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- PDB-1vwi: STREPTAVIDIN-CYCLO-[5-S-VALERAMIDE-HPQGPPC]K-NH2, PH 1.5, I222 COMPLEX -

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Basic information

Entry
Database: PDB / ID: 1vwi
TitleSTREPTAVIDIN-CYCLO-[5-S-VALERAMIDE-HPQGPPC]K-NH2, PH 1.5, I222 COMPLEX
Components
  • PEPTIDE LIGAND CONTAINING HPQ
  • STREPTAVIDIN
KeywordsCOMPLEX (BIOTIN-BINDING PROTEIN/PEPTIDE) / COMPLEX (BIOTIN-BINDING PROTEIN-PEPTIDE) / LINEAR THIOETHER-CONTAINING PEPTIDE ENGINEERED / COMPLEX (BIOTIN-BINDING PROTEIN-PEPTIDE) complex
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
PENTANOIC ACID / Streptavidin
Similarity search - Component
Biological speciesStreptomyces avidinii (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 1.5 Å
AuthorsKatz, B.A. / Cass, R.T.
Citation
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.
#1: 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.
#2: Journal: J.Am.Chem.Soc. / Year: 1996
Title: Preparation of a Protein-Dimerizing Ligand by Topochemistry and Structure-Based Design
Authors: Katz, B.A.
#3: 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.
#4: 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.
#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 Cyclic Peptide Ligands Containing Thioether Cross-Links
Authors: Katz, B.A. / Johnson, C.R. / Cass, R.T.
History
DepositionMar 3, 1997Processing site: BNL
Revision 1.0Mar 18, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 27, 2011Group: Atomic model / Derived calculations
Revision 2.0Jun 5, 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_conn / 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_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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.ptnr1_label_seq_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_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.1Oct 30, 2024Group: Advisory / Structure summary
Category: pdbx_entry_details / pdbx_modification_feature ...pdbx_entry_details / pdbx_modification_feature / pdbx_validate_close_contact / pdbx_validate_symm_contact
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: STREPTAVIDIN
D: STREPTAVIDIN
M: PEPTIDE LIGAND CONTAINING HPQ
P: PEPTIDE LIGAND CONTAINING HPQ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8606
Polymers27,6564
Non-polymers2042
Water2,630146
1
B: STREPTAVIDIN
D: STREPTAVIDIN
M: PEPTIDE LIGAND CONTAINING HPQ
P: PEPTIDE LIGAND CONTAINING HPQ
hetero molecules

B: STREPTAVIDIN
D: STREPTAVIDIN
M: PEPTIDE LIGAND CONTAINING HPQ
P: PEPTIDE LIGAND CONTAINING HPQ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,72112
Polymers55,3128
Non-polymers4094
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area13800 Å2
ΔGint-76 kcal/mol
Surface area21830 Å2
MethodPISA
2
B: STREPTAVIDIN
D: STREPTAVIDIN
M: PEPTIDE LIGAND CONTAINING HPQ
P: PEPTIDE LIGAND CONTAINING HPQ
hetero molecules

B: STREPTAVIDIN
D: STREPTAVIDIN
M: PEPTIDE LIGAND CONTAINING HPQ
P: PEPTIDE LIGAND CONTAINING HPQ
hetero molecules

B: STREPTAVIDIN
D: STREPTAVIDIN
M: PEPTIDE LIGAND CONTAINING HPQ
P: PEPTIDE LIGAND CONTAINING HPQ
hetero molecules

B: STREPTAVIDIN
D: STREPTAVIDIN
M: PEPTIDE LIGAND CONTAINING HPQ
P: PEPTIDE LIGAND CONTAINING HPQ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,44124
Polymers110,62416
Non-polymers8178
Water28816
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
Buried area31000 Å2
ΔGint-178 kcal/mol
Surface area40270 Å2
MethodPISA
3
B: STREPTAVIDIN
D: STREPTAVIDIN
M: PEPTIDE LIGAND CONTAINING HPQ
P: PEPTIDE LIGAND CONTAINING HPQ
hetero molecules

