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- PDB-4jnj: Structure based engineering of streptavidin monomer with a reduce... -

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Basic information

Entry
Database: PDB / ID: 4jnj
TitleStructure based engineering of streptavidin monomer with a reduced biotin dissociation rate
ComponentsStreptavidin/Rhizavidin Hybrid
KeywordsPROTEIN BINDING / Beta barrel / Engineered Streptavidin Variant / Biotin / Biotin-Binding Protein
Function / homologyAvidin-like / Lipocalin / Beta Barrel / Mainly Beta / BIOTIN
Function and homology information
Biological speciesStreptomyces avidinii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.902 Å
AuthorsDeMonte, D. / Drake, E.J. / Hong Lim, K. / Gulick, A.M. / Park, S.
CitationJournal: Proteins / Year: 2013
Title: Structure-based engineering of streptavidin monomer with a reduced biotin dissociation rate.
Authors: Demonte, D. / Drake, E.J. / Lim, K.H. / Gulick, A.M. / Park, S.
History
DepositionMar 15, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 29, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2013Group: Database references
Revision 1.2Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.ptnr1_label_seq_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_conn.ptnr2_label_seq_id / _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/Rhizavidin Hybrid
B: Streptavidin/Rhizavidin Hybrid
C: Streptavidin/Rhizavidin Hybrid
D: Streptavidin/Rhizavidin Hybrid
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,93117
Polymers50,3654
Non-polymers1,56613
Water3,927218
1
A: Streptavidin/Rhizavidin Hybrid
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,0325
Polymers12,5911
Non-polymers4414
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Streptavidin/Rhizavidin Hybrid
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,0325
Polymers12,5911
Non-polymers4414
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Streptavidin/Rhizavidin Hybrid
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,9013
Polymers12,5911
Non-polymers3102
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Streptavidin/Rhizavidin Hybrid
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,9664
Polymers12,5911
Non-polymers3753
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
B: Streptavidin/Rhizavidin Hybrid
hetero molecules

D: Streptavidin/Rhizavidin Hybrid
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,9989
Polymers25,1832
Non-polymers8167
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_545x+1/2,-y-1/2,-z1
Buried area790 Å2
ΔGint-88 kcal/mol
Surface area12810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.117, 64.058, 108.493
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Streptavidin/Rhizavidin Hybrid


Mass: 12591.332 Da / Num. of mol.: 4 / Fragment: unp residues 12-134
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces avidinii (bacteria) / Production host: Escherichia coli (E. coli)
#2: Chemical
ChemComp-BTN / BIOTIN


Mass: 244.311 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16N2O3S
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 218 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.11 Å3/Da / Density % sol: 41.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 18-24% PEG 1000, 40-80 mM zinc acetate, 100 mM sodium acetate , pH 5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97945 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: May 18, 2012
RadiationMonochromator: Curved Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97945 Å / Relative weight: 1
ReflectionResolution: 1.9→29 Å / Num. all: 33053 / Num. obs: 34185 / % possible obs: 97.3 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.095 / Net I/σ(I): 10.7
Reflection shellResolution: 1.9→1.95 Å / Rmerge(I) obs: 0.716 / Mean I/σ(I) obs: 2.2 / % possible all: 97.1

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.902→29 Å / SU ML: 0.22 / σ(F): 1.36 / Phase error: 24.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2518 1992 6.03 %
Rwork0.1959 --
obs0.1993 33023 96.62 %
all-164674 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.902→29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3451 0 73 218 3742
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073621
X-RAY DIFFRACTIONf_angle_d1.4424929
X-RAY DIFFRACTIONf_dihedral_angle_d16.3011259
X-RAY DIFFRACTIONf_chiral_restr0.095501
X-RAY DIFFRACTIONf_plane_restr0.004661
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9021-1.94970.33571340.24582135X-RAY DIFFRACTION94
1.9497-2.00240.30191400.24122246X-RAY DIFFRACTION99
2.0024-2.06130.27841520.21842211X-RAY DIFFRACTION99
2.0613-2.12780.26321420.20732240X-RAY DIFFRACTION99
2.1278-2.20380.27781450.20662237X-RAY DIFFRACTION99
2.2038-2.2920.26611410.20382248X-RAY DIFFRACTION99
2.292-2.39630.26571400.20382224X-RAY DIFFRACTION98
2.3963-2.52260.26741520.20482205X-RAY DIFFRACTION97
2.5226-2.68050.26181360.20082244X-RAY DIFFRACTION98
2.6805-2.88730.26861450.21212202X-RAY DIFFRACTION97
2.8873-3.17760.26061330.20582217X-RAY DIFFRACTION96
3.1776-3.63670.26611470.18182183X-RAY DIFFRACTION95
3.6367-4.5790.19831400.16212206X-RAY DIFFRACTION94
4.579-29.41750.22911450.19512233X-RAY DIFFRACTION91

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