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- PDB-2izc: APOSTREPTAVIDIN PH 2.0 I222 COMPLEX -

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Basic information

Entry
Database: PDB / ID: 2izc
TitleAPOSTREPTAVIDIN PH 2.0 I222 COMPLEX
ComponentsSTREPTAVIDIN
KeywordsBIOTIN-BINDING PROTEIN / APOSTREPTAVIDIN
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 ...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 / Resolution: 1.4 Å
AuthorsKatz, B.A.
Citation
Journal: J.Mol.Biol. / Year: 1997
Title: Binding of biotin to streptavidin stabilizes intersubunit salt bridges between Asp61 and His87 at low pH.
Authors: Katz, B.A.
#1: Journal: J.Biol.Chem. / Year: 1997
Title: In Crystals of Complexes of Streptavidin with Peptide Ligands Containing the Hpq Sequence the Pka of the Peptide Histidine is Less Than 3.0
Authors: Katz, B.A. / Cass, R.T.
#2: Journal: J.Am.Chem.Soc. / Year: 1996
Title: Structure-Based Design Tools: Structural and Thermodynamic Comparison with Biotin of a Small Molecule that Binds Streptavidin with Micromolar Affinity
Authors: Katz, B.A. / Liu, B. / Cass, R.T.
#3: Journal: J.Am.Chem.Soc. / Year: 1996
Title: Preparation of a Protein-Dimerizing Ligand by Topochemistry and Structure-Based Design
Authors: Katz, B.A.
#4: Journal: J.Biol.Chem. / Year: 1995
Title: Topochemical catalysis achieved by structure-based ligand design.
Authors: Katz, B.A. / Cass, R.T. / Liu, B. / Arze, R. / Collins, N.
#5: Journal: Biochemistry / Year: 1995
Title: Binding to Protein Targets of Peptidic Leads Discovered by Phage Display: Crystal Structures of Streptavidin-Bound Linear and Cyclic Peptide Ligands Containing the Hpq Sequence
Authors: Katz, B.A.
#6: Journal: J.Am.Chem.Soc. / Year: 1995
Title: Structure-Based Design of High Affinity Streptavidin Binding Ligands Containing Thioether Crosslinks
Authors: Katz, B.A. / Johnson, C.R. / Cass, R.T.
History
DepositionAug 13, 1997Processing site: BNL
Revision 1.0Sep 16, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 8, 2017Group: Database references
Revision 1.4Feb 21, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / software / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _software.name / _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_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_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
B: STREPTAVIDIN
D: STREPTAVIDIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,0827
Polymers25,9302
Non-polymers1525
Water2,108117
1
B: STREPTAVIDIN
D: STREPTAVIDIN
hetero molecules

B: STREPTAVIDIN
D: STREPTAVIDIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,16514
Polymers51,8604
Non-polymers30510
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area10550 Å2
ΔGint-189 kcal/mol
Surface area19380 Å2
MethodPISA
2
B: STREPTAVIDIN
D: STREPTAVIDIN
hetero molecules

B: STREPTAVIDIN
D: STREPTAVIDIN
hetero molecules

B: STREPTAVIDIN
D: STREPTAVIDIN
hetero molecules

B: STREPTAVIDIN
D: STREPTAVIDIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,33028
Polymers103,7208
Non-polymers60920
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
crystal symmetry operation3_655-x+1,y,-z1
crystal symmetry operation4_555x,-y,-z1
MethodPQS
Unit cell
Length a, b, c (Å)94.850, 105.630, 48.140
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11B-1460-

HOH

21D-1465-

HOH

Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.999876, -0.01572, 0.000628), (-0.010776, 0.713407, 0.700667), (-0.011463, 0.700573, -0.713488)
Vector: 51.6258, 0.3097, 0.1027)

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Components

#1: Protein STREPTAVIDIN


Mass: 12965.025 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Streptomyces avidinii (bacteria) / References: UniProt: P22629
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 117 / 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: 2.32 Å3/Da / Density % sol: 24 %
Description: REJECTION CRITERIA: (I(H)I - ) > [0.30 * () + 0.10*I(H)I], WHERE I(H)I IS THE ITH OBSERVATION OF THE INTENSITY OF REFLECTION H (M.G.ROSSMANN ET AL., J.APPL.CRYST. 12, 570-581). THIS ...Description: REJECTION CRITERIA: (I(H)I - ) > [0.30 * () + 0.10*I(H)I], WHERE I(H)I IS THE ITH OBSERVATION OF THE INTENSITY OF REFLECTION H (M.G.ROSSMANN ET AL., J.APPL.CRYST. 12, 570-581). THIS REJECTION CRITERION IS THE DEFAULT OF THE MSC PROGRAM BIOTEX.
Crystal growpH: 2
Details: SYNTHETIC MOTHER LIQUOR = 75 % SATURATED AMMONIUM SULFATE, 25 % 1.0 M SODIUM FORMATE ADJUSTED TO PH 2.0.
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 4 / Method: vapor diffusion, hanging drop / Details: Pahler, A., (1987) J. Biol. Chem., 262, 13933.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
130-32 %satammonium sulfate1reservoir
20.1 Mpotassium acetate1reservoir
330 mg/mlprotein1drop

