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- PDB-6vlp: Hop phytocystatin in space group C2221 -

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Basic information

Entry
Database: PDB / ID: 6vlp
TitleHop phytocystatin in space group C2221
ComponentsHop1
KeywordsPROTEIN BINDING / cystatin / domain-swap / inhibitor / hop
Biological speciesHumulus lupulus (European hop)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.681 Å
AuthorsValadares, N.F. / Moura, G.T.
Funding support Brazil, 1items
OrganizationGrant numberCountry
Brazilian National Council for Scientific and Technological Development (CNPq) Brazil
CitationJournal: Biochim Biophys Acta Proteins Proteom / Year: 2020
Title: Crystal structure and physicochemical characterization of a phytocystatin from Humulus lupulus: Insights into its domain-swapped dimer
Authors: Moura, G.T. / Souza, A.A. / Garay, A.V. / Freitas, S.M. / Valadares, N.F.
History
DepositionJan 24, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 14, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 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: Hop1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,7105
Polymers11,2591
Non-polymers4514
Water1,26170
1
A: Hop1
hetero molecules

A: Hop1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,42010
Polymers22,5182
Non-polymers9038
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area6210 Å2
ΔGint-131 kcal/mol
Surface area9380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.551, 63.280, 72.383
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-202-

SO4

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Components

#1: Protein Hop1


Mass: 11258.755 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Humulus lupulus (European hop) / Plasmid: pET24a / Production host: Escherichia coli (E. coli) / Strain (production host): Lemo21
#2: Chemical ChemComp-TAM / TRIS(HYDROXYETHYL)AMINOMETHANE / Tris


Mass: 163.215 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H17NO3 / Comment: pH buffer*YM
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 70 / Source method: isolated from a natural source / Formula: H2O
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: 2.16 Å3/Da / Density % sol: 43.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 30% w/v PEG8000, 100 mM sodium cacodylate, pH 6.5, 200 mM sodium acetate trihydrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.45 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 11, 2018
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.45 Å / Relative weight: 1
ReflectionResolution: 1.681→28.99 Å / Num. obs: 11170 / % possible obs: 97.44 % / Redundancy: 2 % / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.01952 / Rrim(I) all: 0.02761 / Net I/σ(I): 21.64
Reflection shellResolution: 1.681→1.741 Å / Redundancy: 2 % / Rmerge(I) obs: 0.4666 / Num. unique obs: 1011 / CC1/2: 0.629 / Rrim(I) all: 0.6599 / % possible all: 89.62

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Processing

Software
NameVersionClassification
PHENIXv1.16-3549refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4TX4

4tx4


Resolution: 1.681→28.99 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.2092 --
Rwork0.1911 --
obs-11170 97.44 %
Displacement parametersBiso mean: 32.04 Å2
Refinement stepCycle: LAST / Resolution: 1.681→28.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms643 0 26 70 739
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074682
X-RAY DIFFRACTIONf_angle_d0.9522922
X-RAY DIFFRACTIONf_chiral_restr0.062499
X-RAY DIFFRACTIONf_plane_restr0.0059114
X-RAY DIFFRACTIONf_dihedral_angle_d14.8137408

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