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Basic information

Entry
Database: PDB / ID: 4gjs
TitleStreptavidin-K121H
ComponentsStreptavidin
KeywordsBiotin-binding protein / artificial metalloenyzme / artificial transfer hydrogenase / beta barrel / tetramer / biotin / iridium pentamethylcyclopentadienyl
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
Chem-0OD / Rhodium / Streptavidin
Similarity search - Component
Biological speciesStreptomyces avidinii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsHeinisch, T. / Schirmer, T.
CitationJournal: J.Am.Chem.Soc. / Year: 2013
Title: A dual anchoring strategy for the localization and activation of artificial metalloenzymes based on the biotin-streptavidin technology.
Authors: Zimbron, J.M. / Heinisch, T. / Schmid, M. / Hamels, D. / Nogueira, E.S. / Schirmer, T. / Ward, T.R.
History
DepositionAug 10, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 13, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 10, 2013Group: Database references
Revision 1.2Apr 24, 2013Group: Database references
Revision 1.3Feb 28, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_ncs_dom_lim / 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_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _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

Downloads & links

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Assembly

Deposited unit
A: Streptavidin
B: Streptavidin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,5636
Polymers33,1582
Non-polymers1,4054
Water5,891327
1
A: Streptavidin
B: Streptavidin
hetero molecules

A: Streptavidin
B: Streptavidin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,12712
Polymers66,3164
Non-polymers2,8118
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_554-x,y,-z-11
Buried area9680 Å2
ΔGint-57 kcal/mol
Surface area18720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.652, 81.331, 47.002
Angle α, β, γ (deg.)90.000, 104.830, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-501-

HOH

21B-504-

HOH

31B-600-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A and (resseq 13:134 )
21chain B and (resseq 13:134 )

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ASP / Beg label comp-ID: ASP / End auth comp-ID: LYS / End label comp-ID: LYS / Auth seq-ID: 13 - 134 / Label seq-ID: 13 - 134

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1chain 'A' and (resseq 13:134 )AA
2chain 'B' and (resseq 13:134 )BB

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Components

#1: Protein Streptavidin


Mass: 16578.984 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces avidinii (bacteria) / Plasmid: pLysS / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P22629
#2: Chemical ChemComp-0OD / trichloro{(1,2,3,4,5-eta)-1,2,3,4-tetramethyl-5-[2-({5-[(3aS,4S,6aR)-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]pentanoyl}amino)ethyl]cyclopentadienyl}rhodium(1+) / [Cp*(Biot-methylene)RhCl(H2O)2]+


Mass: 599.827 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H32Cl3N3O2RhS
#3: Chemical ChemComp-RH / Rhodium


Mass: 102.906 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Rh
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 327 / 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: 2.3 Å3/Da / Density % sol: 46.4 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.1 M MES, 19 % PEG500, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 3, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionNumber: 66292
ReflectionResolution: 1.85→40.67 Å / Num. obs: 24972 / % possible obs: 98.46 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 2.65 % / Rmerge(I) obs: 0.081 / Net I/σ(I): 5.9541
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique all% possible all
1.85-1.952.140.183.557608356196.35
1.95-2.072.550.163.688899349299.52
2.07-2.212.680.154.248703324699.55
2.21-2.392.760.124.968433305299.52
2.39-2.622.780.087.477765279699.19
2.62-2.932.80.078.167044251598.8
2.93-3.382.810.078.556267223198.61
3.38-4.142.830.069.095285186897.94
4.14-5.852.840.077.444072143297.01
5.85-40.672.840.15.55221677994.75

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Processing

Software
NameVersionClassificationNB
SCALACCP4_3.3.20 2011/05/18data scaling
PHENIXdev_1050refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→28.321 Å / Occupancy max: 1 / Occupancy min: 0.11 / SU ML: 0.24 / σ(F): 1.37 / Phase error: 25.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.25 1277 5.12 %
Rwork0.203 --
obs0.205 24960 98.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 73.07 Å2 / Biso mean: 22.53 Å2 / Biso min: 6.33 Å2
Refinement stepCycle: LAST / Resolution: 1.85→28.321 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1828 0 60 327 2215
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A914X-RAY DIFFRACTIONPOSITIONAL0.025
12B914X-RAY DIFFRACTIONPOSITIONAL0.025
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.5968-0.1462-0.32541.93760.17491.71740.0556-0.0644-0.09780.1122-0.0865-0.22890.08940.18250.00970.09090.0148-0.01910.06870.04170.223613.4001-13.2485-19.4834
22.02040.26690.14052.15580.28571.7890.06760.04170.0154-0.1275-0.0732-0.2764-0.14060.1643-0.00080.089-0.01280.02040.06850.02950.176213.46212.6569-25.9331
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain A and resid 13:134A13 - 134
2X-RAY DIFFRACTION2chain B and resid 13:134B13 - 134

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