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- PDB-1hxl: MINIPROTEIN MP-2 (V10A) COMPLEX WITH STREPTAVIDIN -

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Basic information

Entry
Database: PDB / ID: 1hxl
TitleMINIPROTEIN MP-2 (V10A) 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 16, 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 1.3Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_initial_refinement_model / pdbx_modification_feature / refine
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine.pdbx_starting_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)30,0714
Polymers30,0714
Non-polymers00
Water1,72996
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)60,1428
Polymers60,1428
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Unit cell
Length a, b, c (Å)81.989, 82.583, 89.385
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
DetailsThe biological assembly is a tetramer generated from the dimer in the asymmetric unit generated 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: 1625.917 Da / Num. of mol.: 2 / Mutation: V10A / Source method: obtained synthetically / Details: THE PEPTIDE WAS CHEMICALLY SYNTHESIZED.
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 96 / 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: 2.52 Å3/Da / Density % sol: 51.1 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.8
Details: 100 MM POTASSIUM ACETATE, AMMONIUM SULFATE, pH 4.80, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 108 K
Diffraction sourceSource: ROTATING ANODE / Type: MACSCIENCE / Wavelength: 1.5418
DetectorType: MACSCIENCE / Detector: IMAGE PLATE / Date: Jan 13, 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→50 Å / Num. obs: 28454 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 7.86 % / Biso Wilson estimate: 10.9 Å2 / Rmerge(I) obs: 0.076 / Rsym value: 0.076 / Net I/σ(I): 11.7
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 8.2 % / Rmerge(I) obs: 0.221 / Rsym value: 0.221 / % possible all: 99.9

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→41.29 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 745224.08 / 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
Rfree0.236 2797 9.9 %SHELLS
Rwork0.215 ---
obs-28207 98.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 42.68 Å2 / ksol: 0.351 e/Å3
Displacement parametersBiso mean: 17.1 Å2
Baniso -1Baniso -2Baniso -3
1--0.33 Å20 Å20 Å2
2---1.4 Å20 Å2
3---1.73 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a-0.02 Å
Refinement stepCycle: LAST / Resolution: 1.8→41.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1974 0 0 96 2070
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_d26.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.58
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.411.5
X-RAY DIFFRACTIONc_mcangle_it2.362
X-RAY DIFFRACTIONc_scbond_it2.112
X-RAY DIFFRACTIONc_scangle_it3.22.5
LS refinement shellResolution: 1.8→1.83 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.245 112 8.3 %
Rwork0.222 1240 -
obs--96 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP

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