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- PDB-4aqo: CRYSTAL STRUCTURE OF THE CALCIUM BOUND PKD-like DOMAIN OF COLLAGE... -

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Basic information

Entry
Database: PDB / ID: 4aqo
TitleCRYSTAL STRUCTURE OF THE CALCIUM BOUND PKD-like DOMAIN OF COLLAGENASE G FROM CLOSTRIDIUM HISTOLYTICUM AT 0.99 ANGSTROM RESOLUTION.
ComponentsCOLLAGENASE
KeywordsHYDROLASE / PKD-LIKE DOMAIN / COLLAGENOLYSIS / COLLAGEN / RECRUITMENT / TWO- TIERED BETA BARREL
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: 0.99 Å
AuthorsEckhard, U. / Brandstetter, H.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: Structural Basis for Activity Regulation and Substrate Preference of Clostridial Collagenases G, H, and T.
Authors: Eckhard, U. / Schonauer, E. / Brandstetter, H.
History
DepositionApr 19, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 5, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 31, 2013Group: Database references
Revision 1.2Dec 20, 2023Group: 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: COLLAGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,7132
Polymers9,6731
Non-polymers401
Water2,414134
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)19.753, 70.896, 23.379
Angle α, β, γ (deg.)90.00, 95.24, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein COLLAGENASE / COLLAGENASE G


Mass: 9672.577 Da / Num. of mol.: 1 / Fragment: PKD-LIKE DOMAIN, RESIDUES 792-880
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CLOSTRIDIUM HISTOLYTICUM (bacteria) / Plasmid: PET-15B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9X721, microbial collagenase
#2: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 134 / 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: 1.79 Å3/Da / Density % sol: 31.4 % / Description: NONE
Crystal growDetails: 0.1 M POTASSIUM THIOCYANATE, 30% W/V POLYETHYLENE GLYCOL MONOMETHYL ETHER 2000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.8856
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 24, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8856 Å / Relative weight: 1
ReflectionResolution: 0.99→35.4 Å / Num. obs: 32608 / % possible obs: 91.8 % / Observed criterion σ(I): 12.1 / Redundancy: 3.4 % / Biso Wilson estimate: 5.4 Å2 / Rmerge(I) obs: 0.02 / Net I/σ(I): 27.3
Reflection shellResolution: 0.99→1.04 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.06 / Mean I/σ(I) obs: 12.1 / % possible all: 77.1

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2Y72

2y72


Resolution: 0.99→35.45 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.969 / SU B: 0.485 / SU ML: 0.013 / Cross valid method: THROUGHOUT / ESU R: 0.024 / ESU R Free: 0.025 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.14998 1623 5 %RANDOM
Rwork0.12386 ---
obs0.12515 30951 91.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 8.086 Å2
Baniso -1Baniso -2Baniso -3
1--0.16 Å20 Å2-0.13 Å2
2---0.45 Å20 Å2
3---0.59 Å2
Refinement stepCycle: LAST / Resolution: 0.99→35.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms637 0 1 134 772
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.02700
X-RAY DIFFRACTIONr_bond_other_d0.0030.02456
X-RAY DIFFRACTIONr_angle_refined_deg1.5451.941956
X-RAY DIFFRACTIONr_angle_other_deg0.80231136
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9025103
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.22125.71428
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.29315117
X-RAY DIFFRACTIONr_dihedral_angle_4_deg7.053152
X-RAY DIFFRACTIONr_chiral_restr0.0940.2111
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02814
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02136
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr2.31131156
X-RAY DIFFRACTIONr_sphericity_free37.681521
X-RAY DIFFRACTIONr_sphericity_bonded5.28451244
LS refinement shellResolution: 0.99→1.016 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.17 79 -
Rwork0.158 1674 -
obs--66.53 %
Refinement TLS params.Method: refined / Origin x: 4.0466 Å / Origin y: 7.1492 Å / Origin z: 6.1441 Å
111213212223313233
T0.0072 Å2-0.0019 Å20.001 Å2-0.017 Å2-0.0046 Å2--0.0117 Å2
L0.0355 °2-0.1748 °20.0043 °2-1.5514 °2-0.2929 °2--0.2273 °2
S-0.0064 Å °-0.0148 Å °0.004 Å °0.0841 Å °0.0075 Å °-0.0031 Å °-0.0214 Å °0.0227 Å °-0.0011 Å °

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