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- PDB-1hxz: MINIPROTEIN MP-2 COMPLEX WITH STREPTAVIDIN -

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Basic information

Entry
Database: PDB / ID: 1hxz
TitleMINIPROTEIN MP-2 COMPLEX WITH STREPTAVIDIN
Components
  • MP-2
  • 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: 1.8 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: Derived calculations / 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

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Assembly

Deposited unit
A: STREPTAVIDIN
B: STREPTAVIDIN
C: MP-2
D: MP-2


Theoretical massNumber of molelcules
Total (without water)30,1274
Polymers30,1274
Non-polymers00
Water2,918162
1
A: STREPTAVIDIN
B: STREPTAVIDIN
C: MP-2
D: MP-2

A: STREPTAVIDIN
B: STREPTAVIDIN
C: MP-2
D: MP-2


Theoretical massNumber of molelcules
Total (without water)60,2548
Polymers60,2548
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area13650 Å2
ΔGint-76 kcal/mol
Surface area21420 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)81.926, 82.599, 89.340
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
DetailsThe second part of the biological assembly is generated from the dimer by the two fold axis: -x,y,1/2-z

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Components

#1: Protein STREPTAVIDIN


Mass: 13409.466 Da / Num. of mol.: 2
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-2 / MINI-PROTEIN 2


Mass: 1653.970 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: THE PEPTIDE WAS CHEMICALLY SYNTHESIZED.
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 162 / 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: 2.51 Å3/Da / Density % sol: 50.95 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 100mM potassium acetate, 32% AMMONIUM SULFATE , pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: ROTATING ANODE / Type: MACSCIENCE / Wavelength: 1.5418
DetectorType: MACSCIENCE / Detector: IMAGE PLATE / Date: Jan 14, 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: 1.8→29.1 Å / Num. obs: 28243 / % possible obs: 99.2 % / Observed criterion σ(I): 0 / Redundancy: 4.87 % / Biso Wilson estimate: 8.4 Å2 / Rmerge(I) obs: 0.061 / Rsym value: 0.061 / Net I/σ(I): 12.9
Reflection shellResolution: 1.78→1.81 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.134 / Rsym value: 0.134 / % possible all: 98.7

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
GLRFphasing
CNS0.5refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1SLD STREPTAVIDIN TETRAMER

1sld


Resolution: 1.8→29.1 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 747543.62 / 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
Rfree0.23 2793 9.9 %RANDOM
Rwork0.209 ---
obs-28149 98.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 39.54 Å2 / ksol: 0.331 e/Å3
Displacement parametersBiso mean: 18.4 Å2
Baniso -1Baniso -2Baniso -3
1--0.15 Å20 Å20 Å2
2---1.08 Å20 Å2
3---1.23 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.13 Å0.08 Å
Refinement stepCycle: LAST / Resolution: 1.8→29.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1998 0 0 162 2160
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.004
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_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d26
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.6
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.441.5
X-RAY DIFFRACTIONc_mcangle_it2.452
X-RAY DIFFRACTIONc_scbond_it9.32
X-RAY DIFFRACTIONc_scangle_it6.12.5
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.257 441 9.6 %
Rwork0.219 4134 -
obs--98.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER_REP.TOP

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