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- PDB-7wss: Collagenase from Grimontia (Vibrio) hollisae 1706B -

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Basic information

Entry
Database: PDB / ID: 7wss
TitleCollagenase from Grimontia (Vibrio) hollisae 1706B
ComponentsMicrobial 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
DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / microbial collagenase
Similarity search - Component
Biological speciesGrimontia hollisae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.19 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
DepositionFeb 1, 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 1.2Apr 3, 2024Group: 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

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Assembly

Deposited unit
A: Microbial collagenase
B: Microbial collagenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,70743
Polymers123,8032
Non-polymers2,90441
Water8,611478
1
A: Microbial collagenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,04818
Polymers61,9011
Non-polymers1,14717
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area100 Å2
ΔGint-34 kcal/mol
Surface area23080 Å2
MethodPISA
2
B: Microbial collagenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,65925
Polymers61,9011
Non-polymers1,75724
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area100 Å2
ΔGint-35 kcal/mol
Surface area23080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)182.939, 75.120, 135.148
Angle α, β, γ (deg.)90.000, 128.180, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,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...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1GLUTHRA1 - 55
d_12ens_1THRLYSA57 - 122
d_13ens_1LEULEUA124 - 141
d_14ens_1VALLEUA143 - 195
d_15ens_1ALAASPA197 - 201
d_16ens_1THRALAA203 - 224
d_17ens_1TYRALAA226 - 263
d_18ens_1TYRLEUA265 - 281
d_19ens_1ASPILEA283 - 291
d_110ens_1SERHISA293 - 308
d_111ens_1ALAALAA310 - 311
d_112ens_1ASPGLYA313 - 503
d_113ens_1TRPALAA505 - 506
d_114ens_1TYRGLYA508 - 533
d_115ens_1ZNZNB
d_116ens_1CACAC
d_117ens_1CACAD
d_118ens_1CACAE
d_21ens_1GLUTHRH1 - 55
d_22ens_1THRLYSH57 - 122
d_23ens_1LEULEUH124 - 141
d_24ens_1VALLEUH143 - 195
d_25ens_1ALAASPH197 - 201
d_26ens_1THRALAH203 - 224
d_27ens_1TYRALAH226 - 263
d_28ens_1TYRLEUH265 - 281
d_29ens_1ASPILEH283 - 291
d_210ens_1SERHISH293 - 308
d_211ens_1ALAALAH310 - 311
d_212ens_1ASPGLYH313 - 503
d_213ens_1TRPALAH505 - 506
d_214ens_1TYRGLYH508 - 533
d_215ens_1ZNZNI
d_216ens_1CACAJ
d_217ens_1CACAK
d_218ens_1CACAL

NCS oper: (Code: givenMatrix: (0.255775391295, 0.00308398753244, 0.966731316462), (0.0221509436387, -0.999751068896, -0.00267131766683), (0.966482428657, 0.0220972682263, -0.255780034079)Vector: 75. ...NCS oper: (Code: given
Matrix: (0.255775391295, 0.00308398753244, 0.966731316462), (0.0221509436387, -0.999751068896, -0.00267131766683), (0.966482428657, 0.0220972682263, -0.255780034079)
Vector: 75.7922690825, -30.5250290174, -97.2293058134)

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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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Non-polymers , 7 types, 519 molecules

#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.: 8 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#5: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 478 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.94 Å3/Da / Density % sol: 58.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.2 M Calcium acetate, 0.1 M MES/ Sodium hydroxide pH 6.0, 20% (w/v) Polyethylene glycol 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 X 4M / Detector: PIXEL / Date: Oct 23, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.19→50 Å / Num. obs: 72941 / % possible obs: 98 % / Redundancy: 4.26 % / Biso Wilson estimate: 44.27 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.075 / Rrim(I) all: 0.088 / Net I/σ(I): 13.3
Reflection shellResolution: 2.19→2.32 Å / Redundancy: 3.61 % / Rmerge(I) obs: 0.75 / Mean I/σ(I) obs: 2.05 / Num. unique obs: 11564 / CC1/2: 0.779 / Rrim(I) all: 0.88 / % possible all: 97.2

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSver. Feb 5, 2021data reduction
XDSver. Feb 5, 2021data scaling
MOLREP11. 7. 01phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AlphaFold2

Resolution: 2.19→44.48 Å / SU ML: 0.316 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.5143
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2272 3643 5 %
Rwork0.1859 69217 -
obs0.188 72860 98.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 44.81 Å2
Refinement stepCycle: LAST / Resolution: 2.19→44.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8436 0 170 478 9084
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00678945
X-RAY DIFFRACTIONf_angle_d0.819712112
X-RAY DIFFRACTIONf_chiral_restr0.04741257
X-RAY DIFFRACTIONf_plane_restr0.00771593
X-RAY DIFFRACTIONf_dihedral_angle_d15.75973117
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.571613754381 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.19-2.220.36951340.34712538X-RAY DIFFRACTION94.82
2.22-2.250.41561400.34652654X-RAY DIFFRACTION97.49
2.25-2.280.35731360.30862593X-RAY DIFFRACTION97.46
2.28-2.320.3481410.28072670X-RAY DIFFRACTION99.19
2.32-2.350.31321410.25882671X-RAY DIFFRACTION97.84
2.35-2.390.30181380.2552623X-RAY DIFFRACTION99.03
2.39-2.430.30041380.24372652X-RAY DIFFRACTION98.1
2.43-2.480.30391410.242676X-RAY DIFFRACTION99.12
2.48-2.530.31061390.23222639X-RAY DIFFRACTION98.44
2.53-2.580.30991420.2212682X-RAY DIFFRACTION99.05
2.58-2.630.27151400.24492662X-RAY DIFFRACTION98.84
2.63-2.690.32691400.23522664X-RAY DIFFRACTION98.35
2.69-2.760.30971420.22152679X-RAY DIFFRACTION99.37
2.76-2.840.2981400.22362661X-RAY DIFFRACTION98.91
2.84-2.920.25921410.20392690X-RAY DIFFRACTION98.85
2.92-3.010.25921400.19292653X-RAY DIFFRACTION98.62
3.01-3.120.23831420.20112688X-RAY DIFFRACTION98.95
3.12-3.250.23091390.20272651X-RAY DIFFRACTION99.04
3.25-3.390.24921420.18072685X-RAY DIFFRACTION98.88
3.39-3.570.21771400.16652677X-RAY DIFFRACTION98.6
3.57-3.80.19881410.1572680X-RAY DIFFRACTION97.95
3.8-4.090.16181400.14472650X-RAY DIFFRACTION97.83
4.09-4.50.16061410.12492682X-RAY DIFFRACTION98.36
4.5-5.150.16541430.13182713X-RAY DIFFRACTION98.93
5.15-6.490.1921420.16022699X-RAY DIFFRACTION98.58
6.49-44.480.1641400.16322685X-RAY DIFFRACTION94.89

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