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- PDB-6x5x: Crystal structure o BmooMP-I, a P-I metalloproteinase from Bothro... -

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Basic information

Entry
Database: PDB / ID: 6x5x
TitleCrystal structure o BmooMP-I, a P-I metalloproteinase from Bothrops moojeni
ComponentsSnake venom metalloproteinase BmooMP-I
KeywordsHYDROLASE / Metalloproteinase P-I / Fibrinogenolytic metalloproteinase
Biological speciesBothrops moojeni (Brazilian lancehead)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.92 Å
AuthorsSalvador, G.H.M. / Borges, R.J. / Fontes, M.R.M.
Funding support Brazil, 1items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)2015/24167-7 Brazil
CitationJournal: Biochimie / Year: 2020
Title: Biochemical, pharmacological and structural characterization of BmooMP-I, a new P-I metalloproteinase from Bothrops moojeni venom.
Authors: Salvador, G.H.M. / Borges, R.J. / Eulalio, M.M.C. / Dos Santos, L.D. / Fontes, M.R.M.
History
DepositionMay 27, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 7, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Snake venom metalloproteinase BmooMP-I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,0666
Polymers22,5741
Non-polymers4925
Water4,216234
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)70.344, 70.344, 97.205
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Snake venom metalloproteinase BmooMP-I


Mass: 22574.480 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bothrops moojeni (Brazilian lancehead)

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Non-polymers , 5 types, 239 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 234 / 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: 3.08 Å3/Da / Density % sol: 60.01 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: PEG 400, Tris HCl pH 8.5, Lithium sulfate, sodium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.425 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 11, 2016 / Details: Mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.425 Å / Relative weight: 1
ReflectionResolution: 1.92→40 Å / Num. obs: 21808 / % possible obs: 99.9 % / Redundancy: 14.2 % / Biso Wilson estimate: 24.13 Å2 / Rmerge(I) obs: 0.156 / Rpim(I) all: 0.043 / Rrim(I) all: 0.162 / Χ2: 1.021 / Net I/σ(I): 4.7 / Num. measured all: 310194
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.92-214.60.87423950.8940.2350.9061.015100
2-2.0914.50.60523530.9330.1630.6271.058100
2.09-2.213.80.4324030.9660.1180.4461.095100
2.2-2.3414.70.38423780.9730.1030.3971.042100
2.34-2.5214.50.27524280.9820.0740.2850.992100
2.52-2.7714.20.23623970.9870.0640.2441.04100
2.77-3.1714.80.14924300.9950.040.1540.938100
3.17-3.9913.10.10624570.9960.030.1111.032100
3.99-4013.80.08225670.9970.0230.0850.98299.5

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation1.92 Å23.83 Å
Translation1.92 Å23.83 Å

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHASER2.5.6phasing
PHENIX1.13_2998refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3GBO

3gbo


Resolution: 1.92→23.831 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 17.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1806 1090 5.01 %
Rwork0.16 20682 -
obs0.1611 21772 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 79.87 Å2 / Biso mean: 27.7416 Å2 / Biso min: 12.36 Å2
Refinement stepCycle: final / Resolution: 1.92→23.831 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1656 0 24 234 1914
Biso mean--50.94 39.29 -
Num. residues----200
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.92-2.00690.23381310.1957252399
2.0069-2.11270.20361360.17862554100
2.1127-2.2450.18791330.15652538100
2.245-2.41810.19471370.17282570100
2.4181-2.66120.21271360.16112576100
2.6612-3.04560.1821320.16092597100
3.0456-3.83450.15041350.14352600100
3.8345-23.8310.17331500.15912724100
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)
12.3233-0.0140.78492.0382-0.90592.9289-0.0366-0.21780.13430.09770.01230.0235-0.1677-0.2789-0.00850.13850.00240.02440.166-0.0160.174421.1864-21.5916.1859
22.0017-0.40820.92611.7531-0.58071.9853-0.19-0.32690.19510.22920.12990.1565-0.4972-0.5020.08810.21670.0310.00570.2188-0.02150.220819.9627-15.209116.1743
32.3583-0.49781.02032.0137-0.94253.18090.0077-0.2576-0.17760.17240.0460.00120.0471-0.1247-0.07730.1867-0.03840.01690.1893-0.01020.176424.0496-28.613819.5404
45.23010.33011.67581.54260.05482.62160.05870.0157-0.32350.02950.0083-0.05930.16410.0609-0.05430.1674-0.0009-0.00290.1430.00740.145727.4847-31.394914.1312
53.68961.56791.49314.82321.394.14430.08210.0083-0.1430.24580.0033-0.19130.11720.1326-0.10750.11950.00440.02470.12370.02420.106627.5463-26.312410.615
62.24790.9126-0.87462.712-1.42911.7482-0.06150.01670.0287-0.0250.041-0.0604-0.24410.04760.00080.2167-0.0288-0.01030.16230.00340.186330.5278-15.51413.9107
77.08274.8567-1.2164.9483-2.33223.8268-0.23240.22550.0839-0.48020.24690.1805-0.0447-0.01-0.01210.2246-0.0317-0.0340.1936-0.0020.199518.6633-23.4278-4.3046
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 24 )A1 - 24
2X-RAY DIFFRACTION2chain 'A' and (resid 25 through 46 )A25 - 46
3X-RAY DIFFRACTION3chain 'A' and (resid 47 through 69 )A47 - 69
4X-RAY DIFFRACTION4chain 'A' and (resid 70 through 110 )A70 - 110
5X-RAY DIFFRACTION5chain 'A' and (resid 111 through 131 )A111 - 131
6X-RAY DIFFRACTION6chain 'A' and (resid 132 through 177 )A132 - 177
7X-RAY DIFFRACTION7chain 'A' and (resid 178 through 200 )A178 - 200

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