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- PDB-2izk: STREPTAVIDIN-GLYCOLURIL PH 2.58 I4122 COMPLEX -

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Basic information

Entry
Database: PDB / ID: 2izk
TitleSTREPTAVIDIN-GLYCOLURIL PH 2.58 I4122 COMPLEX
ComponentsSTREPTAVIDIN
KeywordsBIOTIN-BINDING PROTEIN / STREPTAVIDIN-SMALL MOLECULE LIGAND / DESIGNED SMALL MOLECULE LIGAND WITH MICROMOLAR AFFINITY
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
ACETATE ION / GLYCOLURIL / Streptavidin
Similarity search - Component
Biological speciesStreptomyces avidinii (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 1.3 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 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: Derived calculations
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
A: STREPTAVIDIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,2624
Polymers12,9651
Non-polymers2973
Water1,33374
1
A: STREPTAVIDIN
hetero molecules

A: STREPTAVIDIN
hetero molecules

A: STREPTAVIDIN
hetero molecules

A: STREPTAVIDIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,04916
Polymers51,8604
Non-polymers1,18912
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z1
crystal symmetry operation10_555-x,-y,z1
crystal symmetry operation15_555y,x,-z1
Buried area12400 Å2
ΔGint-138 kcal/mol
Surface area19120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.040, 58.040, 174.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11A-305-

HOH

21A-546-

HOH

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Components

#1: Protein STREPTAVIDIN /


Mass: 12965.025 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Streptomyces avidinii (bacteria) / References: UniProt: P22629
#2: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GLL / GLYCOLURIL / Glycoluril


Mass: 142.116 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6N4O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 74 / 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: 2.83 Å3/Da / Density % sol: 37.7 %
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: 2.58
Details: SYNTHETIC MOTHER LIQUOR = 75 % SATURATED AMMONIUM SULFATE, 25% 1.0M POTASSIUM ACETATE ADJUSTED TO PH 2.58. COMPLEX PRODUCED BY SOAKING STREPTAVIDIN-2-IMINOBIOTIN CO-CRYSTAL.
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 4.5 / Method: vapor diffusion, hanging drop / Details: Pahler, A., (1987) J. Biol. Chem., 262, 13933.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110-20 mg/mlprotein1drop
250 mMpotassium acetate1drop
3200 mM1dropNaCl
430 %satammonium sulfate1reservoir

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Data collection

DiffractionAmbient temp details: ROOM
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: RIGAKU / 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: 24284 / Redundancy: 4.1 % / Rmerge(I) obs: 0.058
Reflection
*PLUS
Highest resolution: 1.32 Å / Num. measured all: 99961

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
bioteXdata reduction
X-PLORphasing
RefinementHighest resolution: 1.3 Å / Cross valid method: FREE R / σ(F): 1
Details: THE FOLLOWING ATOMS HAD WEAK DENSITY AND OCCUPANCIES WERE REFINED: ALA13, GLU14, ALA15, (SIDE CHAIN OF ALA35), (CG, OD1, AND OD2 OF ASP36), (CG, HG1, HG2, CD, OE1, OE2 OF GLU44), (CA AND HA1 ...Details: THE FOLLOWING ATOMS HAD WEAK DENSITY AND OCCUPANCIES WERE REFINED: ALA13, GLU14, ALA15, (SIDE CHAIN OF ALA35), (CG, OD1, AND OD2 OF ASP36), (CG, HG1, HG2, CD, OE1, OE2 OF GLU44), (CA AND HA1 AND HA2 OF GLY48), (SIDE CHAIN OF ASN49), (SIDE CAHIN OF ALA50) (CG, HG1, HG2, CD, OE1, OE2 OF GLU51), (TERMINUS OF ARG53), (CG, HG1, HG2 OF ARG84), (CD, HD1, HD2, NE, HE, CZ NH1, HH11, HH12, NH2, HH21, HH22 OF ARG84), (CB, HB1, HB2, HB3 OF ALA100), (CG, HG1, HG2, CD, OE1, OE2 OF GLU101), (TERMINUS OF ARG103), (CD, OE1, OE2 OF GLU116), (CE, HE1, HE2 OF LYS121), (NZ, HZ1, HZ2, HZ3 OF LYS121), (CB, HB1, HB2, CG, HG1, HG2, CD, HD1, HD2) OF LYS134, (CE, HE1, HE2, NZ, HZ1, HZ2, HZ3 OF LYS134), PRO135. RESIDUES 60 - 69 WERE REFINED IN 2 CONFORMATIONS BECAUSE UPON PROTONATION OF ASP61 AT LOW PH, ASP61 UNDERGOES A LARGE SHIFT IN CONFORMATION AND CHANGE IN HYDROGEN BONDING. THE LOOP COMRISING RESIDUES 61 - 69 ALSO UNDERGOES CORRESPONDING CONFORMATIONAL CHANGES. HOWEVER SOME OF THESE RESIDUES ARE DISORDERED AND NOT VISIBLE IN EITHER CONFORMATION.
RfactorNum. reflection% reflection
Rfree0.202 -10 %
Rwork0.178 --
obs0.178 16913 69.8 %
Refinement stepCycle: LAST / Highest resolution: 1.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms918 0 19 74 1011
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: 1.5→1.57 Å / % reflection obs: 23.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARMALLH3X.PROTOPALLH6X_BAK.PRO
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.32 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
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: 0.178

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