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- PDB-4ny6: Neutron structure of leucine and valine methyl protonated type II... -

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Basic information

Entry
Database: PDB / ID: 4ny6
TitleNeutron structure of leucine and valine methyl protonated type III antifreeze
ComponentsType-3 ice-structuring protein HPLC 12
KeywordsANTIFREEZE PROTEIN
Function / homology
Function and homology information


extracellular region
Similarity search - Function
Antifreeze, type III / Type Iii Antifreeze Protein Isoform Hplc 12 / Antifreeze-like/N-acetylneuraminic acid synthase C-terminal domain / Antifreeze-like/N-acetylneuraminic acid synthase C-terminal / Antifreeze protein-like domain profile. / Antifreeze-like/N-acetylneuraminic acid synthase C-terminal domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
DEUTERATED WATER / Type-3 ice-structuring protein HPLC 12
Similarity search - Component
Biological speciesZoarces americanus (ocean pout)
MethodNEUTRON DIFFRACTION / X-RAY DIFFRACTION / SYNCHROTRON / NUCLEAR REACTOR / Resolution: 1.05 Å
AuthorsFisher, S.J. / Blakeley, M.P. / Howard, E.I. / Petite-Haertlein, I. / Haertlein, M. / Mitschler, A. / Cousido-Siah, A. / Salvaya, A.G. / Popov, A. / Muller-Dieckmann, C. ...Fisher, S.J. / Blakeley, M.P. / Howard, E.I. / Petite-Haertlein, I. / Haertlein, M. / Mitschler, A. / Cousido-Siah, A. / Salvaya, A.G. / Popov, A. / Muller-Dieckmann, C. / Petrova, T. / Podjarny, A.D.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: Perdeuteration: improved visualization of solvent structure in neutron macromolecular crystallography.
Authors: Fisher, S.J. / Blakeley, M.P. / Howard, E.I. / Petit-Haertlein, I. / Haertlein, M. / Mitschler, A. / Cousido-Siah, A. / Salvay, A.G. / Popov, A. / Muller-Dieckmann, C. / Petrova, T. / Podjarny, A.
History
DepositionDec 10, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 24, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software
Revision 1.2Jun 13, 2018Group: Data collection / Refinement description
Category: diffrn / diffrn_detector ...diffrn / diffrn_detector / diffrn_radiation / diffrn_radiation_wavelength / diffrn_source / refine / refine_ls_shell / reflns / reflns_shell
Item: _diffrn.ambient_temp / _diffrn_detector.detector ..._diffrn.ambient_temp / _diffrn_detector.detector / _diffrn_detector.pdbx_collection_date / _diffrn_detector.type / _diffrn_radiation.monochromator / _diffrn_radiation.pdbx_diffrn_protocol / _diffrn_radiation.pdbx_monochromatic_or_laue_m_l / _diffrn_radiation.pdbx_scattering_type / _diffrn_radiation_wavelength.wavelength / _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.pdbx_synchrotron_site / _diffrn_source.pdbx_wavelength / _diffrn_source.pdbx_wavelength_list / _diffrn_source.source / _diffrn_source.type / _refine.B_iso_mean / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.ls_d_res_high / _refine.ls_d_res_low / _refine.ls_number_reflns_R_free / _refine.ls_number_reflns_obs / _refine.ls_percent_reflns_R_free / _refine.ls_percent_reflns_obs / _refine.occupancy_max / _refine.occupancy_min / _refine.overall_SU_ML / _refine.pdbx_ls_sigma_F / _refine.pdbx_overall_phase_error / _refine.pdbx_refine_id / _refine_ls_shell.R_factor_R_free / _refine_ls_shell.R_factor_R_work / _refine_ls_shell.d_res_high / _refine_ls_shell.d_res_low / _refine_ls_shell.number_reflns_R_free / _refine_ls_shell.number_reflns_R_work / _refine_ls_shell.pdbx_refine_id / _refine_ls_shell.percent_reflns_obs / _reflns.d_resolution_high / _reflns.d_resolution_low / _reflns.number_all / _reflns.number_obs / _reflns.pdbx_Rmerge_I_obs / _reflns.pdbx_netI_over_sigmaI / _reflns.pdbx_redundancy / _reflns.percent_possible_obs / _reflns_shell.Rmerge_I_obs / _reflns_shell.d_res_high / _reflns_shell.d_res_low / _reflns_shell.meanI_over_sigI_obs / _reflns_shell.pdbx_redundancy / _reflns_shell.percent_possible_all
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / refine_hist / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.d_res_high / _refine_hist.d_res_low / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Type-3 ice-structuring protein HPLC 12


Theoretical massNumber of molelcules
Total (without water)6,8941
Polymers6,8941
Non-polymers00
Water75742
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)32.730, 39.120, 46.540
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Type-3 ice-structuring protein HPLC 12 / Antifreeze protein QAE(HPLC 12) / ISP type III HPLC 12


