PDB-1vwc: STREPTAVIDIN-CYCLO-AC-[CHPQFC]-NH2, PH 2.0

Basic information

• Entry: Database: PDB / ID: 1vwc
• Title: STREPTAVIDIN-CYCLO-AC-[CHPQFC]-NH2, PH 2.0

Components

• PEPTIDE LIGAND CONTAINING HPQ
• STREPTAVIDIN

• Keywords: COMPLEX (BIOTIN-BINDING PROTEIN/PEPTIDE) / COMPLEX (BIOTIN-BINDING PROTEIN-PEPTIDE) / CYCLIC PEPTIDE DISCOVERED BY PHAGE DISPLAY / COMPLEX (BIOTIN-BINDING PROTEIN-PEPTIDE) complex

Function / homology

Function:

biotin binding / extracellular region

Domain/homology:

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

Component:

Streptavidin

• Biological species: Streptomyces avidinii (bacteria)
• Method: X-RAY DIFFRACTION / Resolution: 1.86 Å
• Authors: Katz, 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

Deposition	Mar 3, 1997	Processing site: BNL
Revision 1.0	Mar 18, 1998	Provider: repository / Type: Initial release
Revision 1.1	Mar 24, 2008	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Version format compliance

Assembly

Deposited unit

B: STREPTAVIDIN

P: PEPTIDE LIGAND CONTAINING HPQ

Summary:

• 13.7 kDa, 2 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	13,724	2
Polymers	13,724	2
Non-polymers	0	0
Water	1,171	65

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

Summary:

• defined by author
• 54.9 kDa, 8 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	54,896	8
Polymers	54,896	8
Non-polymers	0	0
Water	72	4

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1
crystal symmetry operation	15_555	y,x,-z	1
crystal symmetry operation	10_555	-x,-y,z	1
crystal symmetry operation	8_555	-y,-x,-z	1

Unit cell

Length a, b, c (Å)	59.210, 59.210, 175.910
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	98
Space group name H-M	I4122

Components

#1: Protein

B STREPTAVIDIN /

Details:

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

P PEPTIDE LIGAND CONTAINING HPQ

Details:

Mass: 758.911 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source

#3: Water

ChemComp-HOH / water / Water

Details:

Mass: 18.015 Da / Num. of mol.: 65 / Source method: isolated from a natural source / Formula: H₂O

Experimental details

Experiment

• Experiment: Method: X-RAY DIFFRACTION / Number of used crystals: 1

Sample preparation

• Crystal: Density Matthews: 2.81 ų/Da / Density % sol: 36 %
• Crystal grow: pH: 2 ; Details: SYNTHETIC MOTHER LIQUOR = 75 % SATURATED AMMONIUM SULFATE, 25 % 1.0 M SODIUM FORMATE ADJUSTED TO PH 2.0.
• Crystal grow: Temperature: 20 ℃ / pH: 4.5 / Method: vapor diffusion, hanging drop / Details: Pahler, A., (1987) J. Biol. Chem., 262, 13933.

Components of the solutions

ID	Conc.	Common name	Crystal-ID	Sol-ID	Chemical formula	Details
1	10-20 mg/ml	protein	1	drop
2	50 mM	potassium acetate	1	drop
3	200 mM		1	drop	NaCl	pH4.5
4	30 %sat	ammonium sulfate	1	reservoir
5	50 mM	potassium acetate	1	reservoir
6	200 mM		1	reservoir	NaCl

Data collection

• Diffraction: Mean temperature: 295 K
• Diffraction source: Wavelength: 1.5418
• Detector: Type: SIEMENS / Detector: AREA DETECTOR
• Radiation: Monochromatic (M) / Laue (L): M / Scattering type: x-ray
• Radiation wavelength: Wavelength: 1.5418 Å / Relative weight: 1
• Reflection: Num. obs: 12424 / Redundancy: 3.9 % / R_merge(I) obs: 0.053
• Reflection: Highest resolution: 1.79 Å / Num. measured all: 49532

Processing

Software

Name	Classification
SADIE	data collection
SAINT	data scaling
X-PLOR	model building
X-PLOR	refinement
SADIE	data reduction
SAINT	data reduction
X-PLOR	phasing

