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- PDB-3h6q: Macrocypin, a beta-trefoil cysteine protease inhibitor -

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Basic information

Entry
Database: PDB / ID: 3h6q
TitleMacrocypin, a beta-trefoil cysteine protease inhibitor
ComponentsMacrocypin 1a
KeywordsHYDROLASE/HYDROLASE INHIBITOR / Macrocypin / mycocypin / cysteine protease inhibitor / Kunitz type inhibitor / beta trefoil / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homologyTrefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / cysteine-type endopeptidase inhibitor activity / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil / Mainly Beta / Macrocypin-1a
Function and homology information
Biological speciesMacrolepiota procera (parasol mushroom)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.643 Å
AuthorsRenko, M. / Sabotic, J. / Brzin, J. / Turk, D.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Versatile loops in mycocypins inhibit three protease families.
Authors: Renko, M. / Sabotic, J. / Mihelic, M. / Brzin, J. / Kos, J. / Turk, D.
History
DepositionApr 23, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 20, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Macrocypin 1a


Theoretical massNumber of molelcules
Total (without water)19,2121
Polymers19,2121
Non-polymers00
Water5,783321
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Macrocypin 1a

A: Macrocypin 1a


Theoretical massNumber of molelcules
Total (without water)38,4252
Polymers38,4252
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+2/31
Buried area1990 Å2
ΔGint-8 kcal/mol
Surface area17330 Å2
Unit cell
Length a, b, c (Å)77.11, 77.11, 60.92
Angle α, β, γ (deg.)90, 90, 120
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-273-

HOH

21A-274-

HOH

31A-277-

HOH

Details1

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Components

#1: Protein Macrocypin 1a


Mass: 19212.455 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macrolepiota procera (parasol mushroom)
Plasmid: PET3a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3 / References: UniProt: B9V973
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 321 / Source method: isolated from a natural source / Formula: H2O

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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: 2.72 Å3/Da / Density % sol: 54.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: BisTrisPropane buffer, pH=7.0, 200 mM sodium citrate, 20% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1.1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jun 20, 2008
RadiationMonochromator: Double Crystal Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.64→50 Å / Num. all: 2612 / Num. obs: 25746 / % possible obs: 98.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 10.3 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 69.034
Reflection shellResolution: 1.64→1.7 Å / Redundancy: 8.3 % / Rmerge(I) obs: 0.142 / Num. unique all: 2206 / % possible all: 86.5

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Processing

Software
NameClassification
MAR345dtbdata collection
AMoREphasing
MAINrefinement
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.643→27.714 Å
RfactorNum. reflection% reflectionSelection details
Rfree0.1932 1282 -random
Rwork0.162 ---
obs-25722 100 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-22.755 Å2-0.479 Å2-0.239 Å2
2---0.479 Å20 Å2
3---0.718 Å2
Refinement stepCycle: LAST / Resolution: 1.643→27.714 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1424 0 0 321 1745
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_refined_d0.023
X-RAY DIFFRACTIONr_angle_refined_deg2.259
LS refinement shellResolution: 1.643→1.686 Å
RfactorNum. reflection% reflection
Rfree0.225 75 -
Rwork0.257 --
obs--100 %

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