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- PDB-9l5o: Crystal structure of the mutant Y549A of collagenase VhaC -

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Basic information

Entry
Database: PDB / ID: 9l5o
TitleCrystal structure of the mutant Y549A of collagenase VhaC
Components
  • ASP-TYR-ALA-PRO-THR-LYS-LEU-LEU-PRO-GLN-GLN-PRO
  • LEU-SER-GLU-PRO-SER-GLN-GLN-VAL-THR-GLU-ILE-TYR-GLN-HIS-HIS-ALA-HIS-GLN-ASN-GLY-ASN
  • microbial collagenase
KeywordsHYDROLASE / collagenase / M9 family
Function / homology
Function and homology information


microbial collagenase / metalloendopeptidase activity / proteolysis / extracellular region / zinc ion binding
Similarity search - Function
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 ...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 / Immunoglobulin-like fold
Similarity search - Domain/homology
microbial collagenase
Similarity search - Component
Biological speciesVibrio harveyi VHJR7 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsZhao, W.X.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, China) China
CitationJournal: To Be Published
Title: Crystal structure of the mutant Y549A of collagenase VhaC
Authors: Zhao, W.X.
History
DepositionDec 23, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Nov 5, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: microbial collagenase
B: LEU-SER-GLU-PRO-SER-GLN-GLN-VAL-THR-GLU-ILE-TYR-GLN-HIS-HIS-ALA-HIS-GLN-ASN-GLY-ASN
C: ASP-TYR-ALA-PRO-THR-LYS-LEU-LEU-PRO-GLN-GLN-PRO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,51715
Polymers63,5953
Non-polymers92212
Water8,899494
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6490 Å2
ΔGint-99 kcal/mol
Surface area23280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.366, 49.478, 90.225
Angle α, β, γ (deg.)90.000, 103.790, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb

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Components

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Protein , 1 types, 1 molecules A

#1: Protein microbial collagenase


Mass: 59802.547 Da / Num. of mol.: 1 / Mutation: Y549A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio harveyi VHJR7 (bacteria) / Gene: DS957_010145 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A8B3DGT3, microbial collagenase

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Protein/peptide , 2 types, 2 molecules BC

#2: Protein/peptide LEU-SER-GLU-PRO-SER-GLN-GLN-VAL-THR-GLU-ILE-TYR-GLN-HIS-HIS-ALA-HIS-GLN-ASN-GLY-ASN


Mass: 2420.528 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio harveyi VHJR7 (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria)
#3: Protein/peptide ASP-TYR-ALA-PRO-THR-LYS-LEU-LEU-PRO-GLN-GLN-PRO


Mass: 1371.556 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio harveyi VHJR7 (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria)

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Non-polymers , 4 types, 506 molecules

#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 494 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 2.5 Å3/Da / Density % sol: 50.82 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop
Details: In the buffer containing 0.2 M lithium chloride, 0.1 M Tris-HCl (pH 8.0), and 24% (w/v) polyethylene glycol 8000.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 19, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.9→63.14 Å / Num. obs: 47171 / % possible obs: 94.7 % / Redundancy: 2.4 % / CC1/2: 0.998 / Rmerge(I) obs: 0.062 / Net I/σ(I): 13.2
Reflection shellResolution: 1.9→1.94 Å / Num. unique obs: 432 / CC1/2: 0.999

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→49.78 Å / SU ML: 0.2065 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.6191
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2209 2000 4.24 %
Rwork0.178 45127 -
obs0.1798 47161 94.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.92 Å2
Refinement stepCycle: LAST / Resolution: 1.9→49.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4489 0 52 494 5035
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064656
X-RAY DIFFRACTIONf_angle_d0.75126317
X-RAY DIFFRACTIONf_chiral_restr0.0446653
X-RAY DIFFRACTIONf_plane_restr0.005828
X-RAY DIFFRACTIONf_dihedral_angle_d9.5549633
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.950.28481190.26722683X-RAY DIFFRACTION79.6
1.95-20.26311330.24113011X-RAY DIFFRACTION88.29
2-2.060.2491450.21093274X-RAY DIFFRACTION95.4
2.06-2.130.2571430.19593218X-RAY DIFFRACTION96.52
2.13-2.20.26081480.20253325X-RAY DIFFRACTION97.8
2.2-2.290.24751480.19013338X-RAY DIFFRACTION98.5
2.29-2.390.23861490.1953363X-RAY DIFFRACTION98.29
2.39-2.520.26541470.19493312X-RAY DIFFRACTION97.79
2.52-2.680.23341460.19233328X-RAY DIFFRACTION97.09
2.68-2.880.25321460.19143286X-RAY DIFFRACTION96.89
2.88-3.170.22531460.1883289X-RAY DIFFRACTION96.11
3.17-3.630.21541450.16323271X-RAY DIFFRACTION94.94
3.63-4.580.16971430.14013224X-RAY DIFFRACTION93.45
4.58-49.780.18541420.15683205X-RAY DIFFRACTION90.19

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