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- PDB-4ar9: Crystal structure of the peptidase domain of collagenase T from C... -

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Basic information

Entry
Database: PDB / ID: 4ar9
TitleCrystal structure of the peptidase domain of collagenase T from Clostridium tetani at 1.69 angstrom resolution.
ComponentsCOLLAGENASE COLT
KeywordsHYDROLASE / COLLAGEN / METALLOPROTEASE / PEPTIDASE / COLLAGENOLYSIS
Function / homology
Function and homology information


microbial collagenase / metalloendopeptidase activity / endopeptidase activity / calcium ion binding / proteolysis / zinc ion binding / extracellular region
Similarity search - Function
Neutral Protease; domain 2 - #20 / Collagenase ColT, N-terminal domain / Threonyl-tRNA Synthetase; Chain A, domain 2 - #50 / 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 / Threonyl-tRNA Synthetase; Chain A, domain 2 ...Neutral Protease; domain 2 - #20 / Collagenase ColT, N-terminal domain / Threonyl-tRNA Synthetase; Chain A, domain 2 - #50 / 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 / Threonyl-tRNA Synthetase; Chain A, domain 2 / Peptidase, C-terminal, archaeal/bacterial / Bacterial pre-peptidase C-terminal domain / Neutral Protease; domain 2 / Neutral zinc metallopeptidases, zinc-binding region signature. / Glutaredoxin / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesCLOSTRIDIUM TETANI (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.69 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 22, 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.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_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

Downloads & links

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Assembly

Deposited unit
A: COLLAGENASE COLT
B: COLLAGENASE COLT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,7136
Polymers91,5022
Non-polymers2114
Water10,251569
1
A: COLLAGENASE COLT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,8563
Polymers45,7511
Non-polymers1052
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: COLLAGENASE COLT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,8563
Polymers45,7511
Non-polymers1052
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)76.890, 102.110, 104.750
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 COLLAGENASE COLT / COLLAGENASE T


Mass: 45750.816 Da / Num. of mol.: 2 / Fragment: PEPTIDASE DOMAIN, RESIDUES 340-730
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CLOSTRIDIUM TETANI (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q899Y1, microbial collagenase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 569 / 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: 2.26 Å3/Da / Density % sol: 45.58 % / Description: NONE
Crystal growpH: 6.5 / Details: 25% PEG 3350, 100MM NACL, 0.1M MES PH 6.5

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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: Sep 11, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8856 Å / Relative weight: 1
ReflectionResolution: 1.69→39.85 Å / Num. obs: 88975 / % possible obs: 96.2 % / Observed criterion σ(I): 2 / Redundancy: 5.7 % / Biso Wilson estimate: 20 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 8.7
Reflection shellResolution: 1.69→1.78 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 2 / % possible all: 94.5

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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 2Y3U

2y3u


Resolution: 1.69→38.45 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.942 / SU B: 5.314 / SU ML: 0.078 / Cross valid method: THROUGHOUT / ESU R: 0.168 / ESU R Free: 0.11 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.22105 4451 5 %RANDOM
Rwork0.17234 ---
obs0.17482 84407 95.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.463 Å2
Baniso -1Baniso -2Baniso -3
1-1.15 Å20 Å20 Å2
2---1.52 Å20 Å2
3---0.38 Å2
Refinement stepCycle: LAST / Resolution: 1.69→38.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6325 0 4 569 6898
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.026526
X-RAY DIFFRACTIONr_bond_other_d0.0050.024421
X-RAY DIFFRACTIONr_angle_refined_deg1.3931.9378818
X-RAY DIFFRACTIONr_angle_other_deg1.13310686
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1275792
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.32525.075335
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.632151094
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.5621518
X-RAY DIFFRACTIONr_chiral_restr0.0840.2920
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.027370
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021383
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_restr2.935310947
X-RAY DIFFRACTIONr_sphericity_free26.8885196
X-RAY DIFFRACTIONr_sphericity_bonded7.004511148
LS refinement shellResolution: 1.69→1.734 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.339 323 -
Rwork0.268 5690 -
obs--92.51 %
Refinement TLS params.

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)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.81050.2903-0.17671.49310.17171.11430.025-0.021-0.0252-0.0663-0.02820.00880.00930.03710.00320.0066-0.0043-0.00270.0359-0.00390.031-5.64314.7357-25.4257
20.9877-0.34580.29511.20170.27441.42110.11610.05740.0494-0.0273-0.0629-0.10470.1503-0.0051-0.05320.0365-0.01130.0040.03680.01440.04332.491212.2537-25.7698
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A339 - 730
2X-RAY DIFFRACTION2B339 - 730

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