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- PDB-9cme: Room Temperature Crystal Structure of Collagenase ColH from Hathe... -

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Basic information

Entry
Database: PDB / ID: 9cme
TitleRoom Temperature Crystal Structure of Collagenase ColH from Hathewaya histolytica at 2.7 Angstrom resolution
ComponentsCollagenase ColH
KeywordsHYDROLASE / endopeptidase / peptidase M9B family / catalytic module / bacterial collagenase / zinc metalloproteinase
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. / Concanavalin A-like lectin/glucanase domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Biological speciesHathewaya histolytica (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsSakon, J. / Bonsu, A. / Oki, H. / Kawahara, K. / Matsushita, O. / Mima, T. / Takebe, K.
Funding support United States, Japan, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)103429 United States
Japan Society for the Promotion of Science (JSPS)23K06545 Japan
CitationJournal: To Be Published
Title: Room Temperature Crystal Structure of Collagenase ColH from Hathewaya histolytica at 2.7 Angstrom resolution
Authors: Sakon, J. / Bonsu, A. / Oki, H. / Kawahara, K. / Matsushita, O. / Mima, T. / Takebe, K. / Koide, T. / Fujii, K.
History
DepositionJul 15, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 14, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Collagenase ColH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,7093
Polymers79,6031
Non-polymers1052
Water4,378243
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.075, 125.961, 131.521
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 ColH / Class II collagenase / Gelatinase ColH / Microbial collagenase


Mass: 79603.023 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hathewaya histolytica (bacteria) / Gene: colH / Production host: Escherichia coli (E. coli) / References: UniProt: Q46085, microbial collagenase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 243 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.33 Å3/Da / Density % sol: 47.23 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M Bis-Tris pH 6.5 buffer containing 0.2 M magnesium chloride hexahydrate salt and 25% w/v polyethylene glycol (PEG) 3,350

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Data collection

DiffractionMean temperature: 297 K / Ambient temp details: Room Temperature / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: RIGAKU PhotonJet-S / Wavelength: 1.54 Å
DetectorType: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Mar 1, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
Reflection twin
TypeCrystal-IDIDOperatorDomain-IDFraction
pseudo-merohedral11H, K, L10.7991
pseudo-merohedral22-H, -L, -K20.2009
ReflectionResolution: 2.7→22.29 Å / Num. obs: 118655 / % possible obs: 99.5 % / Redundancy: 5.7 % / CC1/2: 0.962 / Rmerge(I) obs: 0.224 / Rpim(I) all: 0.111 / Net I/σ(I): 6.4
Reflection shellResolution: 2.7→2.83 Å / Num. unique obs: 2722 / CC1/2: 0.439

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
CrysalisProdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→22.29 Å / SU ML: 0 / Cross valid method: FREE R-VALUE / σ(F): 24.85 / Phase error: 31.49 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2714 1069 5.15 %
Rwork0.2305 --
obs0.2343 20756 99.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.7→22.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5531 0 2 243 5776
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0025661
X-RAY DIFFRACTIONf_angle_d0.4787655
X-RAY DIFFRACTIONf_dihedral_angle_d4.087758
X-RAY DIFFRACTIONf_chiral_restr0.038807
X-RAY DIFFRACTIONf_plane_restr0.004990
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.840.30551340.27042785X-RAY DIFFRACTION95
2.84-3.020.30171010.25782807X-RAY DIFFRACTION96
3.02-3.250.32561700.25112744X-RAY DIFFRACTION94
3.25-3.580.30361510.22522774X-RAY DIFFRACTION94
3.58-4.090.26641560.2242815X-RAY DIFFRACTION94
4.09-5.150.24271360.20162862X-RAY DIFFRACTION95
5.15-22.290.25311840.23962937X-RAY DIFFRACTION93
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)
11.1846-0.16310.26351.0451-0.42390.5999-0.2056-0.0960.61130.42350.108-0.1626-0.518-0.05620.06520.7186-0.0907-0.09330.24010.15130.584-16.83448.2996-7.6764
20.52330.2431-0.03150.59640.22720.88110.0337-0.2870.23620.1624-0.01280.0143-0.0462-0.0576-0.00710.30890.0599-0.05050.0669-0.13480.2033-23.8983-18.808119.6767
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 6 through 302 )
2X-RAY DIFFRACTION2chain 'A' and (resid 303 through 681 )

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