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- PDB-6vlq: Hop phytocystatin in space group P22121 -

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Basic information

Entry
Database: PDB / ID: 6vlq
TitleHop phytocystatin in space group P22121
ComponentsHop1
KeywordsPROTEIN BINDING / cystatin / domain-swap / inhibitor / hop
Biological speciesHumulus lupulus (European hop)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.799 Å
AuthorsValadares, F.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)11,3552
Polymers11,2591
Non-polymers961
Water25214
1
A: Hop1
hetero molecules

A: Hop1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,7104
Polymers22,5182
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_557x,-y,-z+21
Buried area4130 Å2
ΔGint-46 kcal/mol
Surface area9510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)28.922, 43.823, 56.829
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Space group name HallP22ab(z,x,y)
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y+1/2,-z+1/2
#4: -x,-y+1/2,z+1/2

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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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / 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: 1.6 Å3/Da / Density % sol: 23.09 %
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: 1.799→25.78 Å / Num. obs: 6708 / % possible obs: 93.49 % / Redundancy: 2 % / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.01817 / Rrim(I) all: 0.02569 / Net I/σ(I): 18.35
Reflection shellResolution: 1.799→1.863 Å / Rmerge(I) obs: 0.8923 / Num. unique obs: 506 / CC1/2: 0.463 / CC star: 0.796

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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: 1.799→25.78 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.2666 --
Rwork0.22 --
obs-6708 93.49 %
Displacement parametersBiso mean: 46.85 Å2
Refinement stepCycle: LAST / Resolution: 1.799→25.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms627 0 5 14 646
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062643
X-RAY DIFFRACTIONf_angle_d0.7908869
X-RAY DIFFRACTIONf_chiral_restr0.051696
X-RAY DIFFRACTIONf_plane_restr0.004109
X-RAY DIFFRACTIONf_dihedral_angle_d20.5772384

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