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- PDB-1n4j: STREPTAVIDIN MUTANT N23A AT 2.18A -

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Basic information

Entry
Database: PDB / ID: 1n4j
TitleSTREPTAVIDIN MUTANT N23A AT 2.18A
ComponentsStreptavidin
KeywordsBIOTIN-BINDING PROTEIN / homotetramer
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 / isomorphous / Resolution: 2.18 Å
AuthorsLe Trong, I. / Freitag, S. / Klumb, L.A. / Chu, V. / Stayton, P.S. / Stenkamp, R.E.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2003
Title: Structural studies of hydrogen bonds in the high-affinity streptavidin-biotin complex: mutations of amino acids interacting with the ureido oxygen of biotin.
Authors: Le Trong, I. / Freitag, S. / Klumb, L.A. / Chu, V. / Stayton, P.S. / Stenkamp, R.E.
History
DepositionOct 31, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 2, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Oct 27, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Feb 14, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Streptavidin


Theoretical massNumber of molelcules
Total (without water)13,2381
Polymers13,2381
Non-polymers00
Water1,13563
1
A: Streptavidin

A: Streptavidin

A: Streptavidin

A: Streptavidin


Theoretical massNumber of molelcules
Total (without water)52,9534
Polymers52,9534
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation15_556y,x,-z+11
crystal symmetry operation10_555-x,-y,z1
crystal symmetry operation8_556-y,-x,-z+11
Unit cell
Length a, b, c (Å)59.2, 59.2, 179.8
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11A-6036-

HOH

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Components

#1: Protein Streptavidin


Mass: 13238.311 Da / Num. of mol.: 1 / Fragment: core streptavidin, residues 13-139 / Mutation: N23A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces avidinii (bacteria) / Gene: core streptavidin / Plasmid: pET21a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P22629
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 63 / Source method: isolated from a natural source / Formula: H2O

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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: 2.81 Å3/Da / Density % sol: 58.65 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.2
Details: PEG4000, phosphate buffer, pH 6.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
120-30 mg/mlprotein1drop
210 %PEG40001reservoir
30.1 Mphosphate1reservoirpH6.2

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: SIEMENS / Wavelength: 1.5418 Å
DetectorType: XENTRONICS / Detector: AREA DETECTOR / Date: Jul 3, 1996
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.18→50 Å / Num. all: 26865 / Num. obs: 26865 / % possible obs: 86 % / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.07
Reflection
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 10 Å / Num. obs: 8077
Reflection shell
*PLUS
% possible obs: 62 % / Rmerge(I) obs: 0.25

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Processing

Software
NameClassification
FRAMBOdata collection
SAINTdata reduction
SADABSdata reduction
SHELXL-97refinement
SAINTdata scaling
SADABSdata scaling
RefinementMethod to determine structure: isomorphous
Starting model: 1RST

1rst


Resolution: 2.18→10 Å / Num. parameters: 3649 / Num. restraintsaints: 3560 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.2526 739 10 %RANDOM
Rwork0.188 ---
all-7392 --
obs-7392 85.1 %-
Refine analyzeNum. disordered residues: 0 / Occupancy sum hydrogen: 799 / Occupancy sum non hydrogen: 911.5
Refinement stepCycle: LAST / Resolution: 2.18→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms849 0 0 63 912
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.005
X-RAY DIFFRACTIONs_angle_d0.022
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0237
X-RAY DIFFRACTIONs_zero_chiral_vol0.024
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.034
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.01
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.052
X-RAY DIFFRACTIONs_approx_iso_adps0
Refinement
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 10 Å / % reflection Rfree: 10 % / Rfactor Rfree: 0.253 / Rfactor Rwork: 0.187
Solvent computation
*PLUS
Displacement parameters
*PLUS

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