Mass: 6894.129 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zoarces americanus (ocean pout) / Plasmid: pET-28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P19614
#2: Chemical ChemComp-DOD / water


Mass: 18.015 Da / Num. of mol.: 42 / Source method: isolated from a natural source / Formula: D2O

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Experimental details

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Experiment

Experiment
MethodNumber of used crystals
NEUTRON DIFFRACTION1
X-RAY DIFFRACTION1

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Sample preparation

CrystalDensity Matthews: 2.16 Å3/Da / Density % sol: 43.08 %
Crystal growTemperature: 285 K / Method: vapor diffusion, sitting drop / pH: 5.2
Details: 10mg/ml protein in 50 mM sodium acetate pD 5.2. Drops containing 20 ml protein solution and 30 ml precipitant buffer (2.1 M ammonium sulfate, 9% d8-glycerol) were equilibrated against 1 ml ...Details: 10mg/ml protein in 50 mM sodium acetate pD 5.2. Drops containing 20 ml protein solution and 30 ml precipitant buffer (2.1 M ammonium sulfate, 9% d8-glycerol) were equilibrated against 1 ml precipitant buffer in the reservoir, VAPOR DIFFUSION, SITTING DROP, temperature 285K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
22981
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
SYNCHROTRONESRF ID23-110.6525
NUCLEAR REACTOROTHER23.18-4.22
Detector
TypeIDDetectorDate
DECTRIS PILATUS 6M1PIXEL
Image Plate2LADI-IIIMay 28, 2008
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-IDMonochromator
1SINGLE WAVELENGTHMx-ray1
2LAUELneutron1NiTi Multilayer Filter
Radiation wavelength
IDWavelength (Å)Relative weight
10.65251
23.181
34.221
Reflection

Entry-ID: 4NY6

Resolution (Å)Num. allNum. obs% possible obs (%)Redundancy (%)Rmerge(I) obsDiffraction-IDNet I/σ(I)
1.05-502853499.76.10.048132.5
1.8-46.525916519489.311.10.136214
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.05-1.090.6382.66199.9
1.8-1.93.50.1696.6271.4

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Processing

Software
NameVersionClassification
QLDdata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.8_1069)refinement
LAUEGENdata reduction
LSCALEdata scaling
SCALAdata scaling
PHENIXphasing
Refinement

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Stereochemistry target values: Joint X-ray/neutron ML / Solvent model: FLAT BULK SOLVENT MODEL

Resolution (Å)Refine-IDBiso mean (Å2)Rfactor RfreeRfactor RworkRfactor obsNum. reflection RfreeNum. reflection obs% reflection Rfree (%)% reflection obs (%)Occupancy maxOccupancy minSU MLDiffraction-IDσ(F)Phase error
1.05-18.965X-RAY DIFFRACTION16.96090.18810.17030.1712142628511599.82100.0911.3418.06
1.85-26.772NEUTRON DIFFRACTION0.22450.17570.178224648975.0289.940.16218.78
Refine funct minimized
Refine-IDType
NEUTRON DIFFRACTIONJoint X-ray/neutron ML
X-RAY DIFFRACTIONJoint X-ray/neutron ML
Refinement stepCycle: LAST / Resolution: 1.05→18.965 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms479 0 0 42 521
Refine LS restraints
Refine-IDTypeDev idealNumber
NEUTRON DIFFRACTIONf_bond_d0.0131232
NEUTRON DIFFRACTIONf_angle_d1.3022179
NEUTRON DIFFRACTIONf_dihedral_angle_d15.259323
NEUTRON DIFFRACTIONf_chiral_restr0.08103
NEUTRON DIFFRACTIONf_plane_restr0.006189
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.05-1.08750.27451410.23282676X-RAY DIFFRACTION100
1.0875-1.13110.17031390.16912654X-RAY DIFFRACTION100
1.1311-1.18250.15471410.15082659X-RAY DIFFRACTION100
1.1825-1.24490.18981400.16192677X-RAY DIFFRACTION100
1.2449-1.32290.17841430.15792694X-RAY DIFFRACTION100
1.3229-1.4250.15821400.15022686X-RAY DIFFRACTION100
1.425-1.56830.18971430.16442709X-RAY DIFFRACTION100
1.5683-1.79510.19841430.16912727X-RAY DIFFRACTION100
1.7951-2.2610.16631450.16462743X-RAY DIFFRACTION100
2.261-18.96840.20111510.17712860X-RAY DIFFRACTION99
1.8502-2.33090.21421150.16692186NEUTRON DIFFRACTION87
2.3309-26.77510.23151310.18122465NEUTRON DIFFRACTION93

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