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- PDB-1mm9: Streptavidin Mutant with Insertion of Fibronectin Hexapeptide, in... -

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Basic information

Entry
Database: PDB / ID: 1mm9
TitleStreptavidin Mutant with Insertion of Fibronectin Hexapeptide, including RGD
ComponentsStreptavidin
KeywordsBiotin-binding protein / tetramer
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 / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Biological speciesStreptomyces avidinii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / isomorphous / Resolution: 1.66 Å
AuthorsLe Trong, I. / McDevitt, T.C. / Nelson, K.E. / Stayton, P.S. / Stenkamp, R.E.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2003
Title: Structural characterization and comparison of RGD cell-adhesion recognition sites engineered into streptavidin.
Authors: Le Trong, I. / McDevitt, T.C. / Nelson, K.E. / Stayton, P.S. / Stenkamp, R.E.
History
DepositionSep 3, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 6, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Streptavidin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,8013
Polymers13,5651
Non-polymers2362
Water1,60389
1
A: Streptavidin
hetero molecules

A: Streptavidin
hetero molecules

A: Streptavidin
hetero molecules

A: Streptavidin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,20412
Polymers54,2594
Non-polymers9458
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_556x,-y+1/2,-z+5/41
crystal symmetry operation12_555y,-x+1/2,z+1/41
crystal symmetry operation15_556y,x,-z+11
2
A: Streptavidin
hetero molecules

A: Streptavidin
hetero molecules

A: Streptavidin
hetero molecules

A: Streptavidin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,20412
Polymers54,2594
Non-polymers9458
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_556-y,-x,-z+11
crystal symmetry operation10_555-x,-y,z1
crystal symmetry operation15_556y,x,-z+11
Buried area12060 Å2
ΔGint-40 kcal/mol
Surface area21420 Å2
MethodPISA
3
A: Streptavidin
hetero molecules

A: Streptavidin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,6026
Polymers27,1292
Non-polymers4734
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation15_556y,x,-z+11
MethodPQS
Unit cell
Length a, b, c (Å)56.90, 56.90, 170.80
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-6028-

HOH

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Components

#1: Protein Streptavidin /


Mass: 13564.644 Da / Num. of mol.: 1 / Fragment: Core Streptavidin (residues 13-139)
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: Chemical ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 89 / 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: 2.27 Å3/Da / Density % sol: 51.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: MPD, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 mg/mlprotein1drop
240-50 %MPD1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.98 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 29, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.66→50 Å / Num. all: 17197 / Num. obs: 17197 / % possible obs: 98.8 % / Observed criterion σ(I): -3 / Redundancy: 14 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 28.4
Reflection shellResolution: 1.66→1.68 Å / Rmerge(I) obs: 0.495 / Mean I/σ(I) obs: 3.2 / Num. unique all: 689 / % possible all: 81.4
Reflection
*PLUS
Highest resolution: 1.65 Å / % possible obs: 98.9 % / Num. measured all: 240518
Reflection shell
*PLUS
Highest resolution: 1.65 Å / % possible obs: 81.4 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
SHELXL-97refinement
RefinementMethod to determine structure: isomorphous / Resolution: 1.66→20 Å / Num. parameters: 9480 / Num. restraintsaints: 12020 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY ?
RfactorNum. reflection% reflectionSelection details
Rfree0.1953 1717 10 %RANDOM
Rwork0.1335 ---
all0.1446 17174 --
obs0.1446 17174 99.8 %-
Refine analyzeNum. disordered residues: 3 / Occupancy sum hydrogen: 877 / Occupancy sum non hydrogen: 1038.5
Refinement stepCycle: LAST / Resolution: 1.66→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms941 0 16 89 1046
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.009
X-RAY DIFFRACTIONs_angle_d0.03
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.03
X-RAY DIFFRACTIONs_zero_chiral_vol0.042
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.055
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.024
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.002
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.024
X-RAY DIFFRACTIONs_approx_iso_adps0.077
Software
*PLUS
Name: SHELXL / Version: 97 / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.65 Å / Lowest resolution: 20 Å / Rfactor obs: 0.145 / Rfactor Rfree: 0.195 / Rfactor Rwork: 0.134
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Rfactor Rfree: 0.176 / Rfactor Rwork: 0.119 / Rfactor obs: 0.13

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