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- PDB-1vwl: STREPTAVIDIN-CYCLO-[5-S-VALERAMIDE-HPQGPPC]K-NH2, PH 3.5, I222 COMPLEX -

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Basic information

Entry
Database: PDB / ID: 1vwl
TitleSTREPTAVIDIN-CYCLO-[5-S-VALERAMIDE-HPQGPPC]K-NH2, PH 3.5, 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 / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
PENTANOIC ACID / Streptavidin
Similarity search - Component
Biological speciesStreptomyces avidinii (bacteria)
Bothrops insularis (golden lancehead)
MethodX-RAY DIFFRACTION / Resolution: 1.45 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, 1997-
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 1.3Nov 16, 2011Group: Atomic model

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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
Water3,333185
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
Unit cell
Length a, b, c (Å)94.810, 105.420, 47.910
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-516-

HOH

21B-519-

HOH

31B-852-

HOH

41B-1249-

HOH

51B-1249-

HOH

Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.99989, -0.01486, 0.002413), (-0.00924, 0.731886, 0.681364), (-0.01189, 0.681265, -0.73194)
Vector: 51.682, 0.2784, 0.4884)

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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 natural source / Source: (natural) Bothrops insularis (golden lancehead)
#3: Chemical ChemComp-LEA / PENTANOIC ACID / VALERIC ACID / Valeric acid


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


Mass: 18.015 Da / Num. of mol.: 185 / Source method: isolated from a natural source / Formula: H2O
Compound detailsDISULFIDE BOND OF PHAGE-DISCOVERED PEPTIDE IS REPLACED WITH THIOETHER.

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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: 2.16 Å3/Da / Density % sol: 18.1 %
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 ℃ / Method: vapor diffusion, hanging drop / Details: Pahler, A., (1987) J. Biol. Chem., 262, 13933. / pH: 4
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 / Detector: IMAGE PLATE
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNum. obs: 42836 / Redundancy: 1.9 % / Rmerge(I) obs: 0.07
Reflection
*PLUS
Highest resolution: 1.32 Å / Num. measured all: 79817 / Rmerge(I) obs: 0.07

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Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLORrefinement
BIOTEX(MSC)data reduction
X-PLORphasing
RefinementResolution: 1.45→7.5 Å / σ(F): 1.7
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), (TERMINUS OF ARG B 84) ...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), (TERMINUS OF ARG B 84), (SIDE CHAIN OF GLU B 101), (TERMINUS OF ARG B 103), (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), (TERMINUS OF ARG D 84), (TERMINUS OF ARG D 103), (M 9 AND M 10), (P 9 AND P 10). DISCRETELY DISORDERED ENTIRE RESIDUES WHOSE OCCUPANCIES AND STRUCTURES WERE SIMULTANEOUSLY REFINED ARE: B 60, B 61, B 62, B 63, B 64, B 65, B 66, B 67, B 68, B 69, D 61, D 62, D 63, D 64, D 65, D 66, D 67, D 68, D 69, (ACE P 0 AND CYS P 1), (CYS P 6 AND NH2 P 7). 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. DISCRETELY DISORDERED SIDE CHAINS WHOSE OCCUPANCIES AND STRUCTURES WERE SIMULTANEOUSLY REFINED WERE B 29, B 40, B 42, B 73, B 110, D 32, D 87, D 107, D 110. 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 516, HOH 519, HOH 1249. DISORDERED WATERS ARE HOH 852 AND HOH 1414 WHICH ARE CLOSE TO SYMMETRY-RELATED EQUIVALENTS OF THEMSELVES, RESPECTIVELY; HOH 1284 WHICH IS CLOSE TO A SYMMETRY-RELATED EQUIVALENT OF ITSELF AND OCCUPIES THE SPACE AVAILABLE WHEN ASN D 107 IS IN ONE OF ITS DISCRETE CONFORMATIONS. HOH 624 WHICH IS CLOSE TO HOH 1182; HOH 504 WHICH IS CLOSE TO HOH 1403; HOH 505 WHICH IS CLOSE TO HOH 1390; HOH 727 WHICH IS CLOSE TO A SYMMETRY-RELATED EQUIVALENT OF HOH 1365; HOH 1180 WHICH IS CLOSE TO A SYMMETRY-RELATED EQUIVALENT OF HOH 1414; HOH 1139 THAT OCCUPIES THE REGION OF SPACE AVAILABLE WHEN ASP B 61 IS IN CONFORMATION NO. 2; HOH 1167 THAT OCCUPIES THE REGION OF SPACE AVAILABLE WHEN ASP D 61 IS IN CONFORMATION NO. 2; HOH 1358 WHICH MAKES A H-BOND WITH OG2 OF THR D 32 IN CONFORMATION 1; HOH 513 WHICH IS CLOSE TO MAIN CHAIN CARBONYL OF B 49; HOH 514 WHICH IS CLOSE TO CA OF B 51; HOH 1251 WHICH IS CLOSE TO O OF B 51; HOH 1209 WHICH IS CLOSE TO CA OF B 48; HOH 1375 WHICH IS CLOSE TO O OF D 51. IN REFINEMENT THERE WERE NO ENERGY INTERACTIONS INVOLVING HOH 513, HOH 514, HOH 516, HOH 519, HOH 852, HOH 1249, HOH 1251, HOH 1375, HOH 1284, HOH 1414. DISULFIDE BOND OF PHAGE-DISCOVERED PEPTIDE IS REPLACED WITH THIOETHER. 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), (TERMINUS OF ARG B 84), (SIDE CHAIN OF GLU B 101), (TERMINUS OF ARG B 103), (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), (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 516, HOH 519, HOH 1249.
RfactorNum. reflection% reflection
Rfree0.244 -10 %
Rwork0.2 --
obs0.2 27282 64 %
Refinement stepCycle: LAST / Resolution: 1.45→7.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4100 0 28 555 4683
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_d25.3
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: 1.45→1.52 Å / % reflection obs: 32.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1I2VAL305_PARMALLH3X.PROI2VAL35_TOPALLH6X_BAK.PRO
X-RAY DIFFRACTION2PARAM11_UCSF.WATTOPH19.PEP
X-RAY DIFFRACTION3PARAM19XB2_KBCO.PROTOPH19XB2_KBCO.PRO
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.2 / Rfactor Rwork: 0.2
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25.3

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