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- PDB-2rti: STREPTAVIDIN-GLYCOLURIL COMPLEX, PH 2.50, SPACE GROUP I222 -

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Basic information

Entry
Database: PDB / ID: 2rti
TitleSTREPTAVIDIN-GLYCOLURIL COMPLEX, PH 2.50, SPACE GROUP I222
ComponentsSTREPTAVIDIN
KeywordsBIOTIN-BINDING PROTEIN / STREPTAVIDIN-GLYCOLURIL / PH 2.50
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
FORMIC ACID / GLYCOLURIL / Streptavidin
Similarity search - Component
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: 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 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)28,7857
Polymers28,3632
Non-polymers4225
Water2,270126
1
B: STREPTAVIDIN
D: STREPTAVIDIN
hetero molecules

B: STREPTAVIDIN
D: STREPTAVIDIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,57014
Polymers56,7254
Non-polymers84510
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area11650 Å2
ΔGint-49 kcal/mol
Surface area18450 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)115,14028
Polymers113,4518
Non-polymers1,68920
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)95.030, 104.800, 48.260
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-1539-

HOH

Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.999852, -0.016006, -0.006257), (-0.015869, 0.720178, 0.693608), (-0.006596, 0.693605, -0.720326)
Vector: 51.8848, 0.5013, 0.2503)

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Components

#1: Protein STREPTAVIDIN


Mass: 14181.324 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Streptomyces avidinii (bacteria) / References: UniProt: P22629
#2: Chemical ChemComp-GLL / GLYCOLURIL


Mass: 142.116 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6N4O2
#3: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: CH2O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 126 / 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: 2.12 Å3/Da / Density % sol: 23.9 %
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, 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: 46071 / % possible obs: 66 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.072
Reflection shellResolution: 1.4→1.46 Å / Redundancy: 3.1 % / % possible all: 31.9
Reflection
*PLUS
Highest resolution: 1.26 Å / Num. measured all: 142009

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Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLORrefinement
bioteX(MSC)data reduction
X-PLORphasing
RefinementResolution: 1.4→7.5 Å / σ(F): 2.5
Details: THE FOLLOWING ATOMS HAD WEAK DENSITY AND OCCUPANCIES WERE REFINED: ALA B 13 GLU B 14 ALA B 15 GLU B 51 (CG, HG1, HG2, CD, OE1, OE2) ARG B 53 (NE, HE, CZ, NH1, HH11, HH12, NH2, HH21, HH22) ...Details: THE FOLLOWING ATOMS HAD WEAK DENSITY AND OCCUPANCIES WERE REFINED: ALA B 13 GLU B 14 ALA B 15 GLU B 51 (CG, HG1, HG2, CD, OE1, OE2) ARG B 53 (NE, HE, CZ, NH1, HH11, HH12, NH2, HH21, HH22) ARG B 84 (NE, HE, CZ, NH1, HH11, HH12, NH2, HH21, HH22) GLY B 99 ALA B 100 GLU B 101 (CB, HB1, HB2, CG, HG1, HG2, CD, OE1, OE2) ARG B 103 (NE, HE, CZ, NH1, HH11, HH12, NH2, HH21, HH22) GLU B 116 (CG, HG1, HG2, CD, OE1, OE2) PRO B 135 ALA D 13 GLU D 14 ALA D 15 (EXCEPT C AND O) ASP D 36 (CG, OD1, OD2) GLU D 51 (CA, HA, CB, HB1, HB2, CG, HG1, HG2, CD, OE1, OE2) ARG D 53 (NE, HE, CZ, NH1, HH11, HH12, NH2, HH21, HH22) ASN D 82 (CG, OD1, ND2, HD21, HD22) TYR D 83 ARG D 84 (NE, HE, CZ, NH1, HH11, HH12, NH2, HH21, HH22) GLU D 101 (CB, HB1, HB2, CG, HG1, HG2, CD, OE1, OE2) ARG D 103 (NE, HE, CZ, NH1, HH11, HH12, NH2, HH21, HH22) GLU D 116 (CG, HG1, HG2, CD, OE1, OE2) RESIDUES B 60-B 69 AND D 60-D 69 WERE REFINED IN 2 CONFORMATIONS BECAUSE UPON PROTONATION OF ASP 61 AT LOW PH, ASP B 61 AND ASP D 61 UNDERGO LARGE SHIFTS IN CONFORMATION AND CHANGES IN HYDROGEN BONDING. THE LOOPS COMPRISING RESIDUES B 61-B 69 AND D 61-D 69 ALSO UNDERGO CORRESPONDING CONFORMATIONAL CHANGES. HOWEVER SOME OF THESE RESIDUES ARE DISORDERED AND NOT VISIBLE IN EITHER CONFORMATION. TYR B 22 IS DISORDERED BETWEEN 2 CONFORMATIONS ONE OF WHICH OCCUPIES A SIMILAR REGION OF SPACE AS A 2-FOLD RELATED B 22. 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 B 22: HOH 1468, HOH 1508, AND HOH 1539. NO HYDROGENS ARE INCLUDED FOR THESE "WATERS".
RfactorNum. reflection% reflection
Rfree0.232 --
Rwork0.209 --
obs0.209 31128 66 %
Refinement stepCycle: LAST / Resolution: 1.4→7.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1819 0 28 126 1973
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.018
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_deg4.2
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.8
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: 31.9 %
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_deg24.8
LS refinement shell
*PLUS
Rfactor obs: 0.209

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