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- PDB-3jqx: Crystal structure of Clostridium histolyticum colH collagenase co... -

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Basic information

Entry
Database: PDB / ID: 3jqx
TitleCrystal structure of Clostridium histolyticum colH collagenase collagen binding domain 3 at 2.2 Angstrom resolution in the presence of calcium and cadmium
ComponentsColH protein
KeywordsCELL ADHESION / beta barrel / dual calcium-binding motif / Collagen
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
Jelly Rolls - #380 / 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 ...Jelly Rolls - #380 / 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. / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Immunoglobulin-like fold / Sandwich / Mainly Beta
Similarity search - Domain/homology
: / Collagenase ColH
Similarity search - Component
Biological speciesClostridium histolyticum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsSakon, J. / Philominathan, S.T.L. / Bauer, R. / Matsushita, O.
CitationJournal: J.Bacteriol. / Year: 2013
Title: Structural Comparison of ColH and ColG Collagen-Binding Domains from Clostridium histolyticum.
Authors: Bauer, R. / Wilson, J.J. / Philominathan, S.T. / Davis, D. / Matsushita, O. / Sakon, J.
History
DepositionSep 8, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 29, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 11, 2012Group: Other
Revision 1.3Dec 5, 2012Group: Database references
Revision 1.4Jan 9, 2013Group: Database references
Revision 1.5Sep 6, 2023Group: 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 / struct_ref_seq_dif / struct_site
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_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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_asym_id / _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_asym_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_ref_seq_dif.details / _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: ColH protein
B: ColH protein
C: ColH protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,37015
Polymers40,2383
Non-polymers1,13212
Water3,549197
1
A: ColH protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,7905
Polymers13,4131
Non-polymers3774
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: ColH protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,7905
Polymers13,4131
Non-polymers3774
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: ColH protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,7905
Polymers13,4131
Non-polymers3774
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)61.567, 64.589, 96.010
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein ColH protein / Collagenase


Mass: 13412.737 Da / Num. of mol.: 3 / Fragment: collagen binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium histolyticum (bacteria) / Gene: colH / Production host: Escherichia coli (E. coli) / References: UniProt: Q46085, microbial collagenase
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Cd
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 197 / 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: 2.37 Å3/Da / Density % sol: 48.15 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: sodium acetate, CdSO4,CaCl2, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97937 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97937 Å / Relative weight: 1
ReflectionResolution: 2.2→30 Å / Num. obs: 18873 / % possible obs: 98.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 13.9 % / Rsym value: 0.12 / Net I/σ(I): 9.6
Reflection shellResolution: 2.2→2.5 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 2.4 / Num. unique all: 1431 / Rsym value: 0.54 / % possible all: 97.7

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Processing

Software
NameVersionClassification
HKL-3000data collection
PHASERphasing
CCP4model building
REFMAC5.2.0019refinement
HKL-3000data reduction
HKL-3000data scaling
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2o8o ColG-3b collagen binding domain

2o8o


Resolution: 2.2→28.68 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.908 / SU B: 5.905 / SU ML: 0.15 / Cross valid method: THROUGHOUT / ESU R: 0.262 / ESU R Free: 0.224 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2502 1017 5.1 %RANDOM
Rwork0.17571 ---
obs0.17941 18872 98.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.309 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å20 Å2
2---0.02 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.2→28.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2801 0 12 197 3010
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0222876
X-RAY DIFFRACTIONr_angle_refined_deg1.8891.9533913
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9945355
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.90725.248141
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.18115436
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.297158
X-RAY DIFFRACTIONr_chiral_restr0.1290.2403
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022280
X-RAY DIFFRACTIONr_nbd_refined0.2190.21275
X-RAY DIFFRACTIONr_nbtor_refined0.3210.21937
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1840.2211
X-RAY DIFFRACTIONr_metal_ion_refined0.1150.215
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1780.264
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.290.227
X-RAY DIFFRACTIONr_mcbond_it1.1831.51811
X-RAY DIFFRACTIONr_mcangle_it2.08722866
X-RAY DIFFRACTIONr_scbond_it3.33831250
X-RAY DIFFRACTIONr_scangle_it4.9034.51047
LS refinement shellResolution: 2.196→2.253 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.272 69 -
Rwork0.204 1362 -
obs-1431 98.22 %

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