / Posselt, G. / Serwanja, J. / Blochl, C. / Huber, C.G. / Haupenthal, J. / Brandstetter, H. / Wessler, S. / Hirsch, A.K.H.
History
DepositionMar 24, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 9, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Collagenase ColG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,8316
Polymers47,8861
Non-polymers9465
Water1,31573
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area440 Å2
ΔGint-8 kcal/mol
Surface area17250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.267, 77.787, 97.319
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Collagenase ColG / Class I collagenase / Gelatinase ColG / Microbial collagenase


Mass: 47885.875 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hathewaya histolytica (bacteria) / Gene: colG / Production host: Escherichia coli (E. coli) / References: UniProt: Q9X721, microbial collagenase

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Non-polymers , 5 types, 78 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-ITO / [6,7-bis(chloranyl)-3-phosphono-quinoxalin-2-yl]phosphonic acid


Mass: 358.997 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H6Cl2N2O6P2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-144 / TRIS-HYDROXYMETHYL-METHYL-AMMONIUM


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 73 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.38 Å3/Da / Density % sol: 48.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: Tris-Bicine pH 8.5,pentaethylene glycol, diethylene glycol, triethylene glycol, tetraethylene glycol, PEG 20,000 and PEG 550 MME

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 10, 2021
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.95→60.76 Å / Num. obs: 33936 / % possible obs: 99.69 % / Redundancy: 2 % / Biso Wilson estimate: 30.71 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.03715 / Net I/σ(I): 12.33
Reflection shellResolution: 1.95→2.02 Å / Rmerge(I) obs: 0.3959 / Num. unique obs: 3303 / CC1/2: 0.699 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX1.20_4459refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2y6i

2y6i


Resolution: 1.95→60.76 Å / SU ML: 0.2164 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.6226
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2286 1733 5.11 %
Rwork0.1865 32202 -
obs-33935 99.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 37.46 Å2
Refinement stepCycle: LAST / Resolution: 1.95→60.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3161 0 50 73 3284
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0123286
X-RAY DIFFRACTIONf_angle_d1.16934457
X-RAY DIFFRACTIONf_chiral_restr0.0585463
X-RAY DIFFRACTIONf_plane_restr0.0092600
X-RAY DIFFRACTIONf_dihedral_angle_d5.5697462
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-2.010.31771380.27542653X-RAY DIFFRACTION99.75
2.01-2.070.28391320.24922637X-RAY DIFFRACTION99.78
2.07-2.150.27361430.23892617X-RAY DIFFRACTION99.24
2.15-2.230.2751330.232683X-RAY DIFFRACTION99.79
2.23-2.330.26471230.20622657X-RAY DIFFRACTION99.93
2.33-2.460.25341460.19852663X-RAY DIFFRACTION100
2.46-2.610.24141530.20562689X-RAY DIFFRACTION100
2.61-2.810.25331460.21022659X-RAY DIFFRACTION99.82
2.81-3.10.24061500.20472690X-RAY DIFFRACTION99.75
3.1-3.540.25721510.18742712X-RAY DIFFRACTION99.93
3.54-4.460.1981620.14882708X-RAY DIFFRACTION99.48
4.46-60.760.17161560.15162834X-RAY DIFFRACTION98.94

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