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- PDB-6w78: crystal structure of a plant ice-binding protein -

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Basic information

Entry
Database: PDB / ID: 6w78
Titlecrystal structure of a plant ice-binding protein
ComponentsAntifreeze polypeptide
KeywordsANTIFREEZE PROTEIN / ice-binding / ice recrystallization inhibition
Function / homologyLeucine-rich repeat-containing N-terminal, plant-type / Leucine rich repeat N-terminal domain / Leucine Rich repeat / Leucine rich repeat / Leucine-rich repeat profile. / Leucine-rich repeat / Leucine-rich repeat domain superfamily / Antifreeze polypeptide
Function and homology information
Biological speciesDaucus carota (carrot)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.311 Å
AuthorsWang, Y.N. / Zhang, H.Q.
CitationJournal: Biochem.J. / Year: 2020
Title: Carrot 'antifreeze' protein has an irregular ice-binding site that confers weak freezing point depression but strong inhibition of ice recrystallization.
Authors: Wang, Y. / Graham, L.A. / Han, Z. / Eves, R. / Gruneberg, A.K. / Campbell, R.L. / Zhang, H. / Davies, P.L.
History
DepositionMar 18, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 20, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Antifreeze polypeptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,6033
Polymers37,1601
Non-polymers4422
Water2,054114
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.895, 57.453, 135.538
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Antifreeze polypeptide / Antifreeze protein


Mass: 37160.469 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Daucus carota (carrot) / Gene: AFP, afp / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: O82438
#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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 114 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.04 Å3/Da / Density % sol: 39.64 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 0.2 M sodium malonate (pH 4.0), and 20% w/v polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.978 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Oct 31, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 13160 / % possible obs: 99.8 % / Redundancy: 8.8 % / Rmerge(I) obs: 0.127 / Net I/σ(I): 18
Reflection shellResolution: 2.3→2.36 Å / Rmerge(I) obs: 0.491 / Num. unique obs: 690

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1OGQ

1ogq


Resolution: 2.311→37.414 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.944 / SU B: 13.739 / SU ML: 0.15 / Cross valid method: FREE R-VALUE / ESU R: 0.36 / ESU R Free: 0.232
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2228 688 4.968 %
Rwork0.1622 --
all0.165 --
obs-13848 99.39 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 38.373 Å2
Baniso -1Baniso -2Baniso -3
1-0.107 Å2-0 Å2-0 Å2
2---1.166 Å20 Å2
3---1.058 Å2
Refinement stepCycle: LAST / Resolution: 2.311→37.414 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2413 0 28 114 2555
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0132514
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172310
X-RAY DIFFRACTIONr_angle_refined_deg2.0471.6553427
X-RAY DIFFRACTIONr_angle_other_deg1.3711.5855406
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7225313
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.23823.84125
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.94115421
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.5271512
X-RAY DIFFRACTIONr_chiral_restr0.090.2334
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022795
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02485
X-RAY DIFFRACTIONr_nbd_refined0.2080.2488
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1960.22284
X-RAY DIFFRACTIONr_nbtor_refined0.1710.21242
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0880.21170
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1920.2101
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1420.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2660.217
X-RAY DIFFRACTIONr_nbd_other0.2330.254
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2430.26
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1260.21
X-RAY DIFFRACTIONr_mcbond_it1.662.6831243
X-RAY DIFFRACTIONr_mcbond_other1.6592.6811242
X-RAY DIFFRACTIONr_mcangle_it2.4834.0211553
X-RAY DIFFRACTIONr_mcangle_other2.4824.0241554
X-RAY DIFFRACTIONr_scbond_it2.7553.0531271
X-RAY DIFFRACTIONr_scbond_other2.7553.0551272
X-RAY DIFFRACTIONr_scangle_it4.3144.441872
X-RAY DIFFRACTIONr_scangle_other4.3134.4421873
X-RAY DIFFRACTIONr_lrange_it5.6432.1462673
X-RAY DIFFRACTIONr_lrange_other5.64232.0912667
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.311-2.3710.275500.168880X-RAY DIFFRACTION94.2249
2.371-2.4360.177560.168934X-RAY DIFFRACTION100
2.436-2.5070.27530.158892X-RAY DIFFRACTION100
2.507-2.5840.246390.164909X-RAY DIFFRACTION100
2.584-2.6680.265400.186857X-RAY DIFFRACTION100
2.668-2.7620.276400.163843X-RAY DIFFRACTION99.8869
2.762-2.8660.293450.164792X-RAY DIFFRACTION100
2.866-2.9830.226490.168766X-RAY DIFFRACTION100
2.983-3.1150.225440.162721X-RAY DIFFRACTION100
3.115-3.2670.246360.147740X-RAY DIFFRACTION100
3.267-3.4430.248330.146678X-RAY DIFFRACTION100
3.443-3.6510.229230.149657X-RAY DIFFRACTION100
3.651-3.9030.189340.15617X-RAY DIFFRACTION99.8466
3.903-4.2140.209270.145574X-RAY DIFFRACTION100
4.214-4.6150.208210.148538X-RAY DIFFRACTION99.8214
4.615-5.1560.219340.158466X-RAY DIFFRACTION99.8004
5.156-5.9480.208210.19442X-RAY DIFFRACTION100
5.948-7.2710.274190.185377X-RAY DIFFRACTION100
7.271-10.2240.144170.167304X-RAY DIFFRACTION100
10.224-37.40.16470.233173X-RAY DIFFRACTION90
Refinement TLS params.Method: refined / Origin x: -11.576 Å / Origin y: -12.9385 Å / Origin z: 19.9902 Å
111213212223313233
T0.0133 Å20.0005 Å2-0.0085 Å2-0.0149 Å2-0.0194 Å2--0.0414 Å2
L1.2548 °20.295 °2-1.2369 °2-0.9855 °2-0.5239 °2--3.2655 °2
S0.0579 Å °-0.044 Å °0.0937 Å °0.0375 Å °0.0384 Å °0.0129 Å °-0.1644 Å °0.1191 Å °-0.0963 Å °
Refinement TLS groupSelection: ALL

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