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- PDB-1swt: CORE-STREPTAVIDIN MUTANT D128A IN COMPLEX WITH BIOTIN AT PH 4.5 -

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Basic information

Entry
Database: PDB / ID: 1swt
TitleCORE-STREPTAVIDIN MUTANT D128A IN COMPLEX WITH BIOTIN AT PH 4.5
ComponentsPROTEIN (STREPTAVIDIN)
KeywordsBINDING PROTEIN / BIOTIN BINDING PROTEIN
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
BIOTIN / Streptavidin
Similarity search - Component
Biological speciesStreptomyces avidinii (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsFreitag, S. / Le Trong, I. / Chu, V. / Klumb, L.A. / Stayton, P.S. / Stenkamp, R.E.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 1999
Title: A structural snapshot of an intermediate on the streptavidin-biotin dissociation pathway.
Authors: Freitag, S. / Chu, V. / Penzotti, J.E. / Klumb, L.A. / To, R. / Hyre, D. / Le Trong, I. / Lybrand, T.P. / Stenkamp, R.E. / Stayton, P.S.
History
DepositionOct 22, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Jul 30, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 23, 2023Group: 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: PROTEIN (STREPTAVIDIN)
B: PROTEIN (STREPTAVIDIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,9634
Polymers26,4752
Non-polymers4892
Water1,874104
1
A: PROTEIN (STREPTAVIDIN)
B: PROTEIN (STREPTAVIDIN)
hetero molecules

A: PROTEIN (STREPTAVIDIN)
B: PROTEIN (STREPTAVIDIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,9278
Polymers52,9494
Non-polymers9774
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Buried area11570 Å2
ΔGint-43 kcal/mol
Surface area18680 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)55.700, 84.800, 50.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-201-

HOH

Noncrystallographic symmetry (NCS)NCS oper: (Code: given / Matrix: (1), (1), (1))

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Components

#1: Protein PROTEIN (STREPTAVIDIN)


Mass: 13237.326 Da / Num. of mol.: 2 / Mutation: D128A
Source method: isolated from a genetically manipulated source
Details: PH 4.5 / Source: (gene. exp.) Streptomyces avidinii (bacteria)
Description: T7 EXPRESSION SYSTEM (PET-210, NOVAGEN, INC., MADISON,WI. SYNTHETIC GENE)
Production host: Escherichia coli (E. coli) / References: UniProt: P22629
#2: Chemical ChemComp-BTN / BIOTIN


Mass: 244.311 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N2O3S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 104 / 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: 2.23 Å3/Da / Density % sol: 44.84 %
Crystal growpH: 4.5
Details: INCUBATED IN 2.5 M BIOTIN/HOH, COCRYSTALLIZED IN 52% MPD (PH 4.5)
Crystal grow
*PLUS
Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
130 mg/mlprotein1drop
250 %MPD1drop

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Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Nov 20, 1996
RadiationMonochromator: GRAPHITE CRYSTAL / 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: 14716 / % possible obs: 88 % / Observed criterion σ(I): 1 / Redundancy: 3 % / Rmerge(I) obs: 0.054 / Net I/σ(I): 7
Reflection shellResolution: 2→2.1 Å / Mean I/σ(I) obs: 1 / % possible all: 43
Reflection
*PLUS
% possible obs: 88 % / Num. measured all: 39212
Reflection shell
*PLUS
% possible obs: 43 %

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Processing

Software
NameClassification
AMoREphasing
SHELXL-97refinement
SADIEdata reduction
SAINTdata reduction
SADABSdata scaling
XPREPdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1SWA

1swa


Resolution: 2→10 Å / Num. parameters: 7549 / Num. restraintsaints: 7497 / Cross valid method: RFREE / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.308 1471 10 %EVERY 10TH REFLECTION
all0.214 14716 --
obs0.209 -88 %-
Refine analyzeNum. disordered residues: 0 / Occupancy sum hydrogen: 1675 / Occupancy sum non hydrogen: 1886.5
Refinement stepCycle: LAST / Resolution: 2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1751 0 32 104 1887
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.006
X-RAY DIFFRACTIONs_angle_d0.024
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.166
X-RAY DIFFRACTIONs_zero_chiral_vol0.087
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.089
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.021
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.082
X-RAY DIFFRACTIONs_approx_iso_adps0
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 10 Å / σ(F): 4 / % reflection Rfree: 10 % / Rfactor obs: 0.156 / Rfactor Rwork: 0.209
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 31 Å2

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