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- PDB-5n7x: CRYSTAL STRUCTURE OF STREPTAVIDIN WITH PEPTIDE EWVHPQFEQKAK -

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Basic information

Entry
Database: PDB / ID: 5n7x
TitleCRYSTAL STRUCTURE OF STREPTAVIDIN WITH PEPTIDE EWVHPQFEQKAK
Components
  • GLU-TRP-VAL-HIS-PRO-GLN-PHE-GLU-GLN-LYS-ALA-LYS Peptide
  • Streptavidin
KeywordsBIOTIN BINDING PROTEIN / STREPTAVIDIN / HPQ MOTIF / STREPTAVIDIN PEPTIDE 11101 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
Biological speciesStreptomyces avidinii (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.12 Å
AuthorsLyamichev, V. / Goodrich, L. / Sullivan, E. / Bannen, R. / Benz, J. / Albert, T. / Patel, J.
CitationJournal: Sci Rep / Year: 2017
Title: Stepwise Evolution Improves Identification of Diverse Peptides Binding to a Protein Target.
Authors: Lyamichev, V.I. / Goodrich, L.E. / Sullivan, E.H. / Bannen, R.M. / Benz, J. / Albert, T.J. / Patel, J.J.
History
DepositionFeb 21, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 4, 2017Provider: repository / Type: Initial release
Revision 1.1May 8, 2024Group: Advisory / Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Streptavidin
B: Streptavidin
C: GLU-TRP-VAL-HIS-PRO-GLN-PHE-GLU-GLN-LYS-ALA-LYS Peptide
D: GLU-TRP-VAL-HIS-PRO-GLN-PHE-GLU-GLN-LYS-ALA-LYS Peptide
E: Streptavidin
F: Streptavidin
G: GLU-TRP-VAL-HIS-PRO-GLN-PHE-GLU-GLN-LYS-ALA-LYS Peptide
H: Streptavidin
I: GLU-TRP-VAL-HIS-PRO-GLN-PHE-GLU-GLN-LYS-ALA-LYS Peptide
J: GLU-TRP-VAL-HIS-PRO-GLN-PHE-GLU-GLN-LYS-ALA-LYS Peptide
K: Streptavidin
L: GLU-TRP-VAL-HIS-PRO-GLN-PHE-GLU-GLN-LYS-ALA-LYS Peptide
M: Streptavidin
N: GLU-TRP-VAL-HIS-PRO-GLN-PHE-GLU-GLN-LYS-ALA-LYS Peptide
O: Streptavidin
P: GLU-TRP-VAL-HIS-PRO-GLN-PHE-GLU-GLN-LYS-ALA-LYS Peptide


Theoretical massNumber of molelcules
Total (without water)163,03516
Polymers163,03516
Non-polymers00
Water22,8791270
1
A: Streptavidin
D: GLU-TRP-VAL-HIS-PRO-GLN-PHE-GLU-GLN-LYS-ALA-LYS Peptide
K: Streptavidin
L: GLU-TRP-VAL-HIS-PRO-GLN-PHE-GLU-GLN-LYS-ALA-LYS Peptide


Theoretical massNumber of molelcules
Total (without water)40,7594
Polymers40,7594
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3410 Å2
ΔGint-18 kcal/mol
Surface area14370 Å2
MethodPISA
2
B: Streptavidin
C: GLU-TRP-VAL-HIS-PRO-GLN-PHE-GLU-GLN-LYS-ALA-LYS Peptide
M: Streptavidin
N: GLU-TRP-VAL-HIS-PRO-GLN-PHE-GLU-GLN-LYS-ALA-LYS Peptide


Theoretical massNumber of molelcules
Total (without water)40,7594
Polymers40,7594
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3400 Å2
ΔGint-18 kcal/mol
Surface area14500 Å2
MethodPISA
3
E: Streptavidin
I: GLU-TRP-VAL-HIS-PRO-GLN-PHE-GLU-GLN-LYS-ALA-LYS Peptide
O: Streptavidin
P: GLU-TRP-VAL-HIS-PRO-GLN-PHE-GLU-GLN-LYS-ALA-LYS Peptide


