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- PDB-1hy2: MINIPROTEIN MP-1 COMPLEX WITH STREPTAVIDIN -

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Basic information

Entry
Database: PDB / ID: 1hy2
TitleMINIPROTEIN MP-1 COMPLEX WITH STREPTAVIDIN
Components
  • MP-1
  • STREPTAVIDIN
KeywordsUNKNOWN FUNCTION / CONFORMATIONAL ENSEMBLE / MINI-PROTEINS / DISULPHIDE CONSTRAINED LOOPS / ENTROPICALLY RESTRAINED PROTEINS / PEPTIDES
Function / homology
Function and homology information


biotin binding / extracellular region
Similarity search - Function
Avidin-like / Avidin-like, conserved site / Avidin-like domain signature. / Avidin / : / Avidin/streptavidin / Avidin-like superfamily / Avidin family / Avidin-like domain profile. / Lipocalin ...Avidin-like / Avidin-like, conserved site / Avidin-like domain signature. / Avidin / : / Avidin/streptavidin / Avidin-like superfamily / Avidin family / Avidin-like domain profile. / Lipocalin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Biological speciesStreptomyces avidinii (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsYang, H.W. / Liu, D.Q. / Fan, X. / White, M.A. / Fox, R.O.
CitationJournal: To be Published
Title: Conformational Ensemble Analysis of Ligand Binding in Streptavidin Mini-Protein Complexes
Authors: Yang, H.W. / Liu, D.Q. / Fan, X. / White, M.A. / Fox, R.O.
History
DepositionJan 17, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 17, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 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
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: STREPTAVIDIN
B: STREPTAVIDIN
C: STREPTAVIDIN
D: STREPTAVIDIN
E: MP-1
F: MP-1
G: MP-1
H: MP-1


Theoretical massNumber of molelcules
Total (without water)58,6128
Polymers58,6128
Non-polymers00
Water4,540252
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12940 Å2
ΔGint-75 kcal/mol
Surface area21620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.633, 81.364, 83.307
Angle α, β, γ (deg.)90.00, 105.04, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
STREPTAVIDIN


Mass: 13409.466 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces avidinii (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P22629
#2: Protein/peptide
MP-1 / MINI-PROTEIN 1


Mass: 1243.436 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: THE MP-1 PEPTIDE WAS CHEMICALLY SYNTHESIZED.
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 252 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.53 Å3/Da / Density % sol: 51.38 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 100mM potassium acetate, ammonium sulfate, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 278 K
Diffraction sourceSource: ROTATING ANODE / Type: MACSCIENCE / Wavelength: 1.5418 / Wavelength: 1.5418 Å
DetectorType: MACSCIENCE / Detector: IMAGE PLATE / Date: Dec 17, 1999 / Details: MULTILAYER
RadiationMonochromator: MULTILAYER OPTICS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 38522 / % possible obs: 97.5 % / Observed criterion σ(I): 0 / Redundancy: 4.18 % / Biso Wilson estimate: 5.2 Å2 / Rmerge(I) obs: 0.105 / Rsym value: 0.105 / Net I/σ(I): 7.3
Reflection shellResolution: 2→2.05 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.317 / Rsym value: 0.317 / % possible all: 88.2

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1SLD STREPTAVIDIN TETRAMER

1sld


Resolution: 2→29.8 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 267053.66 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.258 3759 9.9 %RANDOM
Rwork0.214 ---
obs-38025 96 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 40.32 Å2 / ksol: 0.336 e/Å3
Displacement parametersBiso mean: 21.6 Å2
Baniso -1Baniso -2Baniso -3
1-2.52 Å20 Å21.09 Å2
2--3.5 Å20 Å2
3----6.02 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.16 Å0.14 Å
Refinement stepCycle: LAST / Resolution: 2→29.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4000 0 0 252 4252
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d26.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.64
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it0.881.5
X-RAY DIFFRACTIONc_mcangle_it1.62
X-RAY DIFFRACTIONc_scbond_it0.822
X-RAY DIFFRACTIONc_scangle_it1.342.5
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.265 605 10.3 %
Rwork0.223 5296 -
obs--90.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP

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