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- PDB-3vhm: Crystal structure of NPC-biotin-avidin complex -

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Basic information

Entry
Database: PDB / ID: 3vhm
TitleCrystal structure of NPC-biotin-avidin complex
ComponentsAvidin
KeywordsBIOTIN-BINDING PROTEIN / beta barrel
Function / homology
Function and homology information


biotin binding / antibacterial humoral response / 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 speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsTerai, T. / Maki, E. / Sugiyama, S. / Takahashi, Y. / Matsumura, H. / Mori, Y. / Nagano, T.
CitationJournal: Chem.Biol. / Year: 2011
Title: Rational development of caged-biotin protein-labeling agents and some applications in live cells
Authors: Terai, T. / Maki, E. / Sugiyama, S. / Takahashi, Y. / Matsumura, H. / Mori, Y. / Nagano, T.
History
DepositionAug 29, 2011Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 28, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Avidin
B: Avidin
C: Avidin
D: Avidin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,25318
Polymers54,8664
Non-polymers3,38714
Water3,639202
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12890 Å2
ΔGint-103 kcal/mol
Surface area19810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)131.020, 73.535, 81.180
Angle α, β, γ (deg.)90.000, 120.020, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-205-

HOH

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Components

#1: Protein
Avidin


Mass: 13716.431 Da / Num. of mol.: 4 / Fragment: UNP residues 25-147 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / References: UniProt: P02701
#2: Chemical
ChemComp-NPK / 5-[(3aS,4R,6aR)-1-{[(1R)-1-(6-nitro-1,3-benzodioxol-5-yl)ethoxy]carbonyl}-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]pentanoic acid


Mass: 481.476 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C20H23N3O9S
#3: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 202 / 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: 3.09 Å3/Da / Density % sol: 60.14 % / Mosaicity: 0.354 °
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 2.5-2.7M ammonium sulfate, 0.1M sodium citrate(pH 4.0-5.0), vapor diffusion, sitting drop, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Nov 18, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 44266 / % possible obs: 98.2 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.068 / Χ2: 1.086 / Net I/σ(I): 10.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2-2.034.40.42422111.022197.1
2.03-2.074.40.37821740.963197.5
2.07-2.114.40.30721601.065197.6
2.11-2.154.40.30221931.032197.4
2.15-2.24.40.27821831.019197.5
2.2-2.254.40.29922001.892197.6
2.25-2.314.40.24421781.069198.1
2.31-2.374.40.18122170.97198
2.37-2.444.40.16922051.028198.1
2.44-2.524.40.14822010.972198.1
2.52-2.614.40.11522040.977198.2
2.61-2.714.40.1122030.985198.4
2.71-2.844.40.08621880.988198.6
2.84-2.994.30.06622471.053198.7
2.99-3.174.30.05422261.08198.8
3.17-3.424.30.04522271.139199
3.42-3.764.30.03822501.201199.1
3.76-4.314.30.03422371.149199.1
4.31-5.434.30.02722701.058199.2
5.43-504.10.02622921.06198.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→37.52 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.932 / WRfactor Rfree: 0.2244 / WRfactor Rwork: 0.1835 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8462 / SU B: 3.57 / SU ML: 0.101 / SU R Cruickshank DPI: 0.159 / SU Rfree: 0.15 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.15 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2303 2228 5 %RANDOM
Rwork0.1885 ---
obs0.1907 44247 98.19 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 79.04 Å2 / Biso mean: 28.2242 Å2 / Biso min: 8.8 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2→37.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3821 0 218 202 4241
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0290.0224121
X-RAY DIFFRACTIONr_angle_refined_deg2.7091.9815602
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7225484
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.92323.846169
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.03915673
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.6571526
X-RAY DIFFRACTIONr_chiral_restr0.1940.2640
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.023038
X-RAY DIFFRACTIONr_mcbond_it1.5371.52412
X-RAY DIFFRACTIONr_mcangle_it2.65823921
X-RAY DIFFRACTIONr_scbond_it3.83531709
X-RAY DIFFRACTIONr_scangle_it5.8764.51681
LS refinement shellResolution: 2.003→2.055 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.252 144 -
Rwork0.213 3055 -
all-3199 -
obs--97 %

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