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- PDB-2y72: Crystal structure of the PKD Domain of Collagenase G from Clostri... -

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Basic information

Entry
Database: PDB / ID: 2y72
TitleCrystal structure of the PKD Domain of Collagenase G from Clostridium Histolyticum at 1.18 Angstrom Resolution.
ComponentsCOLLAGENASE
KeywordsHYDROLASE / POLYCYSTIC KIDNEY DISEASE DOMAIN / BETA BARREL / COLLAGEN RECOGNITION DOMAIN
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
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 / PKD domain / Peptidase, C-terminal, archaeal/bacterial / Bacterial pre-peptidase C-terminal 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 / 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 zinc metallopeptidases, zinc-binding region signature. / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesCLOSTRIDIUM HISTOLYTICUM (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.18 Å
AuthorsEckhard, 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.
#1: Journal: Biol.Chem / Year: 2011
Title: Polycystic Kidney Disease-Like Domains of Clostridial Collagenases and Their Role in Collagen Recruitment.
Authors: Eckhard, U. / Brandstetter, H.
History
DepositionJan 27, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 28, 2011Provider: repository / Type: Initial release
Revision 1.1Oct 5, 2011Group: Atomic model / Other
Revision 1.2Oct 19, 2011Group: Database references
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: COLLAGENASE
B: COLLAGENASE


Theoretical massNumber of molelcules
Total (without water)17,8942
Polymers17,8942
Non-polymers00
Water6,557364
1
A: COLLAGENASE


Theoretical massNumber of molelcules
Total (without water)8,9471
Polymers8,9471
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: COLLAGENASE


Theoretical massNumber of molelcules
Total (without water)8,9471
Polymers8,9471
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)68.205, 59.300, 55.280
Angle α, β, γ (deg.)90.00, 125.61, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein COLLAGENASE / COLLAGENASE G


Mass: 8946.764 Da / Num. of mol.: 2
Fragment: POLYCYSTIC KIDNEY DISEASE (PKD) DOMAIN, RESIDUES 799-880
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 364 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.55 Å3/Da / Density % sol: 51.74 % / Description: NONE
Crystal growpH: 7 / Details: 2.5M C3H2O4NA2, 10MM CACL2, PH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.98793
DetectorType: MARRESEARCH / Detector: CCD / Date: Aug 12, 2010 / Details: MIRRORS
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98793 Å / Relative weight: 1
ReflectionResolution: 1.18→40.51 Å / Num. obs: 56646 / % possible obs: 96.4 % / Observed criterion σ(I): 3.2 / Redundancy: 6 % / Biso Wilson estimate: 9.7 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 13.9
Reflection shellResolution: 1.18→1.24 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 3.2 / % possible all: 78.4

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2C26

2c26


Resolution: 1.18→44.94 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.964 / SU B: 1.108 / SU ML: 0.023 / Cross valid method: THROUGHOUT / ESU R: 0.037 / ESU R Free: 0.039 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.17997 2843 5 %RANDOM
Rwork0.14564 ---
obs0.14734 53797 96.32 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.061 Å2
Baniso -1Baniso -2Baniso -3
1-1.48 Å20 Å20.7 Å2
2---0.05 Å20 Å2
3----0.62 Å2
Refinement stepCycle: LAST / Resolution: 1.18→44.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1249 0 0 364 1613
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0221354
X-RAY DIFFRACTIONr_bond_other_d0.0020.02910
X-RAY DIFFRACTIONr_angle_refined_deg1.8051.9361850
X-RAY DIFFRACTIONr_angle_other_deg0.91932226
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3875193
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.52524.81554
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.56315226
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.339156
X-RAY DIFFRACTIONr_chiral_restr0.1150.2211
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021592
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02276
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.1361.5882
X-RAY DIFFRACTIONr_mcbond_other0.6551.5378
X-RAY DIFFRACTIONr_mcangle_it3.34121431
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.193472
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.8424.5411
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr1.69532264
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.18→1.211 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.228 150 -
Rwork0.207 2884 -
obs--70.33 %
Refinement TLS params.

T23: -0.0008 Å2 / Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°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)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.10610.09980.01070.32550.03820.09970.0025-0.0022-0.0026-0.00650.0015-0.0114-0.00810.0047-0.0040.00120.0010.00020.0120.00413.2486-5.077915.3339
20.1062-0.0012-0.01850.2674-0.06860.021-0.0076-0.0047-0.00540.00370.00760.00280.0002000.0018-0.0004-0.00060.01150.003611.0329-19.11584.3578
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A796 - 880
2X-RAY DIFFRACTION2B796 - 880

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