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- PDB-2rtk: STREPTAVIDIN-GLYCOLURIL COMPLEX, PH 2.58, SPACE GROUP I4122 PREPA... -

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Basic information

Entry
Database: PDB / ID: 2rtk
TitleSTREPTAVIDIN-GLYCOLURIL COMPLEX, PH 2.58, SPACE GROUP I4122 PREPARED FROM AN APOSTREPTAVIDIN CRYSTAL
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 ...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: 1.82 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: Chem.Biol. / Year: 1995
Title: Topochemistry for Preparing Ligands that Dimerize Receptors
Authors: Katz, B.A. / Stroud, R.M. / Collins, N. / Liu, B. / Arze, R.
#6: 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.
#7: Journal: J.Am.Chem.Soc. / Year: 1995
Title: Structure-Based Design of High Affinity Streptavidin Binding Cyclic Peptide Ligands Containing Thioether Cross-Links
Authors: Katz, B.A. / Johnson, C.R. / Cass, R.T.
History
DepositionSep 11, 1997Processing site: BNL
Revision 1.0Oct 14, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
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)14,4794
Polymers14,1811
Non-polymers2973
Water1,69394
1
A: STREPTAVIDIN
hetero molecules

A: STREPTAVIDIN
hetero molecules

A: STREPTAVIDIN
hetero molecules

A: STREPTAVIDIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,91416
Polymers56,7254
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 area12460 Å2
ΔGint-137 kcal/mol
Surface area19160 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)58.200, 58.200, 176.660
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

31A-558-

HOH

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Components

#1: Protein STREPTAVIDIN


Mass: 14181.324 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


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


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


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


Mass: 18.015 Da / Num. of mol.: 94 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.64 Å3/Da / Density % sol: 33.3 %
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, A.G.W.LESLIE, S.S.ABDEL-MEGUID, T.TSUKIHARA, ...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, A.G.W.LESLIE, S.S.ABDEL-MEGUID, T.TSUKIHARA, J.APPL.CRYST. 12, 570 - 581). THIS REJECTION CRITERION IS THE DEFAULT OF THE MSC PROGRAM BIOTEX.
Crystal growpH: 1.9
Details: SYNTHETIC MOTHER LIQUOR OF 75% SATURATED AMMONIUM SULFATE, 25% 1.0 M SODIUM FORMATE ADJUSTED TO PH 1.90.
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

Diffraction sourceWavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNum. obs: 13194 / % possible obs: 60 % / Redundancy: 2.4 % / Rmerge(I) obs: 0.092
Reflection shellResolution: 1.82→1.9 Å / Redundancy: 2.4 % / % possible all: 33.1
Reflection
*PLUS
Highest resolution: 1.38 Å / Num. measured all: 31257