Refinement

Resolution: 1.86→7.5 Å / σ(F): 2
Details: THE FOLLOWING ATOMS HAD WEAK DENSITY AND OCCUPANCIES WERE REFINED: 13, 14, 15, SIDE CHAIN OF GLN 24, TERMINUS OF ASP 36, SIDE CHAIN OF 47, 48, 50, 51, TERMINUS OF ARG 53, 64, 65, 66, 67, 99, 100, SIDE CHAIN OF 101, TERMINUS OF ARG 103, TERMINUS OF GLU 116, TERMINUS OF LYS 121, (ACE P 0 AND CYS P 1), (CYS P 6 AND NH2 P 7). DISCRETELY DISORDERED SIDE CHAINS WHOSE OCCUPANCIES AND STRUCTURES WERE SIMULTANEOUSLY REFINED WERE 43, 84 (3 CONFORMATIONS), 107, 132. DISORDERED WATERS ARE HOH 207 WHICH IS CLOSE TO A SYMMETRY-RELATED EQUIVALENT OF HOH 354; HOH 244 WHICH IS CLOSE TO A SYMMETRY-RELATED EQUIVALENT OF HOH 298. HOH 305, HOH 313, AND HOH 467 ARE CLOSE TO SYMMETRY-RELATED EQUIVALENTS OF THEMSELVES, RESPECTIVELY. NO ENERGY INTERACTIONS INVOLVING HOH 305, HOH 313, OR HOH 467 WERE TURNED ON DURING REFINEMENT. THE FOLLOWING ATOMS HAD WEAK DENSITY AND OCCUPANCIES WERE REFINED: 13, 14, 15, SIDE CHAIN OF GLN 24, TERMINUS OF ASP 36, SIDE CHAIN OF 47, 48, 50, 51, TERMINUS OF ARG 53, 64, 65, 66, 67, 99, 100, SIDE CHAIN OF 101, TERMINUS OF ARG 103, TERMINUS OF GLU 116, TERMINUS OF LYS 121, (ACE P 0 AND CYS P 1), (CYS P 6 AND NH2 P 7).

	Rfactor	Num. reflection	% reflection
Rfree	0.209	-	10 %
Rwork	0.191	-	-
obs	0.191	10046	75 %

Refinement step

Cycle: LAST / Resolution: 1.86→7.5 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1052	0	0	65	1117

Refine LS restraints

Refine-ID	Type	Dev ideal
X-RAY DIFFRACTION	x_bond_d	0.019
X-RAY DIFFRACTION	x_bond_d_na
X-RAY DIFFRACTION	x_bond_d_prot
X-RAY DIFFRACTION	x_angle_d
X-RAY DIFFRACTION	x_angle_d_na
X-RAY DIFFRACTION	x_angle_d_prot
X-RAY DIFFRACTION	x_angle_deg	3
X-RAY DIFFRACTION	x_angle_deg_na
X-RAY DIFFRACTION	x_angle_deg_prot
X-RAY DIFFRACTION	x_dihedral_angle_d	28.5
X-RAY DIFFRACTION	x_dihedral_angle_d_na
X-RAY DIFFRACTION	x_dihedral_angle_d_prot
X-RAY DIFFRACTION	x_improper_angle_d
X-RAY DIFFRACTION	x_improper_angle_d_na
X-RAY DIFFRACTION	x_improper_angle_d_prot
X-RAY DIFFRACTION	x_mcbond_it
X-RAY DIFFRACTION	x_mcangle_it
X-RAY DIFFRACTION	x_scbond_it
X-RAY DIFFRACTION	x_scangle_it

• LS refinement shell: Resolution: 1.86→1.94 Å / % reflection obs: 28.9 %

Xplor file

Refine-ID	Serial no	Param file	Topol file
X-RAY DIFFRACTION	1	A16PH12_PARAM19XB2_KBCO.P	A16PH12_TOPH19XB2_KBCO.PRO
X-RAY DIFFRACTION	2	PARAM11_UCSF.WAT	TOPH19.PEP
X-RAY DIFFRACTION	3	PARAM19XB2_KBCO.PRO	TOPH19XB2_KBCO.PRO

• Software: Name: X-PLOR / Classification: refinement

Refine LS restraints

Refine-ID	Type	Dev ideal
X-RAY DIFFRACTION	x_dihedral_angle_d
X-RAY DIFFRACTION	x_dihedral_angle_deg	28.5