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- PDB-4irw: Co-crystallization of streptavidin-biotin complex with a lanthani... -

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Basic information

Entry
Database: PDB / ID: 4irw
TitleCo-crystallization of streptavidin-biotin complex with a lanthanide-ligand complex gives rise to a novel crystal form
ComponentsStreptavidin
KeywordsBIOTIN BINDING PROTEIN / beta barrel
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
BIOTIN / PYRIDINE-2,6-DICARBOXYLIC ACID / TERBIUM(III) ION / Streptavidin
Similarity search - Component
Biological speciesStreptomyces avidinii (bacteria)
MethodX-RAY DIFFRACTION / SAD / Resolution: 1.396 Å
AuthorsBandara, R.A.M.S.S. / Liu, D.Q. / Hindupur, A. / Tesh, K.F. / Fox, R.O.
CitationJournal: To be Published
Title: Co-crystallization of streptavidin-biotin complex with a lanthanide-ligand complex gives rise to a novel crystal form
Authors: Bandara, R.A.M.S.S. / Liu, D.Q. / Hindupur, A. / Tesh, K.F. / Fox, R.O.
History
DepositionJan 15, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 29, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_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_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_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.pdbx_ptnr1_label_alt_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_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)16,47720
Polymers13,4091
Non-polymers3,06719
Water2,072115
1
A: Streptavidin
hetero molecules

A: Streptavidin
hetero molecules

A: Streptavidin
hetero molecules

A: Streptavidin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,90780
Polymers53,6384
Non-polymers12,26976
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_565x,-y+1,-z1
Buried area8560 Å2
ΔGint-54 kcal/mol
Surface area20180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.423, 71.395, 55.494
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number21
Space group name H-MC222
Components on special symmetry positions
IDModelComponents
11A-202-

PDC

21A-202-

PDC

31A-202-

PDC

41A-205-

PDC

51A-205-

PDC

61A-205-

PDC

71A-211-

PDC

81A-211-

PDC

91A-211-

PDC

101A-214-

TB

111A-215-

TB

121A-217-

TB

131A-219-

NA

141A-315-

HOH

151A-375-

HOH

161A-386-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Streptavidin


Mass: 13409.466 Da / Num. of mol.: 1 / Fragment: UNP residues 36-163
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces avidinii (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P22629

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Non-polymers , 5 types, 134 molecules

#2: Chemical
ChemComp-PDC / PYRIDINE-2,6-DICARBOXYLIC ACID / DIPICOLINIC ACID


Mass: 167.119 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C7H5NO4
#3: Chemical ChemComp-BTN / BIOTIN


Mass: 244.311 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N2O3S
#4: Chemical
ChemComp-TB / TERBIUM(III) ION


Mass: 158.925 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Tb
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 115 / 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: 2.38 Å3/Da / Density % sol: 48.3 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 1.5 uL protein (pH 8.0) incubated with saturated biotin solution + 1.5 uL 200 mM Na3[Tb(Dpa)3] + 3 uL 60% v/v MPD, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 93.15 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5417 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Aug 13, 2011
RadiationMonochromator: OSMIC VARIMAX HF OPTIC / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5417 Å / Relative weight: 1
ReflectionResolution: 1.396→27.86 Å / Num. obs: 21044 / % possible obs: 81.5 % / Redundancy: 6.26 % / Rmerge(I) obs: 0.066 / Χ2: 1 / Net I/σ(I): 15.4 / Scaling rejects: 996
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allΧ2% possible all
1.396-1.452.080.3771.812155830.5322.9
1.45-1.53.320.3182.8404412170.6247.5
1.5-1.574.670.2714.1911119500.7777.4
1.57-1.656.10.2195.71443423630.8391.9
1.65-1.766.540.1727.61541423480.8692.5
1.76-1.897.020.13410.31697724120.8893.5
1.89-2.087.010.10513.31711624370.8794.2
2.08-2.396.950.08915.51724824780.8595.9
2.39-3.017.080.0819.71819325641.0497.9
3.01-27.866.760.05441.21896226921.7799

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
d*TREKdata scaling
d*TREK9.9.8.9 W9RSSIdata reduction
PHENIXrefinement
PDB_EXTRACT3.11data extraction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.396→27.859 Å / Occupancy max: 1 / Occupancy min: 0.08 / FOM work R set: 0.8637 / SU ML: 0.13 / σ(F): 0 / Phase error: 20.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1536 1957 9.49 %
Rwork0.1226 --
obs0.1256 21015 79.56 %
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 84.62 Å2 / Biso mean: 26.7835 Å2 / Biso min: 7.95 Å2
Refinement stepCycle: LAST / Resolution: 1.396→27.859 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms910 0 151 115 1176
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091129
X-RAY DIFFRACTIONf_angle_d1.4311502
X-RAY DIFFRACTIONf_chiral_restr0.077153
X-RAY DIFFRACTIONf_plane_restr0.005202
X-RAY DIFFRACTIONf_dihedral_angle_d8.92500
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 27

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.396-1.41320.4528110.3711151267
1.4132-1.43180.2732360.284732135720
1.4318-1.45150.3319520.256249154330
1.4515-1.47220.2643730.220263670939
1.4722-1.49420.2464830.194378887148
1.4942-1.51750.2521970.187934103157
1.5175-1.54240.22631240.17351175129971
1.5424-1.5690.22491470.16081396154387
1.569-1.59750.20541560.17261510166690
1.5975-1.62820.181630.15231491165491
1.6282-1.66150.1961620.15521513167591
1.6615-1.69760.191540.15791499165391
1.6976-1.73710.21281550.15221511166692
1.7371-1.78050.19531630.13381536169992
1.7805-1.82860.18171630.12911521168493
1.8286-1.88240.15431610.12881536169793
1.8824-1.94320.17791590.1221536169593
1.9432-2.01260.18091620.12221527168993
2.0126-2.09320.15621660.10991572173895
2.0932-2.18840.14571550.09971566172194
2.1884-2.30370.14961680.10821588175696
2.3037-2.4480.15111670.10661585175297
2.448-2.63680.16691660.10561614178098
2.6368-2.9020.12191670.11831594176198
2.902-3.32130.15281700.11441632180299
3.3213-4.18220.11641650.11191654181999
4.1822-27.8640.13521700.1361605177597

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