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- PDB-4u6t: Crystal structure of the Clostridium histolyticum colH collagenas... -

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Basic information

Entry
Database: PDB / ID: 4u6t
TitleCrystal structure of the Clostridium histolyticum colH collagenase polycystic kidney disease-like domain 2a at 1.76 Angstrom resolution
ComponentsColH protein
KeywordsHYDROLASE / Calcium-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. / Concanavalin A-like lectin/glucanase domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesClostridium histolyticum (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 1.76 Å
AuthorsBauer, R. / Janowska, K. / Sakon, J. / Matsushita, O. / Latimer, E.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM103429 United States
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
DepositionJul 29, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 11, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 10, 2015Group: Database references
Revision 1.2Sep 27, 2017Group: Advisory / Author supporting evidence ...Advisory / Author supporting evidence / Derived calculations / Other / Refinement description / Source and taxonomy
Category: entity_src_gen / pdbx_audit_support ...entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_struct_oper_list / pdbx_validate_close_contact / software
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization ..._entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_oper_list.symmetry_operation / _software.name
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Dec 27, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / refine_hist / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein / _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: ColH protein
B: ColH protein
C: ColH protein
D: ColH protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,7659
Polymers38,1334
Non-polymers1,6325
Water19,9251106
1
A: ColH protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,1863
Polymers9,5331
Non-polymers6532
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: ColH protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,8602
Polymers9,5331
Non-polymers3261
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: ColH protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,1863
Polymers9,5331
Non-polymers6532
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: ColH protein


Theoretical massNumber of molelcules
Total (without water)9,5331
Polymers9,5331
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)88.330, 88.330, 123.560
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: LEU / Beg label comp-ID: LEU / End auth comp-ID: ASP / End label comp-ID: ASP / Refine code: 3 / Auth seq-ID: 687 - 770 / Label seq-ID: 3 - 86

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD

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Components

#1: Protein
ColH protein / Collagenase


Mass: 9533.257 Da / Num. of mol.: 4
Fragment: polycystic kidney disease-like domain (UNP residues 725-810)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium histolyticum (bacteria) / Gene: colH / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(RIL) / References: UniProt: Q46085
#2: Chemical
ChemComp-P33 / 3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL / HEPTAETHYLENE GLYCOL / PEG330


Mass: 326.383 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C14H30O8 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1106 / 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: 3.65 Å3/Da / Density % sol: 66.29 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 3 M ammonium sulfate, 0.1 M MES pH 4.5, 15% (w/v) PEG 4000

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 92 / Detector: CCD / Date: May 14, 2013 / Details: CCD
RadiationMonochromator: Osmic Blue confocal mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.76→65.04 Å / Num. obs: 53717 / % possible obs: 99.5 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.068 / Χ2: 1.11 / Net I/σ(I): 11.5 / Num. measured all: 254417 / Scaling rejects: 1909
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allΧ2Rejects% possible all
1.76-1.822.120.3742.31086751290.96095.7
1.82-1.93.10.30531669253810.99099.9
1.9-1.984.690.254.82531853921.1918100
1.98-2.095.090.1726.82743353831.0718100
2.09-2.225.110.1249.22765253991.0343100
2.22-2.395.280.1110.52846953801.017099.9
2.39-2.635.430.09512.22946754021.0211999.9
2.63-3.015.490.081142981853860.9923399.9
3.01-3.795.360.06318.92942054211.0434199.9
3.79-65.045.180.05923.32928154441.68106799.6

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
d*TREK9.9.9.4 W9RSSIdata reduction
PDB_EXTRACT3.14data extraction
d*TREKdata scaling
RefinementResolution: 1.76→65.04 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.899 / SU B: 5.797 / SU ML: 0.086 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.124 / ESU R Free: 0.135 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2715 2731 5.1 %RANDOM
Rwork0.2067 50932 --
obs0.2099 53663 99.36 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 143.34 Å2 / Biso mean: 31.334 Å2 / Biso min: 12.47 Å2
Baniso -1Baniso -2Baniso -3
1-0.52 Å20.26 Å20 Å2
2--0.52 Å20 Å2
3----0.78 Å2
Refinement stepCycle: final / Resolution: 1.76→65.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2684 0 110 1106 3900
Biso mean--56.65 42.32 -
Num. residues----344
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0222871
X-RAY DIFFRACTIONr_angle_refined_deg1.2291.9873818
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3045340
X-RAY DIFFRACTIONr_dihedral_angle_2_deg43.27726.97132
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.48215514
X-RAY DIFFRACTIONr_chiral_restr0.1190.2388
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212084
X-RAY DIFFRACTIONr_mcbond_it4.0181.51696
X-RAY DIFFRACTIONr_mcangle_it5.82222749
X-RAY DIFFRACTIONr_scbond_it12.90931175
X-RAY DIFFRACTIONr_scangle_it14.3534.51069
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A336TIGHT POSITIONAL0.160.05
2B336TIGHT POSITIONAL0.140.05
3C336TIGHT POSITIONAL0.120.05
4D336TIGHT POSITIONAL0.140.05
1A302LOOSE POSITIONAL0.275
2B302LOOSE POSITIONAL0.25
3C302LOOSE POSITIONAL0.165
4D302LOOSE POSITIONAL0.185
1A336TIGHT THERMAL0.880.5
2B336TIGHT THERMAL0.80.5
3C336TIGHT THERMAL0.90.5
4D336TIGHT THERMAL0.860.5
1A302LOOSE THERMAL1.0410
2B302LOOSE THERMAL0.8710
3C302LOOSE THERMAL0.7710
4D302LOOSE THERMAL0.8310
LS refinement shellResolution: 1.76→1.806 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.32 198 -
Rwork0.268 3563 -
all-3761 -
obs--94.64 %
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)
11.73850.45090.4010.68630.08151.9776-0.08370.04930.0705-0.0160.05410.0098-0.00640.02090.02960.00550.0008-0.00380.01020.00150.004335.485-23.48-29.787
21.8207-0.32360.34960.56130.30471.8427-0.1008-0.13880.06690.03680.095-0.03910.0320.02760.00580.010.0152-0.00710.0353-0.0130.006657.484-27.226-36.56
32.23-0.45770.08281.9746-0.40682.00510.10180.1555-0.3678-0.1596-0.03960.15340.3205-0.0494-0.06220.08980.0044-0.03870.0424-0.05110.088755.9-41.957-53.328
42.1812-0.02340.2032.56830.56481.35530.1797-0.1232-0.39810.19-0.1117-0.27820.29410.0581-0.06810.09210.0008-0.04510.03880.05390.125237.338-39.357-15.391
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A685 - 770
2X-RAY DIFFRACTION2B685 - 770
3X-RAY DIFFRACTION3C685 - 770
4X-RAY DIFFRACTION4D685 - 770

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