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- PDB-3ult: Crystal structure of an ice-binding protein from the perennial ry... -

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Basic information

Entry
Database: PDB / ID: 3ult
TitleCrystal structure of an ice-binding protein from the perennial ryegrass, Lolium perenne
ComponentsIce recrystallization inhibition protein-like protein
KeywordsANTIFREEZE PROTEIN / beta-solenoid / beta-roll / ice-binding / antifreeze / ice / extracellular
Function / homology
Function and homology information


: / Grass antifreeze beta roll / : / Serralysin-like metalloprotease, C-terminal / 2 Solenoid / Alkaline Protease, subunit P, domain 1 / Leucine-rich repeat-containing N-terminal, plant-type / Leucine rich repeat N-terminal domain / Serralysin-like metalloprotease, C-terminal / Leucine Rich Repeat ...: / Grass antifreeze beta roll / : / Serralysin-like metalloprotease, C-terminal / 2 Solenoid / Alkaline Protease, subunit P, domain 1 / Leucine-rich repeat-containing N-terminal, plant-type / Leucine rich repeat N-terminal domain / Serralysin-like metalloprotease, C-terminal / Leucine Rich Repeat / Leucine-rich repeat / Leucine-rich repeat domain superfamily / Mainly Beta
Similarity search - Domain/homology
ETHANOL / Ice recrystallization inhibition protein-like protein
Similarity search - Component
Biological speciesLolium perenne (perennial ryegrass)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.4 Å
AuthorsMiddleton, A.J. / Faucher, F. / Campbell, R.L. / Davies, P.L.
CitationJournal: J.Mol.Biol. / Year: 2012
Title: Antifreeze protein from freeze-tolerant grass has a beta-roll fold with an irregularly structured ice-binding site.
Authors: Middleton, A.J. / Marshall, C.B. / Faucher, F. / Bar-Dolev, M. / Braslavsky, I. / Campbell, R.L. / Walker, V.K. / Davies, P.L.
History
DepositionNov 11, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 15, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 18, 2012Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ice recrystallization inhibition protein-like protein
B: Ice recrystallization inhibition protein-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,63715
Polymers27,0062
Non-polymers63113
Water4,234235
1
A: Ice recrystallization inhibition protein-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,8428
Polymers13,5031
Non-polymers3387
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Ice recrystallization inhibition protein-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,7957
Polymers13,5031
Non-polymers2926
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)94.280, 62.490, 44.000
Angle α, β, γ (deg.)90.000, 113.960, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Ice recrystallization inhibition protein-like protein


Mass: 13503.053 Da / Num. of mol.: 2 / Fragment: UNP residues 137-254
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lolium perenne (perennial ryegrass) / Gene: IRI3 / Plasmid: pET24a+ / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-star(DE3) / References: UniProt: B5T007
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-EOH / ETHANOL


Mass: 46.068 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H6O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 235 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.19 Å3/Da / Density % sol: 43.91 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.2
Details: 45-50% Ethanol, 100 mM Phosphate-citrate, 0-5% PEG 1000, pH 4.2, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 1.13, 1.55
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Feb 14, 2009
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.131
21.551
ReflectionNumber: 51177 / Rmerge(I) obs: 0.073 / D res high: 2.1 Å / Num. obs: 23468 / % possible obs: 87.1
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)Num. obs% possible obs (%)IDRmerge(I) obs
102021694.310.048
61085492.510.052
46254693.310.052
34495092.210.059
2.83193491.610.083
2.72.8119492.410.095
2.62.7141991.510.12
2.52.6162891.510.146
2.42.5191591.410.156
2.32.4220790.610.167
2.22.3263689.910.173
2.12.2196956.910.25
ReflectionResolution: 1.4→20 Å / Num. obs: 45098 / % possible obs: 97.9 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 5.7 % / Biso Wilson estimate: 17.982 Å2 / Rmerge(I) obs: 0.076 / Rsym value: 0.057 / Net I/σ(I): 16.83
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.4-1.50.2935.48472288305196.9
1.5-1.60.1468.83364736343197.2
1.6-1.70.12310.89289755033197.8
1.7-1.80.10113.14227893946198.2
1.8-20.06417.97332285791198.6
2-2.50.04724.69436207643199
2.5-30.04529.04191913388199.1
3-40.04134.17149552701198.1
4-60.04134.7373631366196.8
6-100.04634.242577471196.5
10-200.04935.15558111177.1

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Phasing

PhasingMethod: SIRAS

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
SHARPphasing
PHENIX1.7.1_743refinement
PDB_EXTRACT3.1data extraction
Blu-Icedata collection
XDSdata reduction
RefinementMethod to determine structure: SIRAS / Resolution: 1.4→19.423 Å / Occupancy max: 1 / Occupancy min: 0.01 / SU ML: 0.28 / σ(F): 2 / Phase error: 20 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1873 2242 4.99 %Random
Rwork0.1651 ---
obs0.1662 44891 97.7 %-
Solvent computationShrinkage radii: 0.41 Å / VDW probe radii: 0.6 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 64.897 Å2 / ksol: 0.493 e/Å3
Displacement parametersBiso max: 86.65 Å2 / Biso mean: 17.308 Å2 / Biso min: 6.82 Å2
Baniso -1Baniso -2Baniso -3
1-3.0465 Å20 Å23.1001 Å2
2---0.9361 Å2-0 Å2
3----2.1104 Å2
Refinement stepCycle: LAST / Resolution: 1.4→19.423 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1586 0 41 235 1862
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111908
X-RAY DIFFRACTIONf_angle_d1.4222638
X-RAY DIFFRACTIONf_chiral_restr0.085314
X-RAY DIFFRACTIONf_plane_restr0.006382
X-RAY DIFFRACTIONf_dihedral_angle_d10.678657
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 16

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.4-1.43040.23171370.21562618275597
1.4304-1.46370.22891380.20842621275997
1.4637-1.50030.20461400.18252650279097
1.5003-1.54080.22041380.16742616275497
1.5408-1.58620.19651390.15992630276997
1.5862-1.63730.23261390.15352644278397
1.6373-1.69580.19591400.1572647278798
1.6958-1.76370.18861410.15342683282498
1.7637-1.84390.18861410.1522662280398
1.8439-1.9410.16071360.14232656279298
1.941-2.06250.15991420.14092697283998
2.0625-2.22150.14561420.13582700284299
2.2215-2.44470.17251420.14542713285599
2.4447-2.79760.17521420.1552702284499
2.7976-3.52120.17781430.15992708285199
3.5212-19.42470.21841420.21872702284496

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