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- PDB-7xeb: Collagenase from Grimontia (Vibrio) hollisae 1706B complexed with... -

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Basic information

Entry
Database: PDB / ID: 7xeb
TitleCollagenase from Grimontia (Vibrio) hollisae 1706B complexed with Gly-Pro-Hyp
Components
  • GLY-PRO-HYP peptide
  • GLY-PRO-HYP-GLY-PRO-HYP peptide
  • Microbial collagenase
KeywordsHYDROLASE / Grimontia hollisae / Collagenase
Function / homology
Function and homology information


microbial collagenase / metalloendopeptidase activity / proteolysis / zinc ion binding / extracellular region
Similarity search - Function
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
Similarity search - Domain/homology
microbial collagenase
Similarity search - Component
Biological speciesGrimontia hollisae (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.39 Å
AuthorsIkeuchi, T. / Yasumoto, M. / Takita, T. / Mizutani, K. / Mikami, B. / Tanaka, K. / Hattori, S. / Yasukawa, K.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)18KK0285 Japan
CitationJournal: J.Biol.Chem. / Year: 2022
Title: Crystal structure of Grimontia hollisae collagenase provides insights into its novel substrate specificity toward collagen.
Authors: Ikeuchi, T. / Yasumoto, M. / Takita, T. / Tanaka, K. / Kusubata, M. / Hayashida, O. / Hattori, S. / Mizutani, K. / Mikami, B. / Yasukawa, K.
History
DepositionMar 30, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 29, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 3, 2022Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Microbial collagenase
B: Microbial collagenase
C: GLY-PRO-HYP peptide
D: GLY-PRO-HYP peptide
E: GLY-PRO-HYP-GLY-PRO-HYP peptide
F: GLY-PRO-HYP-GLY-PRO-HYP peptide
G: GLY-PRO-HYP peptide
H: GLY-PRO-HYP peptide
I: GLY-PRO-HYP-GLY-PRO-HYP peptide
J: GLY-PRO-HYP-GLY-PRO-HYP peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,91625
Polymers127,15410
Non-polymers76215
Water2,828157
1
A: Microbial collagenase
C: GLY-PRO-HYP peptide
D: GLY-PRO-HYP peptide
E: GLY-PRO-HYP-GLY-PRO-HYP peptide
F: GLY-PRO-HYP-GLY-PRO-HYP peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,11315
Polymers63,5775
Non-polymers53610
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Microbial collagenase
G: GLY-PRO-HYP peptide
H: GLY-PRO-HYP peptide
I: GLY-PRO-HYP-GLY-PRO-HYP peptide
J: GLY-PRO-HYP-GLY-PRO-HYP peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,80310
Polymers63,5775
Non-polymers2265
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.972, 75.549, 130.551
Angle α, β, γ (deg.)90.000, 103.060, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 90 through 144 or resid 146...
d_2ens_1(chain "B" and (resid 90 through 144 or resid 146...
d_1ens_2chain "C"
d_2ens_2chain "D"
d_3ens_2chain "G"
d_4ens_2chain "H"
d_1ens_3chain "E"
d_2ens_3chain "F"
d_3ens_3chain "I"
d_4ens_3chain "J"

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1GLUTHRA1 - 55
d_12ens_1THRPHEA57 - 85
d_13ens_1ASNILEA87 - 291
d_14ens_1SERALAA293 - 311
d_15ens_1ASPTYRA313 - 475
d_16ens_1TRPGLYA477 - 533
d_17ens_1ZNZNB
d_18ens_1CACAC
d_19ens_1CACAD
d_110ens_1CACAE
d_21ens_1GLUTHRG1 - 55
d_22ens_1THRPHEG57 - 85
d_23ens_1ASNILEG87 - 291
d_24ens_1SERALAG293 - 311
d_25ens_1ASPTYRG313 - 475
d_26ens_1TRPGLYG477 - 533
d_27ens_1ZNZNH
d_28ens_1CACAI
d_29ens_1CACAJ
d_210ens_1CACAK
d_11ens_2GLYHYPM1 - 3
d_21ens_2GLYHYPN1 - 3
d_31ens_2GLYHYPQ1 - 3
d_41ens_2GLYHYPR1 - 3
d_11ens_3GLYHYPO1 - 6
d_21ens_3GLYHYPP1 - 6
d_31ens_3GLYHYPS1 - 6
d_41ens_3GLYHYPT1 - 6

