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- PDB-9mfz: Streptavidin-E101Q-K121A-L124E bound to Fe(III)-biotin-pentyl-dip... -

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Basic information

Entry
Database: PDB / ID: 9mfz
TitleStreptavidin-E101Q-K121A-L124E bound to Fe(III)-biotin-pentyl-dipicolylamine cofactor
ComponentsStreptavidin
KeywordsMETAL BINDING PROTEIN / biotin-streptavidin complex / artificial metalloprotein
Function / homology
Function and homology information


biotin binding / extracellular region
Similarity search - Function
Avidin-like, conserved site / Avidin-like domain signature. / Avidin / : / Avidin/streptavidin / Avidin-like superfamily / Avidin family / Avidin-like domain profile.
Similarity search - Domain/homology
: / : / Streptavidin
Similarity search - Component
Biological speciesStreptomyces avidinii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsBiswas, A. / Follmer, A.H. / Borovik, A.S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM120349 United States
CitationJournal: To Be Published
Title: Streptavidin-L124E bound to Fe(III)-biotin-pentyl-dipicolylamine cofactor
Authors: Follmer, A.H. / Biswas, A. / Borovik, A.S.
History
DepositionDec 10, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 17, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Streptavidin
B: Streptavidin
C: Streptavidin
D: Streptavidin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,53918
Polymers52,8574
Non-polymers2,68214
Water7,981443
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12310 Å2
ΔGint-171 kcal/mol
Surface area19110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)192.511, 57.633, 57.633
Angle α, β, γ (deg.)90.000, 107.420, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11B-394-

HOH

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Components

#1: Protein
Streptavidin


Mass: 13214.229 Da / Num. of mol.: 4 / Mutation: E101Q, K121A, L124E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces avidinii (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P22629
#2: Chemical
ChemComp-A1BLH / N-(5-{bis[(pyridin-2-yl)methyl]amino}pentyl)-5-[(3aS,4S,6aR)-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]pentanamide


Mass: 510.695 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H38N6O2S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 443 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.89 Å3/Da / Density % sol: 57.38 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: ammonium sulfate, sodium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 2, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.55→45.92 Å / Num. obs: 87395 / % possible obs: 99.8 % / Redundancy: 3.7 % / Biso Wilson estimate: 21.51 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.05845 / Rpim(I) all: 0.03466 / Rrim(I) all: 0.06821 / Net I/σ(I): 13.54
Reflection shellResolution: 1.55→1.605 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.7478 / Mean I/σ(I) obs: 2.33 / Num. unique obs: 8722 / CC1/2: 0.666 / Rpim(I) all: 0.4363 / Rrim(I) all: 0.8692 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Cootmodel building
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.55→45.92 Å / SU ML: 0.1874 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 17.2392
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1889 4305 4.93 %
Rwork0.1659 83075 -
obs0.1671 87380 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.51 Å2
Refinement stepCycle: LAST / Resolution: 1.55→45.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3732 0 162 443 4337
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0174115
X-RAY DIFFRACTIONf_angle_d1.55145638
X-RAY DIFFRACTIONf_chiral_restr0.1158611
X-RAY DIFFRACTIONf_plane_restr0.0106716
X-RAY DIFFRACTIONf_dihedral_angle_d20.70521368
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.55-1.570.4161130.35832803X-RAY DIFFRACTION99.86
1.57-1.590.28231370.31242748X-RAY DIFFRACTION99.86
1.59-1.610.30831200.28712801X-RAY DIFFRACTION99.97
1.61-1.630.29281230.24632742X-RAY DIFFRACTION99.79
1.63-1.650.2371570.22362816X-RAY DIFFRACTION99.83
1.65-1.670.21491700.19892644X-RAY DIFFRACTION99.82
1.67-1.690.21481470.19842777X-RAY DIFFRACTION99.73
1.69-1.720.20431550.18542728X-RAY DIFFRACTION99.62
1.72-1.750.21611620.18032741X-RAY DIFFRACTION99.83
1.75-1.770.23131430.16562765X-RAY DIFFRACTION99.9
1.77-1.80.21671200.16192792X-RAY DIFFRACTION99.83
1.8-1.840.21591540.15862714X-RAY DIFFRACTION99.97
1.84-1.870.20891540.16342776X-RAY DIFFRACTION100
1.87-1.910.19871260.17352710X-RAY DIFFRACTION99.89
1.91-1.950.17692110.18422739X-RAY DIFFRACTION99.97
1.95-20.21431470.19322761X-RAY DIFFRACTION100
2-2.050.1981430.14932805X-RAY DIFFRACTION99.9
2.05-2.10.20581360.13932714X-RAY DIFFRACTION99.69
2.1-2.170.14321820.14762734X-RAY DIFFRACTION99.83
2.17-2.240.18561550.15152777X-RAY DIFFRACTION99.76
2.24-2.320.1571860.15132833X-RAY DIFFRACTION99.86
2.32-2.410.19241060.15892816X-RAY DIFFRACTION99.86
2.41-2.520.20451540.162750X-RAY DIFFRACTION99.9
2.52-2.650.14911280.15192769X-RAY DIFFRACTION99.9
2.65-2.820.16321490.14792780X-RAY DIFFRACTION99.86
2.82-3.030.17111180.1552822X-RAY DIFFRACTION99.9
3.03-3.340.15621430.14732783X-RAY DIFFRACTION100
3.34-3.820.17171630.14172795X-RAY DIFFRACTION99.86
3.82-4.810.14941490.14452827X-RAY DIFFRACTION99.6
4.82-45.920.23991540.22813X-RAY DIFFRACTION98.51

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