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- PDB-1vwh: STREPTAVIDIN COMPLEXED WITH THE HEAD-TO-TAIL DISULFIDE-BONDED PEP... -

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Basic information

Entry
Database: PDB / ID: 1vwh
TitleSTREPTAVIDIN COMPLEXED WITH THE HEAD-TO-TAIL DISULFIDE-BONDED PEPTIDE DIMER OF CYCLO-AC-[CHPQGPPC]-NH2, PH 3.5
Components
  • PEPTIDE LIGAND CONTAINING HPQ
  • STREPTAVIDIN
KeywordsCOMPLEX (BIOTIN-BINDING PROTEIN/PEPTIDE) / COMPLEX (BIOTIN-BINDING PROTEIN-PEPTIDE) / CYCLIC PEPTIDE DISCOVERED BY PHAGE DISPLAY / 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
Biological speciesStreptomyces avidinii (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 1.48 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 1.3Jun 5, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / software / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _software.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_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_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 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: STREPTAVIDIN
P: PEPTIDE LIGAND CONTAINING HPQ


Theoretical massNumber of molelcules
Total (without water)13,8282
Polymers13,8282
Non-polymers00
Water1,04558
1
B: STREPTAVIDIN
P: PEPTIDE LIGAND CONTAINING HPQ

B: STREPTAVIDIN
P: PEPTIDE LIGAND CONTAINING HPQ

B: STREPTAVIDIN
P: PEPTIDE LIGAND CONTAINING HPQ

B: STREPTAVIDIN
P: PEPTIDE LIGAND CONTAINING HPQ


Theoretical massNumber of molelcules
Total (without water)55,3128
Polymers55,3128
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation15_555y,x,-z1
crystal symmetry operation10_555-x,-y,z1
crystal symmetry operation8_555-y,-x,-z1
Unit cell
Length a, b, c (Å)58.180, 58.180, 174.950
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122

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Components

#1: Protein STREPTAVIDIN


Mass: 12965.025 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces avidinii (bacteria) / References: UniProt: P22629
#2: Protein/peptide PEPTIDE LIGAND CONTAINING HPQ


Mass: 863.018 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 58 / Source method: isolated from a natural source / Formula: H2O
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: 2.68 Å3/Da / Density % sol: 28.9 %
Crystal growpH: 3.5
Details: SYNTHETIC MOTHER LIQUOR = 75 % SATURATED AMMONIUM SULFATE, 25 % 1.0 M POTASSIUM ACETATE ADJUSTED TO PH 3.5.
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 formulaDetails
110-20 mg/mlprotein1drop
250 mMpotassium acetate1drop
3200 mM1dropNaClpH4.5
430 %satammonium sulfate1reservoir
550 mMpotassium acetate1reservoir
6200 mM1reservoirNaCl

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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: 26527 / Redundancy: 1.7 % / Rmerge(I) obs: 0.059
Reflection
*PLUS
Highest resolution: 1.33 Å / Num. measured all: 45610

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Processing

Software
NameVersionClassification
bioteX(FROM MSC)data collection
X-PLORmodel building
X-PLORrefinement
bioteX(MSC)data reduction
X-PLORphasing
RefinementResolution: 1.48→7.5 Å / σ(F): 1.9
Details: THE FOLLOWING ATOMS HAD WEAK DENSITY AND OCCUPANCIES WERE REFINED: 13, 14, 15, MAIN CHAIN OF GLN 24, SIDE CHAIN OF GLN 24, SIDE CHAIN OF LEU 25, GLY 26, MAIN CHAIN OF ALA 35, SIDE CHAIN OF ...Details: THE FOLLOWING ATOMS HAD WEAK DENSITY AND OCCUPANCIES WERE REFINED: 13, 14, 15, MAIN CHAIN OF GLN 24, SIDE CHAIN OF GLN 24, SIDE CHAIN OF LEU 25, GLY 26, MAIN CHAIN OF ALA 35, SIDE CHAIN OF ALA 35, (CB, HB1, HB2 OF ASP 36), (CG, OD1, AND OD2 OF ASP 36), ALA 46, VAL 47, GLY 48, ASN 49, ALA 50, SIDE CHAIN OF GLU 51, TERMINUS OF ARG 53, 100, (N AND HN OF 101), (CG, HG1, HG2, CD, OE1, OE2 OF GLU 101), TERMINUS OF ARG 103, (N, HN, CA, HA, CB, HB1, HB2, CG, HG1, HG2 OF GLN 116), (CD, OE1, OE2 OF GLN 116), ALA 117, (CG, HG1, HG2, CD, HD1, HD2 OF LYS 121), (CE, HE1, HE2, NZ, HZ1, HZ2, HZ3 OF LYS 121),(ACE P 0 AND CYS P 1), PRO P 7, (CYS P 8 AND NH2 P 9). 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. NO ENERGY INTERACTIONS INVOLVING HOH 255, HOH 305, AND HOH 445 WERE TURNED ON DURING REFINEMENT.
RfactorNum. reflection% reflection
Rfree0.239 -10 %
Rwork0.198 --
obs0.198 14708 57.9 %
Refinement stepCycle: LAST / Resolution: 1.48→7.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2248 0 0 58 2306
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_d26.2
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: 1.48→1.55 Å / % reflection obs: 27.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1CLEC35_PARMALLH3X.PROCLEC35_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_deg26.2

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