NCS ensembles :
ID
ens_1
ens_2
ens_3

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Microbial collagenase


Mass: 61901.473 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Grimontia hollisae (bacteria) / Plasmid: pNY326 / Production host: Brevibacillus (bacteria) / References: UniProt: F7IZI6, microbial collagenase

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Protein/peptide , 2 types, 8 molecules CDGHEFIJ

#2: Protein/peptide
GLY-PRO-HYP peptide


Mass: 285.297 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Protein/peptide
GLY-PRO-HYP-GLY-PRO-HYP peptide


Mass: 552.578 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 4 types, 172 molecules

#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#6: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 157 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.76 Å3/Da / Density % sol: 55.39 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M Cacodylic acid sodium salt, 0.2M Calcium acetate, 18%(w/v) PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å
DetectorType: DECTRIS EIGER R 4M / Detector: PIXEL / Date: Dec 12, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.39→50 Å / Num. obs: 54059 / % possible obs: 98.5 % / Redundancy: 3.71 % / Biso Wilson estimate: 47.74 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.093 / Rrim(I) all: 0.109 / Net I/σ(I): 12.38
Reflection shellResolution: 2.39→2.54 Å / Redundancy: 3.84 % / Rmerge(I) obs: 0.727 / Mean I/σ(I) obs: 2.34 / Num. unique obs: 8681 / CC1/2: 0.787 / Rrim(I) all: 0.844 / % possible all: 98.3

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
PHENIX1.20.1_4487phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7WSS

7wss


Resolution: 2.39→45.41 Å / SU ML: 0.3851 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 30.445
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2548 2702 5 %
Rwork0.2061 51316 -
obs0.2086 54018 98.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 46.9 Å2
Refinement stepCycle: LAST / Resolution: 2.39→45.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8672 0 30 157 8859
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00788962
X-RAY DIFFRACTIONf_angle_d0.945812220
X-RAY DIFFRACTIONf_chiral_restr0.05251281
X-RAY DIFFRACTIONf_plane_restr0.0071617
X-RAY DIFFRACTIONf_dihedral_angle_d14.87023077
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS0.53489363184
ens_2d_2DX-RAY DIFFRACTIONTorsion NCS0.454885280503
ens_2d_3GX-RAY DIFFRACTIONTorsion NCS0.326669676902
ens_2d_4HX-RAY DIFFRACTIONTorsion NCS0.571070181633
ens_3d_2FX-RAY DIFFRACTIONTorsion NCS0.789478517467
ens_3d_3IX-RAY DIFFRACTIONTorsion NCS0.649853345796
ens_3d_4JX-RAY DIFFRACTIONTorsion NCS0.790100581178
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.39-2.440.39631410.34262693X-RAY DIFFRACTION96.62
2.44-2.480.40491390.31392641X-RAY DIFFRACTION99.46
2.48-2.530.35061420.30722697X-RAY DIFFRACTION98
2.53-2.590.35961420.29822685X-RAY DIFFRACTION98.74
2.59-2.650.35491410.28312680X-RAY DIFFRACTION98.88
2.65-2.720.36341420.27672694X-RAY DIFFRACTION98.34
2.72-2.790.33281420.26872695X-RAY DIFFRACTION98.78
2.79-2.870.2941410.27072686X-RAY DIFFRACTION99.02
2.87-2.960.36381420.28112703X-RAY DIFFRACTION98.68
2.96-3.070.35141420.27642695X-RAY DIFFRACTION98.75
3.07-3.190.31211440.24312720X-RAY DIFFRACTION98.9
3.19-3.340.29111410.23812698X-RAY DIFFRACTION98.99
3.34-3.510.25171430.20962706X-RAY DIFFRACTION98.72
3.51-3.730.23681430.19452725X-RAY DIFFRACTION98.59
3.73-4.020.21611420.17732683X-RAY DIFFRACTION98.16
4.02-4.430.19821420.1442713X-RAY DIFFRACTION98.25
4.43-5.070.15651440.13542718X-RAY DIFFRACTION98.96
5.07-6.380.20371440.16242742X-RAY DIFFRACTION98.67
6.38-45.410.18391450.15182742X-RAY DIFFRACTION96.17

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