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- PDB-4tn9: Crystal structure of Clostridium histolyticum ColG collagenase po... -

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Basic information

Entry
Database: PDB / ID: 4tn9
TitleCrystal structure of Clostridium histolyticum ColG collagenase polycystic kidney disease-like domain at 1.4 Angstrom resolution
ComponentsCollagenase
KeywordsMETAL BINDING PROTEIN
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. / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesClostridium histolyticum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.4 Å
AuthorsBauer, R. / Sakon, J. / Philominathan, S.T.L. / Matsushita, O. / Gann, S.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2015
Title: Structures of three polycystic kidney disease-like domains from Clostridium histolyticum collagenases ColG and ColH.
Authors: Bauer, R. / Janowska, K. / Taylor, K. / Jordan, B. / Gann, S. / Janowski, T. / Latimer, E.C. / Matsushita, O. / Sakon, J.
History
DepositionJun 3, 2014Deposition site: RCSB / Processing site: RCSB
SupersessionMar 11, 2015ID: 3JQU
Revision 1.0Mar 11, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2015Group: Database references
Revision 1.2Jul 20, 2016Group: Data collection
Revision 1.3Nov 22, 2017Group: Derived calculations / Refinement description / Category: pdbx_struct_oper_list / software / Item: _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Collagenase
B: Collagenase


Theoretical massNumber of molelcules
Total (without water)18,3462
Polymers18,3462
Non-polymers00
Water7,476415
1
A: Collagenase


Theoretical massNumber of molelcules
Total (without water)9,1731
Polymers9,1731
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Collagenase


Theoretical massNumber of molelcules
Total (without water)9,1731
Polymers9,1731
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)24.998, 71.763, 47.894
Angle α, β, γ (deg.)90.000, 95.560, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: ASN / End label comp-ID: ASN / Refine code: 3 / Auth seq-ID: 685 - 770 / Label seq-ID: 1 - 86

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
DetailsThe biological unit is a monomer.

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Components

#1: Protein Collagenase


Mass: 9172.991 Da / Num. of mol.: 2 / Fragment: UNP residues 797-881
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium histolyticum (bacteria) / Gene: colG / Production host: Escherichia coli (E. coli) / References: UniProt: Q9X721
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 415 / 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: 2.33 Å3/Da / Density % sol: 47.22 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 41-49% MPD, 100 mM Bis-Tris (pH 5.5), 0.1-0.3% ammonium acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.919 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Apr 5, 2008
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.919 Å / Relative weight: 1
ReflectionResolution: 1.4→50 Å / Num. obs: 30393 / % possible obs: 92.5 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.068 / Χ2: 1.492 / Net I/av σ(I): 21.321 / Net I/σ(I): 8.4 / Num. measured all: 99029
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.4-1.452.40.35827380.68883.7
1.45-1.513.10.31231740.76497.7
1.51-1.583.40.23432520.8299.3
1.58-1.663.50.18932970.98199.7
1.66-1.763.50.14932491.21999.6
1.76-1.93.30.12326541.44881.2
1.9-2.093.30.132273.08298.4
2.09-2.393.20.06824901.89475.9
2.39-3.023.50.05133141.71699.9
3.02-503.20.0429982.04789.6

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
HKL-3000data reduction
PDB_EXTRACT3.14data extraction
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 1.4→20.36 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.942 / SU B: 2.006 / SU ML: 0.042 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.083 / ESU R Free: 0.078 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2178 1539 5.1 %RANDOM
Rwork0.167 28786 --
obs0.1696 28786 92.23 %-
Solvent computationSolvent model: BABINET MODEL
Displacement parametersBiso max: 95.12 Å2 / Biso mean: 18.343 Å2 / Biso min: 5.93 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å20 Å2-0.52 Å2
2---0.71 Å20 Å2
3---0.55 Å2
Refinement stepCycle: final / Resolution: 1.4→20.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1281 0 0 415 1696
Biso mean---31.18 -
Num. residues----173
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0221343
X-RAY DIFFRACTIONr_angle_refined_deg1.651.9431808
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6585171
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.74225.08857
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.24115242
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.688156
X-RAY DIFFRACTIONr_chiral_restr0.1350.2203
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.02992
X-RAY DIFFRACTIONr_mcbond_it2.7051.5851
X-RAY DIFFRACTIONr_mcangle_it3.8221375
X-RAY DIFFRACTIONr_scbond_it5.3183492
X-RAY DIFFRACTIONr_scangle_it7.5024.5433
X-RAY DIFFRACTIONr_rigid_bond_restr2.71231343
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
344TIGHT POSITIONAL0.120.05
271LOOSE POSITIONAL0.335
344TIGHT THERMAL0.80.5
271LOOSE THERMAL0.7810
LS refinement shellResolution: 1.4→1.439 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.356 94 -
Rwork0.283 1771 -
all-1865 -
obs--78.53 %

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