B: STREPTAVIDIN
D: STREPTAVIDIN
M: PEPTIDE LIGAND CONTAINING HPQ
P: PEPTIDE LIGAND CONTAINING HPQ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,72112
Polymers55,3128
Non-polymers4094
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z1
MethodPQS
Unit cell
Length a, b, c (Å)94.840, 105.570, 47.980
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-519-

HOH

21B-852-

HOH

31B-1239-

HOH

41B-1284-

HOH

Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.99997, -0.005, 0.005996), (0.000427, 0.731744, 0.681579), (-0.007796, 0.681561, -0.73172)
Vector: 51.5276, 0.0266, 0.3927)

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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: Protein/peptide PEPTIDE LIGAND CONTAINING HPQ


Mass: 863.017 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
#3: Chemical ChemComp-LEA / PENTANOIC ACID / VALERIC ACID


Mass: 102.132 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H10O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 146 / Source method: isolated from a natural source / Formula: H2O
Compound detailsDISULFIDE BOND OF PHAGE-DISCOVERED PEPTIDE IS REPLACED WITH THIOETHER.
Has protein modificationY

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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: 2.17 Å3/Da / Density % sol: 18.7 %
Crystal growpH: 1.5
Details: SYNTHETIC MOTHER LIQUOR = 75 % SATURATED AMMONIUM SULFATE, 25 % 1.0 M SODIUM FORMATE ADJUSTED TO PH 1.5.
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-IDDetails
130-32 %satammonium salfate1reservoir
20.1 Mpotassium acetate1reservoirpH4.0
315 mg/mlprotein1drop
415-16 %satammonium salfate1drop
50.05 Mpotassium acetate1drop

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Data collection

DiffractionMean temperature: 293 K
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: 41504 / Redundancy: 2.2 % / Rmerge(I) obs: 0.056
Reflection
*PLUS
Highest resolution: 1.32 Å / Num. measured all: 89532

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Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLORrefinement
bioteX(MSC)data reduction
X-PLORphasing
RefinementResolution: 1.5→7.5 Å / σ(F): 1.8
Details: THE FOLLOWING ATOMS HAD WEAK DENSITY AND OCCUPANCIES WERE REFINED: B 13, B 14, B 15, B 22, B 46, B 47, B 48, B 49, B 50, (TERMINUS OF ARG B 53), (TERMINUS OF ARG B 59), B 62, B 63, B 64, B ...Details: THE FOLLOWING ATOMS HAD WEAK DENSITY AND OCCUPANCIES WERE REFINED: B 13, B 14, B 15, B 22, B 46, B 47, B 48, B 49, B 50, (TERMINUS OF ARG B 53), (TERMINUS OF ARG B 59), B 62, B 63, B 64, B 65, B 66, B 67, B 68, (TERMINUS OF ARG B 84), (SIDE CHAIN OF GLU B 101), TERMINUS OF ARG B 103, (CB, HB1, HB2 OF GLU B 116), (CG, HG1, HG2, CD, OE1, OE2 OF GLU B 116), B 135, D 13, D 14, D 15, D 46, D 47, D 48, D 49, D 50, (TERMINUS OF ARG D 53), (TERMINUS OF ARG D 59), D 62, D 63, D 64, D 65, D 66, D 67, D 68, (TERMINUS OF ARG D 84), (TERMINUS OF ARG D 103), (M 9 AND M 10), (P 9 AND P 10). B 22 IS DISORDERED BETWEEN 2 CONFORMATIONS ONE OF WHICH OCCUPIES A SIMILAR REGION OF SPACE AS A TWO-FOLD RELATED B 22. 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 B 22: HOH 519, HOH 1239.
RfactorNum. reflection% reflection
Rfree0.235 -10 %
Rwork0.202 --
obs0.202 25381 65.7 %
Refinement stepCycle: LAST / Resolution: 1.5→7.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1939 0 12 146 2097
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_d24.9
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: 1.5→1.57 Å / % reflection obs: 34.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1I2VAL15_PARMALLH3X.PROI2VAL15_TOPALLH6X_BAK.PRO
X-RAY DIFFRACTION2PARAM11_UCSF.WATTOPH19.PEP
X-RAY DIFFRACTION3PARAM19XB2_KBCO.PROTOPH19XB2_KBCO.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_deg24.9

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