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- PDB-4gjv: Streptavidin-S112H -

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Basic information

Entry
Database: PDB / ID: 4gjv
TitleStreptavidin-S112H
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: 2.4 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 1.3Sep 13, 2023Group: 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 / pdbx_initial_refinement_model / struct_conn / 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.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_seq_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_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,4667
Polymers16,6211
Non-polymers8456
Water39622
1
A: Streptavidin
hetero molecules

A: Streptavidin
hetero molecules

A: Streptavidin
hetero molecules

A: Streptavidin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,86328
Polymers66,4844
Non-polymers3,37824
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z1
crystal symmetry operation10_665-x+1,-y+1,z1
crystal symmetry operation15_555y,x,-z1
Buried area11250 Å2
ΔGint-152 kcal/mol
Surface area18340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.580, 57.580, 183.760
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11A-402-

CL

21A-502-

HOH

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Components

#1: Protein Streptavidin /


Mass: 16621.086 Da / Num. of mol.: 1 / Mutation: S112H
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.: 1 / Source method: obtained synthetically / Formula: C21H32Cl3N3O2RhS
#3: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-RH / Rhodium / Rhodium


Mass: 102.906 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Rh
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 22 / 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: 46.9 %
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
ReflectionResolution: 2.4→54.946 Å / Num. all: 11694 / Num. obs: 10084

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Processing

Software
NameVersionClassificationNB
REFMACrefinement
SCALAdata scaling
PDB_EXTRACT3.006data extraction
PHENIXdev_1050refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2QCB

2qcb


Resolution: 2.4→19.876 Å / Occupancy max: 1 / Occupancy min: 0 / SU ML: 0.32 / σ(F): 1.34 / Phase error: 25.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.23 1000 9.99 %
Rwork0.185 --
obs0.189 10013 87.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 83.66 Å2 / Biso mean: 35.641 Å2 / Biso min: 20.01 Å2
Refinement stepCycle: LAST / Resolution: 2.4→19.876 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms917 0 33 22 972
Refinement TLS params.Method: refined / Origin x: 14.4174 Å / Origin y: 24.8201 Å / Origin z: -3.3717 Å
111213212223313233
T0.2388 Å20.0011 Å2-0.0027 Å2-0.2474 Å20.0043 Å2--0.3063 Å2
L1.8428 °20.0823 °20.0461 °2-1.7445 °20.0207 °2--1.8521 °2
S0.0181 Å °-0.0288 Å °0.0901 Å °0.0787 Å °0.077 Å °0.1325 Å °-0.0485 Å °-0.1797 Å °-0.0924 Å °
Refinement TLS groupSelection details: chain A and resid 13:134

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