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Data collection

DiffractionAmbient temp details: ROOM
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Details: MSC MIRRORS
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNum. obs: 48869 / Redundancy: 4.1 % / Rmerge(I) obs: 0.067
Reflection
*PLUS
Highest resolution: 1.32 Å / Num. measured all: 200364

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
bioteXdata reduction
X-PLORphasing
RefinementResolution: 1.4→7.5 Å / Cross valid method: FREE R / σ(F): 2
Details: THE FOLLOWING ATOMS HAD WEAK DENSITY AND OCCUPANCIES WERE REFINED: B13, B14, B15, (CG, HG1, HG2, CD, OE1, OE2 OF GLU B51), (NE, HE, CZ, NH1, HH11, HH12, NH2, HH21, HH22 OF ARG B53), SER B62, ...Details: THE FOLLOWING ATOMS HAD WEAK DENSITY AND OCCUPANCIES WERE REFINED: B13, B14, B15, (CG, HG1, HG2, CD, OE1, OE2 OF GLU B51), (NE, HE, CZ, NH1, HH11, HH12, NH2, HH21, HH22 OF ARG B53), SER B62, ALA B63, PRO B64, ALA B65, THR B66, ASP B67, GLY B68 (NE, HE, CZ, NH1, HH11, HH12, NH2, HH21, HH22 OF ARG B84), (SIDE CHAIN OF HIS B87), (NE, HE, CZ, NH1, HH11, HH12, NH2, HH21, HH22 OF ARG B103), (CG, HG1, HG2, CD, OE1, OE2 OF GLU B116), (CB, HB1, HB2, CG, HG1, HG2 OF LYS B134), (CD, HD1, HD2 OF LYS B134), PRO B135, ALA D13, (N, HN, CA, HA, CB, HB1, HB2, C, O OF GLU D14), (CG, HG1, HG2, CD, OE1, OE2 OF GLU D14), ALA D15 (CG, OD1, OD2 OF ASP D36), (OG AND HG1 OF SER D45), ALA D46, VAL D47, GLY D48, ASN D49, ALA D50, (GLU D51, EXCEPT C AND O) (NE, HE, CZ, NH1, HH11, HH12, NH2, HH21, HH22 OF ARG D53), (CG, OD1, ND2, HD21, HD22 OF ASN D82), (CG AND OUTWARD OF TYR D83), (NE, HE, CZ, NH1, HH11, HH12, NH2, HH21, HH22 OF ARG D84), (CG, HG1, HG2, CD, OE1, OE2 OF GLU D101), (NE, HE, CZ, NH1, HH11, HH12, NH2, HH21, HH22 OF ARG D103), (CG, HG1, HG2, CD, OE1, OE2 OF GLU D116). TYR B22 IS DISORDERED BETWEEN 2 CONFORMATIONS ONE OF WHICH OCCUPIES A SIMILAR REGION OF SPACE AS A 2-FOLD RELATED B22. PROPER REFINEMENT WITH X-PLOR IS NOT POSSIBLE BECAUSE OF THE OVERLAP OF ONE CONFORMER WITH THE SYMMETRY RELATED COUNTERPART. THE FOLLOWING WATERS WERE USED TO ACCOUNT FOR DENSITY DUE TO THIS CONFORMER OF TYR B22: HOH 491, HOH 1460,AND HOH 1465. NO HYDROGENS ARE INCLUDED FOR THESE "WATERS".
RfactorNum. reflection% reflection
Rfree0.241 -10 %
Rwork0.207 --
obs0.207 31325 66 %
Refinement stepCycle: LAST / Resolution: 1.4→7.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1819 0 5 117 1941
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.019
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg4.3
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.5
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 1.4→1.46 Å / % reflection obs: 29 %
Xplor fileSerial no: 1 / Param file: PARMALLH3X.PRO / Topol file: TOPALLH6X_BAK.PRO
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.5
LS refinement shell
*PLUS
Rfactor obs: 0.207

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