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- PDB-4cpf: Wild-type streptavidin in complex with love-hate ligand 3 (LH3) -

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Basic information

Entry
Database: PDB / ID: 4cpf
TitleWild-type streptavidin in complex with love-hate ligand 3 (LH3)
ComponentsSTREPTAVIDIN
KeywordsBIOTIN-BINDING PROTEIN / AVIDIN / BIOTIN / BIOTINYLATED / STERIC CLASH / STRAINED / HINDERED / FORCE / LIGAND SERIES / AFFINITY
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
Chem-LH3 / Streptavidin
Similarity search - Component
Biological speciesSTREPTOMYCES AVIDINII (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.14 Å
AuthorsFairhead, M. / Shen, D. / Chan, L.K.M. / Lowe, E.D. / Donohoe, T.J. / Howarth, M.
CitationJournal: Bioorg.Med.Chem. / Year: 2014
Title: Love-Hate Ligands for High Resolution Analysis of Strain in Ultra-Stable Protein/Small Molecule Interaction.
Authors: Fairhead, M. / Shen, D. / Chan, L.K.M. / Lowe, E.D. / Donohoe, T.J. / Howarth, M.
History
DepositionFeb 6, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 6, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 27, 2014Group: Database references
Revision 1.2Oct 1, 2014Group: Database references
Revision 1.3May 8, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.4Dec 20, 2023Group: 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 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: STREPTAVIDIN
B: STREPTAVIDIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,1653
Polymers26,5632
Non-polymers6031
Water4,071226
1
A: STREPTAVIDIN
B: STREPTAVIDIN
hetero molecules

A: STREPTAVIDIN
B: STREPTAVIDIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,3316
Polymers53,1254
Non-polymers1,2052
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z1
Buried area8780 Å2
ΔGint-54.5 kcal/mol
Surface area19310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.080, 94.120, 104.790
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
11A-22-

TYR

21A-2093-

HOH

31B-2096-

HOH

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Components

#1: Protein STREPTAVIDIN


Mass: 13281.336 Da / Num. of mol.: 2 / Fragment: RESIDUES 37-163
Source method: isolated from a genetically manipulated source
Details: WILD-TYPE CORE STREPTAVIDIN / Source: (gene. exp.) STREPTOMYCES AVIDINII (bacteria) / Plasmid: PET21 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): RIPL / References: UniProt: P22629
#2: Chemical ChemComp-LH3 / methyl 4-(2-{5-[(3aS,4S,6aR)-2-oxo-hexahydro-1H- thieno[3,4-d]imidazolidin-4-yl]pentanehydrazido}-3- [4-(methoxycarbonyl)phenyl]phenyl)benzoate


Mass: 602.701 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C32H34N4O6S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 226 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsMETHYL 4-(2-{5-[(3AS,4S,6AR)-2-OXO-HEXAHYDRO-1H- THIENO[3, 4-D]IMIDAZOLIDIN-4-YL]PENTANEHYDRAZIDO}- ...METHYL 4-(2-{5-[(3AS,4S,6AR)-2-OXO-HEXAHYDRO-1H- THIENO[3, 4-D]IMIDAZOLIDIN-4-YL]PENTANEHYDRAZIDO}-3- [4-(METHOXYCARBONYL)PHENYL]PHENYL)BENZOATE (LH3): LOVE-HATE LIGAND 3
Sequence detailsN-TERMINAL METHIONINE REMOVED IN MATURE PROTEIN

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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: 2.2 Å3/Da / Density % sol: 45 % / Description: NONE
Crystal growMethod: vapor diffusion, sitting drop / pH: 4.5
Details: 75% SATURATED AMMONIUM SULPHATE, 25% 1M SODIUM ACETATE PH4.5. SITTING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.98
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 13, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.14→32.75 Å / Num. obs: 79019 / % possible obs: 93 % / Observed criterion σ(I): 0 / Redundancy: 6.1 % / Biso Wilson estimate: 11.68 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 18.8
Reflection shellResolution: 1.14→1.18 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 2.83 / % possible all: 65

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
xia2data reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3RY1

3ry1


Resolution: 1.14→32.748 Å / SU ML: 0.07 / σ(F): 1.34 / Phase error: 14.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1646 3970 5 %
Rwork0.1388 --
obs0.1401 79019 92.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19 Å2
Refinement stepCycle: LAST / Resolution: 1.14→32.748 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1785 0 43 226 2054
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012067
X-RAY DIFFRACTIONf_angle_d1.3932859
X-RAY DIFFRACTIONf_dihedral_angle_d11.619708
X-RAY DIFFRACTIONf_chiral_restr0.09312
X-RAY DIFFRACTIONf_plane_restr0.007394
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.14-1.15390.2232750.19381682X-RAY DIFFRACTION58
1.1539-1.16850.21041060.18011864X-RAY DIFFRACTION66
1.1685-1.18390.2079860.16492112X-RAY DIFFRACTION73
1.1839-1.20010.16871230.16352259X-RAY DIFFRACTION79
1.2001-1.21730.19791420.16052410X-RAY DIFFRACTION85
1.2173-1.23550.20341350.14932568X-RAY DIFFRACTION90
1.2355-1.25480.17271450.14762711X-RAY DIFFRACTION96
1.2548-1.27530.16381660.13922825X-RAY DIFFRACTION99
1.2753-1.29730.17881360.12672849X-RAY DIFFRACTION100
1.2973-1.32090.15421620.12322871X-RAY DIFFRACTION100
1.3209-1.34630.13981400.1192887X-RAY DIFFRACTION100
1.3463-1.37380.14971270.11732862X-RAY DIFFRACTION100
1.3738-1.40370.15371690.11512855X-RAY DIFFRACTION100
1.4037-1.43630.13551540.11712851X-RAY DIFFRACTION100
1.4363-1.47230.16431050.1122914X-RAY DIFFRACTION100
1.4723-1.51210.13211780.10942853X-RAY DIFFRACTION100
1.5121-1.55660.15371640.10842831X-RAY DIFFRACTION100
1.5566-1.60680.13571530.11182872X-RAY DIFFRACTION100
1.6068-1.66420.14081600.11142877X-RAY DIFFRACTION100
1.6642-1.73080.13861550.11642879X-RAY DIFFRACTION100
1.7308-1.80960.14061560.11432894X-RAY DIFFRACTION100
1.8096-1.9050.12551640.11832865X-RAY DIFFRACTION100
1.905-2.02430.14521440.11692885X-RAY DIFFRACTION100
2.0243-2.18060.14551530.11782920X-RAY DIFFRACTION100
2.1806-2.40.14771520.13172904X-RAY DIFFRACTION100
2.4-2.74710.1631520.14782933X-RAY DIFFRACTION100
2.7471-3.46050.17581480.15492846X-RAY DIFFRACTION96
3.4605-32.7610.26081200.22791964X-RAY DIFFRACTION64

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