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- PDB-5chk: Crystal structure of avidin - HABA complex (hexagonal crystal form) -

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Basic information

Entry
Database: PDB / ID: 5chk
TitleCrystal structure of avidin - HABA complex (hexagonal crystal form)
ComponentsAvidin
KeywordsGLYCOPROTEIN / complex
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 ...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 / Resolution: 2.2 Å
AuthorsStrzelczyk, P. / Bujacz, A. / Bujacz, G.
Funding support Poland, 1items
OrganizationGrant numberCountry
National Science CentreDEC-2013/11/N/ST5/01296 Poland
CitationJournal: J.Mol.Struct. / Year: 2016
Title: Crystal structure and ligand affinity of avidin in the complex with 4-hydroxyazobenzene-2-carboxylic acid
Authors: Strzelczyk, P. / Bujacz, G.
History
DepositionJul 10, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Mar 23, 2016Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _atom_site.occupancy / _chem_comp.name ..._atom_site.occupancy / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Avidin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,8143
Polymers14,3501
Non-polymers4632
Water91951
1
A: Avidin
hetero molecules

A: Avidin
hetero molecules

A: Avidin
hetero molecules

A: Avidin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,25412
Polymers57,4004
Non-polymers1,8548
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555-x,-y,z1
crystal symmetry operation7_555y,x,-z+1/31
crystal symmetry operation10_555-y,-x,-z+1/31
Buried area10460 Å2
ΔGint-39 kcal/mol
Surface area21900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.310, 61.310, 120.530
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422
Components on special symmetry positions
IDModelComponents
11A-321-

HOH

21A-336-

HOH

31A-342-

HOH

41A-346-

HOH

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Components

#1: Protein Avidin


Mass: 14350.081 Da / Num. of mol.: 1 / Fragment: UNP residues 25-152 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / References: UniProt: P02701
#2: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
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
#3: Chemical ChemComp-55R / 2-[2-(4-oxocyclohexa-2,5-dien-1-ylidene)hydrazinyl]benzoic acid


Mass: 242.230 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C13H10N2O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 51 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.28 Å3/Da / Density % sol: 46.02 %
Crystal growTemperature: 292.15 K / Method: vapor diffusion
Details: 0.1M sodium citrate tribasic dehydrate pH 4.5, 24% w/v polyethylene glycol 1000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.977609 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 30, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.977609 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 7329 / % possible obs: 100 % / Redundancy: 5.1 % / Net I/σ(I): 31.92

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1VYO

1vyo


Resolution: 2.2→40.18 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.951 / SU B: 15.725 / SU ML: 0.188 / Cross valid method: THROUGHOUT / ESU R: 0.216 / ESU R Free: 0.196 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22746 368 5 %RANDOM
Rwork0.1607 ---
obs0.16401 6957 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 72.69 Å2
Baniso -1Baniso -2Baniso -3
1--2.03 Å2-1.02 Å2-0 Å2
2---2.03 Å20 Å2
3---6.59 Å2
Refinement stepCycle: LAST / Resolution: 2.2→40.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms946 0 32 51 1029
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.019999
X-RAY DIFFRACTIONr_bond_other_d0.0030.02920
X-RAY DIFFRACTIONr_angle_refined_deg2.0031.9331354
X-RAY DIFFRACTIONr_angle_other_deg1.1342.9912112
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.3595120
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.05424.04842
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.18815166
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.006156
X-RAY DIFFRACTIONr_chiral_restr0.1150.2155
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021120
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02243
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_it3.8194.898483
X-RAY DIFFRACTIONr_mcbond_other3.8024.887482
X-RAY DIFFRACTIONr_mcangle_it6.4917.328602
X-RAY DIFFRACTIONr_mcangle_other6.4917.34603
X-RAY DIFFRACTIONr_scbond_it4.2235.494516
X-RAY DIFFRACTIONr_scbond_other4.2195.493517
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.8588.003753
X-RAY DIFFRACTIONr_long_range_B_refined11.32340.1761097
X-RAY DIFFRACTIONr_long_range_B_other11.31840.1951098
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.287 27 -
Rwork0.313 491 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 15.6265 Å / Origin y: 0.2207 Å / Origin z: 22.1386 Å
111213212223313233
T0.0374 Å20.0318 Å2-0.0117 Å2-0.2404 Å2-0.0926 Å2--0.1294 Å2
L3.1042 °20.9012 °20.0235 °2-2.2411 °2-0.4046 °2--2.8976 °2
S0.0832 Å °-0.0814 Å °0.1393 Å °0.1741 Å °0.1295 Å °-0.2718 Å °-0.075 Å °0.6746 Å °-0.2127 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 46
2X-RAY DIFFRACTION1A47 - 95
3X-RAY DIFFRACTION1A96 - 122

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