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- PDB-1hqq: MINIPROTEIN MP-2 (M9A) COMPLEX WITH STREPTAVIDIN -

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Basic information

Entry
Database: PDB / ID: 1hqq
TitleMINIPROTEIN MP-2 (M9A) 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: 1.7 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
DepositionDec 19, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 16, 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
E: MP-2
B: STREPTAVIDIN
F: MP-2
C: STREPTAVIDIN
G: MP-2
D: STREPTAVIDIN
H: MP-2


Theoretical massNumber of molelcules
Total (without water)60,0138
Polymers60,0138
Non-polymers00
Water3,099172
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13550 Å2
ΔGint-78 kcal/mol
Surface area21690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.133, 89.299, 58.137
Angle α, β, γ (deg.)90.00, 90.57, 90.00
Int Tables number4
Space group name H-MP1211

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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-2 / MINI-PROTEIN 2


Mass: 1593.852 Da / Num. of mol.: 4 / Mutation: M9A / Source method: obtained synthetically / Details: The peptide was chemically synthesized.
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 172 / 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: 51.07 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 100 mM potassium acetate, ammonium sulfate, pH 4.0, 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 Å
DetectorType: MACSCIENCE / Detector: IMAGE PLATE / Date: Oct 20, 2000 / 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: 1.7→20.84 Å / Num. all: 63318 / Num. obs: 163318 / % possible obs: 96.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.46 % / Biso Wilson estimate: 12.5 Å2 / Limit h max: 34 / Limit h min: -34 / Limit k max: 52 / Limit k min: -34 / Limit l max: 33 / Limit l min: 0 / Observed criterion F max: 569614.15 / Observed criterion F min: 0.316 / Rmerge(I) obs: 0.086 / Rsym value: 0.086 / Net I/σ(I): 8.1
Reflection shellResolution: 1.7→1.73 Å / Rmerge(I) obs: 0.302 / Mean I/σ(I) obs: 4.2 / Num. unique all: 2754 / Rsym value: 0.302 / % possible all: 84.8

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Processing

Software
NameVersionClassificationNB
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
EPMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→20.84 Å / Rfactor Rfree error: 0.003 / Occupancy max: 1 / Occupancy min: 1 / Data cutoff high rms absF: 569571.22 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.249 6283 10.1 %shells
Rwork0.224 ---
all-65226 --
obs-62190 95.3 %-
Solvent computationSolvent model: CNS bulk solvent model used / Bsol: 38.6719 Å2 / ksol: 0.351859 e/Å3
Displacement parametersBiso max: 48.9 Å2 / Biso mean: 17.08 Å2 / Biso min: 3.77 Å2
Baniso -1Baniso -2Baniso -3
1--3.6 Å20 Å20.32 Å2
2--4.09 Å20 Å2
3----0.5 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.12 Å0.12 Å
Luzzati d res high-1.7
Refinement stepCycle: LAST / Resolution: 1.7→20.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3944 0 0 172 4116
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.004
X-RAY DIFFRACTIONx_angle_deg1.2
X-RAY DIFFRACTIONx_torsion_deg26.2
X-RAY DIFFRACTIONx_torsion_impr_deg0.57
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRfactor Rfree errorNum. reflection allNum. reflection obs% reflection obs (%)
1.7-1.780.29174610.50.28363620.0118136708787.5
1.78-1.870.2387569.30.23966300.0098169738690.4
1.87-1.990.2267038.60.22668800.0098127758393.3
1.99-2.140.2197689.40.21870390.0088137780795.9
2.14-2.360.21982410.10.21871260.0088137795097.7
2.36-2.70.2287879.70.22872350.0088143802298.5
2.7-3.40.22584910.40.22572740.0088202812399
3.4-20.840.21285010.30.21373820.0078264823299.6
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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