Theoretical massNumber of molelcules
Total (without water)40,7594
Polymers40,7594
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3490 Å2
ΔGint-18 kcal/mol
Surface area14270 Å2
MethodPISA
4
F: Streptavidin
G: GLU-TRP-VAL-HIS-PRO-GLN-PHE-GLU-GLN-LYS-ALA-LYS Peptide
H: Streptavidin
J: GLU-TRP-VAL-HIS-PRO-GLN-PHE-GLU-GLN-LYS-ALA-LYS Peptide


Theoretical massNumber of molelcules
Total (without water)40,7594
Polymers40,7594
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3490 Å2
ΔGint-17 kcal/mol
Surface area14270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.913, 64.806, 81.156
Angle α, β, γ (deg.)96.31, 97.15, 84.09
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Streptavidin /


Mass: 18849.672 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces avidinii (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P22629
#2: Protein/peptide
GLU-TRP-VAL-HIS-PRO-GLN-PHE-GLU-GLN-LYS-ALA-LYS Peptide


Mass: 1529.714 Da / Num. of mol.: 8 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1270 / Source method: isolated from a natural source / Formula: H2O

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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: 1.83 Å3/Da / Density % sol: 32.97 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1M Magnesium acetate 0.1M Sodium cacodylate pH 6.5 15% PEG6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9999 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 1, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 1.12→80.13 Å / Num. obs: 403025 / % possible obs: 90.4 % / Redundancy: 1.66 % / CC1/2: 0.99 / Rmerge(I) obs: 0.031 / Net I/σ(I): 10.03
Reflection shellResolution: 1.12→1.22 Å / Redundancy: 1.58 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 0.94 / Num. unique obs: 86936 / CC1/2: 0.37 / % possible all: 86.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
SADABSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.12→80.13 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.97 / SU B: 1.63 / SU ML: 0.031 / Cross valid method: THROUGHOUT / ESU R: 0.034 / ESU R Free: 0.035 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18554 20178 5 %RANDOM
Rwork0.16023 ---
obs0.16149 382815 90.36 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 18.773 Å2
Baniso -1Baniso -2Baniso -3
1--0.25 Å2-1 Å2-0.24 Å2
2---0.16 Å20.95 Å2
3---0.08 Å2
Refinement stepCycle: 1 / Resolution: 1.12→80.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8074 0 0 1270 9344
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.028640
X-RAY DIFFRACTIONr_bond_other_d0.0020.027367
X-RAY DIFFRACTIONr_angle_refined_deg1.581.8911914
X-RAY DIFFRACTIONr_angle_other_deg0.937317118
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.67151162
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.55424.072388
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.586151207
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9871535
X-RAY DIFFRACTIONr_chiral_restr0.1130.21308
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0210031
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021952
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.7431.2884352
X-RAY DIFFRACTIONr_mcbond_other1.7421.2874351
X-RAY DIFFRACTIONr_mcangle_it2.2041.9255442
X-RAY DIFFRACTIONr_mcangle_other2.2041.9265443
X-RAY DIFFRACTIONr_scbond_it2.1711.5074288
X-RAY DIFFRACTIONr_scbond_other2.1711.5084289
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.5762.1636413
X-RAY DIFFRACTIONr_long_range_B_refined3.40525.68537294