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Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLORrefinement
bioteX(MSC)data reduction
X-PLORphasing
RefinementResolution: 1.82→7.5 Å / σ(F): 2.5
Details: THE FOLLOWING ATOMS HAD WEAK DENSITY AND OCCUPANCIES WERE REFINED: ALA 13, GLU 14, ALA 15 (EXCEPT C AND O), GLY 26 (SIDE CHAIN) ASP 36 (N, HN, CA, HA, CB, HB1, HB2, C, O, CG, OD1, OD2) GLU ...Details: THE FOLLOWING ATOMS HAD WEAK DENSITY AND OCCUPANCIES WERE REFINED: ALA 13, GLU 14, ALA 15 (EXCEPT C AND O), GLY 26 (SIDE CHAIN) ASP 36 (N, HN, CA, HA, CB, HB1, HB2, C, O, CG, OD1, OD2) GLU 44 (CG, HG1, HG2, CD, OE1, OE2), ALA 46, VAL 47, GLY 48, ASN 49, ALA 50 GLU 51, SER 52 (SIDE CHAIN OF SER52), ARG 53 (NE, HE, CZ, NH1, HH11, HH12, NH2, HH21, HH22) ARG 84 (CG, HG1, HG2, CD, HD1, HD2, NE, HE, CZ, NH1, HH11, HH12, NH2, HH21, HH22) GLY 99, ALA 100, GLU 101 (N, HN, CA, HA, CB, HB1, HB2, C, O, CG, HG1, HG2, CD, OE1, OE2) ARG 103 (NE, HE, CZ, NH1, HH11, HH12, NH2, HH21, HH22) GLU 116 (N, HN, CA, HA, CB, HB1, HB2, CG, HG1, HG2, C, O CD, OE1, OE2), ALA 117, ASN 118 (SIDE CHAIN) LYS 121 (CG, HG1, HG2, CD, HD1, HD2, CE, HE1, HE2, NZ, HZ1, HZ2, HZ3) LYS 134 (CB, HB1, HB2, CD, HD1, HD2, CE, HE1, HE2, NZ, HZ1, HZ2, HZ3), PRO 135 DISCRETELY DISORDERED ENTIRE RESIDUES WHOSE OCCUPANCIES AND STRUCTURES WERE SIMULTANEOUSLY REFINED ARE: 60, 61, 62, 63, 64, 65, 66, 67, 68, 69. DISCRETELY DISORDERED SIDE CHAINS WHOSE OCCUPANCIES AND STRUCTURES WERE SIMULTANEOUSLY REFINED ARE: PHE 29, LEU 73, HIS 87, GLN 107, LEU 110, LYS 132. RESIDUES 60-69 WERE REFINED IN 2 CONFORMATIONS BECAUSE UPON PROTONATION OF ASP 61 AT LOW PH, ASP 61 UNDERGOES A LARGE SHIFT IN CONFORMATION AND CHANGE IN HYDROGEN BONDING. THE LOOP COMPRISING RESIDUES 61-69 ALSO UNDERGO CORRESPONDING CONFORMATIONAL CHANGES. HOWEVER SOME OF THESE RESIDUES ARE DISORDERED AND NOT VISIBLE IN EITHER CONFORMATION. DISORDERED WATERS ARE: HOH 136 WHICH OCCUPIES THE SPACE AVAILABLE WHEN ASP 61 IS IN CONFORMATION 2 HOH 207 WHICH IS CLOSE TO A SYMMETRY RELATED EQUIVALENT OF HOH 354 HOH 228 WHICH IS CLOSE TO HOH 229 AND HOH 230 HOH 305 WHICH IS CLOSE TO A SYMMETRY RELATED EQUIVALENT OF ITSELF HOH 546 WHICH IS CLOSE TO A SYMMETRY RELATED EQUIVALENT OF ITSELF HOH 558 WHICH IS CLOSE TO A SYMMETRY RELATED EQUIVALENT OF ITSELF HOH 559 WHICH IS CLOSE TO A SYMMETRY RELATED EQUIVALENT OF ITSELF HOH 624 WHICH IS CLOSE TO A SYMMETRY RELATED EQUIVALENT OF ITSELF THE FOLLOWING ATOMS HAD WEAK DENSITY AND OCCUPANCIES WERE REFINED: ALA 13 GLU 14 ALA 15 (EXCEPT C AND O) GLY 26 (SIDE CHAIN) ASP 36 (N, HN, CA, HA, CB, HB1, HB2, C, O, CG, OD1, OD2) GLU 44 (CG, HG1, HG2, CD, OE1, OE2) ALA 46 VAL 47 GLY 48 ASN 49 ALA 50 GLU 51 SER 52 (SIDE CHAIN OF SER52) ARG 53 (NE, HE, CZ, NH1, HH11, HH12, NH2, HH21, HH22) ARG 84 (CG, HG1, HG2, CD, HD1, HD2, NE, HE, CZ, NH1, ARG 84 HH11, HH12, NH2, HH21, HH22) GLY 99 ALA 100 GLU 101 (N, HN, CA, HA, CB, HB1, HB2, C, O, CG, HG1, HG2, CD, OE1, OE2) ARG 103 (NE, HE, CZ, NH1, HH11, HH12, NH2, HH21, HH22) GLU 116 (N, HN, CA, HA, CB, HB1, HB2, CG, HG1, HG2, C, O CD, OE1, OE2) ALA 117 ASN 118 (SIDE CHAIN) LYS 121 (CG, HG1, HG2, CD, HD1, HD2, CE, HE1, HE2, NZ, HZ1, HZ2, HZ3) LYS 134 (CB, HB1, HB2, CD, HD1, HD2, CE, HE1, HE2, NZ, HZ1, HZ2, HZ3) PRO 135 RESIDUES 60-69 WERE REFINED IN 2 CONFORMATIONS BECAUSE UPON PROTONATION OF ASP 61 AT LOW PH, ASP 61 UNDERGOES A LARGE SHIFT IN CONFORMATION AND CHANGE IN HYDROGEN BONDING. THE LOOP COMPRISING RESIDUES 61-69 ALSO UNDERGO CORRESPONDING CONFORMATIONAL CHANGES. HOWEVER SOME OF THESE RESIDUES ARE DISORDERED AND NOT VISIBLE IN EITHER CONFORMATION.
RfactorNum. reflection% reflection
Rfree0.276 --
Rwork0.196 --
obs0.196 8280 60 %
Refinement stepCycle: LAST / Resolution: 1.82→7.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms918 0 19 94 1031
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.02
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_d23.9
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: 1.8→1.92 Å / % reflection obs: 33.1 %
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_deg23.9
LS refinement shell
*PLUS
Highest resolution: 1.9 Å / Rfactor obs: 0.196

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