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- PDB-2izd: APOSTREPTAVIDIN pH 3.0 I222 COMPLEX -

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Basic information

Entry
Database: PDB / ID: 2izd
TitleAPOSTREPTAVIDIN pH 3.0 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
IODIDE ION / AMMONIUM ION / Streptavidin
Similarity search - Component
Biological speciesStreptomyces avidinii (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 1.6 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 23, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 27, 2011Group: Atomic model / Derived calculations
Revision 1.4Nov 16, 2011Group: Atomic model
Revision 1.5Feb 8, 2017Group: Database references
Revision 2.0Feb 21, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Other / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / software / struct_site
Item: _atom_site.occupancy / _database_2.pdbx_DOI ..._atom_site.occupancy / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _software.name / _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)26,2427
Polymers25,9302
Non-polymers3125
Water2,558142
1
B: STREPTAVIDIN
D: STREPTAVIDIN
hetero molecules

B: STREPTAVIDIN
D: STREPTAVIDIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,48414
Polymers51,8604
Non-polymers62410
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area10760 Å2
ΔGint-144 kcal/mol
Surface area18790 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)104,96828
Polymers103,7208
Non-polymers1,24820
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)94.880, 105.340, 47.400
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-491-

HOH

21B-1460-

HOH

31B-1460-

HOH

Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.999699, -0.022536, -0.009715), (-0.023005, 0.722762, 0.690714), (-0.008544, 0.690729, -0.723063)
Vector: 51.9126, 0.7101, 0.3315)

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Components

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Protein , 1 types, 2 molecules BD

#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

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Non-polymers , 5 types, 147 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: I
#5: Chemical ChemComp-NH4 / AMMONIUM ION


Mass: 18.038 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H4N
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 142 / 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: 2.28 Å3/Da / Density % sol: 46.14 %
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: 3
Details: SYNTHETIC MOTHER LIQUOR = 75 % SATURATED AMMONIUM SULFATE, 25 % 1.0 M POTASSIUM ACETATE ADJUSTED TO PH 3.0.
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
ReflectionResolution: 1.6→7.5 Å / Num. obs: 40359 / Redundancy: 2.5 % / Rmerge(I) obs: 0.083
Reflection
*PLUS
Highest resolution: 1.31 Å / Num. measured all: 99140

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
bioteXdata reduction
X-PLORphasing
RefinementResolution: 1.6→7.5 Å / Cross valid method: FREE R / σ(F): 2.5
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). RESIDUES TYR B60 THROUGH SER B69 AND TYR D60 THROUGH SER D69 WERE REFINED IN TWO CONFORMATIONS BECAUSE UPON PROTONATION OF ASP61 AT LOW PH, ASP61 UNDERGOES A LARGE SHIFT IN CONFORMATION AND CHANGE IN HYDROGEN BONDING. THE LOOPS COMRISING RESIDUES ASP B61 THROUGH SER B69 AND ASP D61 THROUGH SER D69 ALSO UNDERGO CORRESPONDING CONFORMATIONAL CHANGES. HOWEVER SOME OF THESE RESIDUES ARE DISORDERED AND NOT VISIBLE IN EITHER CONFORMATION. TYR B22 IS DISORDERED BETWEEN 2 CONFORMATIONS ONE OF WHICH OCCUPIES A SIMILAR REGION OF SPACE AS A 2 - FOLD RELATED TYR B22. PROPER REFINEMENT WITH XPLOR 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: HOH491, AND HOH1460. IN REFINEMENT THERE WERE NO ENERGY INTERACTIONS INVOLVING HOH491, HOH1460.
RfactorNum. reflection% reflection
Rfree0.252 -10 %
Rwork0.2059 --
obs0.2059 20118 64 %
Refinement stepCycle: LAST / Resolution: 1.6→7.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1819 0 9 142 1970
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: 1.6→1.67 Å / % reflection obs: 29.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARMALLH3X.PROTOPALLH6X_BAK.PRO
X-RAY DIFFRACTION2
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
Lowest resolution: 1.76 Å / Rfactor obs: 0.208

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