X-RAY DIFFRACTIONr_long_range_B_other2.78324.19735839
X-RAY DIFFRACTIONr_rigid_bond_restr2.438316007
X-RAY DIFFRACTIONr_sphericity_free32.3275182
X-RAY DIFFRACTIONr_sphericity_bonded11.585516813
LS refinement shellResolution: 1.12→1.149 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.365 1396 -
Rwork0.341 26734 -
obs--85.35 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.2239-0.0809-0.08170.0990.01940.1946-0.0254-0.0047-0.02940.01290.00710.0059-0.0075-0.03260.01830.04240.02620.00030.0294-0.01680.0274-87.1658-112.8953-16.8744
20.1442-0.0502-0.04220.19560.00720.095-0.0125-0.05840.00240.01470.0078-0.00640.01940.0260.00470.04470.02810.00090.0498-0.01840.0289-102.9053-95.295123.9778
30.2872-0.2528-0.38110.47660.44830.5578-0.013-0.08510.05570.05140.0918-0.08240.03530.1114-0.07890.03420.0281-0.00890.0704-0.04970.0487-89.6246-87.627520.7389
40.7342-0.49570.13640.3357-0.13662.3899-0.0269-0.0013-0.09240.01970.00960.06020.0085-0.30130.01730.02360.01510.00360.0685-0.03020.0505-98.8298-119.0864-24.8822
50.1938-0.0459-0.08440.13850.02290.1709-0.0348-0.0222-0.04230.02860.02-0.00040.0260.0190.01470.04810.02990.00110.0251-0.0120.0358-73.4044-122.5023-15.0749
60.2132-0.0838-0.10370.14660.02350.139-0.0107-0.05990.020.01110.01350.00610.00970.0086-0.00280.04020.0228-0.00010.0459-0.0260.0312-116.9609-86.021723.9035
70.1479-0.18190.28670.2891-0.11171.4515-0.0078-0.0238-0.03120.01570.0030.05630.0289-0.13150.00480.03280.01560.00270.0409-0.02440.039-129.1112-92.03616.4757
80.2317-0.0848-0.08730.11030.02990.20030.01170.0110.015-0.0198-0.0134-0.00240.0219-0.00060.00170.04260.0262-0.00080.0266-0.01610.0259-104.4843-94.6178-4.061
90.082-0.3313-0.01081.5237-0.19420.3084-0.024-0.01520.03320.06410.016-0.14880.03760.05960.0080.0370.0302-0.00980.0373-0.02190.0442-59.9523-115.6071-18.0405
100.2067-0.08710.30540.8420.1470.79410.03010.0271-0.04710.0185-0.01060.02930.1002-0.0201-0.01950.06270.016-0.00210.0311-0.02530.0346-113.9395-106.155-0.8776
110.2726-0.0788-0.14080.11260.07660.2165-0.01740.0517-0.0432-0.0025-0.00940.00190.0184-0.02240.02680.03270.01810.00110.0401-0.03080.0362-72.6449-124.0174-43.0595
120.03030.03630.21820.5505-0.11422.43270.0070.008-0.0243-0.0287-0.0174-0.01410.1977-0.12890.01040.0612-0.01280.02430.0809-0.07640.0883-83.0968-135.0455-39.8641
130.1767-0.0626-0.09980.09710.06220.13820.03030.01050.0506-0.0265-0.0153-0.0084-0.0307-0.0209-0.01490.04370.02790.0040.0248-0.01280.0406-110.6097-79.0894-2.3829
140.5249-0.25660.3810.2061-0.05451.20730.0324-0.00770.1647-0.02210.0094-0.0688-0.12080.0286-0.04180.05650.01740.0260.0196-0.02150.1089-101.7653-68.91195.4093
150.1696-0.0575-0.10140.10480.08670.14850.01810.06040.0027-0.0229-0.018-0.0035-0.0318-0.0427-0.00010.03860.0285-0.00160.0466-0.01640.0254-78.4967-108.1172-42.9784
160.3905-0.2693-0.21970.20160.26931.04950.0457-0.00090.0732-0.03630.0089-0.0541-0.12150.0074-0.05460.0560.02590.01130.026-0.01410.0395-69.9435-97.7142-35.3612
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A14 - 135
2X-RAY DIFFRACTION2B14 - 134
3X-RAY DIFFRACTION3C1 - 11
4X-RAY DIFFRACTION4D1 - 11
5X-RAY DIFFRACTION5E14 - 135
6X-RAY DIFFRACTION6F14 - 135
7X-RAY DIFFRACTION7G1 - 11
8X-RAY DIFFRACTION8H14 - 135
9X-RAY DIFFRACTION9I1 - 11
10X-RAY DIFFRACTION10J1 - 11
11X-RAY DIFFRACTION11K14 - 135
12X-RAY DIFFRACTION12L1 - 11
13X-RAY DIFFRACTION13M14 - 134
14X-RAY DIFFRACTION14N1 - 11
15X-RAY DIFFRACTION15O14 - 135
16X-RAY DIFFRACTION16P1 - 11

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