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- PDB-5j6y: Crystal structure of PA14 domain of MpAFP Antifreeze protein -

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Basic information

Entry
Database: PDB / ID: 5j6y
TitleCrystal structure of PA14 domain of MpAFP Antifreeze protein
ComponentsAntifreeze protein
KeywordsCELL ADHESION / Sugar binding / Antifreeze protein / PA14
Function / homology
Function and homology information


Cadherin-like domain / : / : / : / Cadherin-like domain / Bacterial antifreeze protein repeat / Serralysin-like metalloprotease, C-terminal / Immunoglobulin-like fold
Similarity search - Domain/homology
beta-D-glucopyranose / alpha-D-glucopyranose / Antifreeze protein
Similarity search - Component
Biological speciesMarinomonas primoryensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.03 Å
AuthorsGuo, S.
CitationJournal: Sci Adv / Year: 2017
Title: Structure of a 1.5-MDa adhesin that binds its Antarctic bacterium to diatoms and ice.
Authors: Guo, S. / Stevens, C.A. / Vance, T.D.R. / Olijve, L.L.C. / Graham, L.A. / Campbell, R.L. / Yazdi, S.R. / Escobedo, C. / Bar-Dolev, M. / Yashunsky, V. / Braslavsky, I. / Langelaan, D.N. / ...Authors: Guo, S. / Stevens, C.A. / Vance, T.D.R. / Olijve, L.L.C. / Graham, L.A. / Campbell, R.L. / Yazdi, S.R. / Escobedo, C. / Bar-Dolev, M. / Yashunsky, V. / Braslavsky, I. / Langelaan, D.N. / Smith, S.P. / Allingham, J.S. / Voets, I.K. / Davies, P.L.
History
DepositionApr 5, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 7, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Refinement description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / refine / refine_hist / reflns / reflns_shell / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.label_alt_id / _chem_comp.name ..._atom_site.label_alt_id / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_nonpoly_scheme.ndb_seq_num / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.ls_d_res_high / _refine.ls_percent_reflns_obs / _refine_hist.d_res_high / _reflns.pdbx_CC_half / _reflns_shell.number_unique_obs / _reflns_shell.pdbx_CC_half
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Mar 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _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 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,75811
Polymers20,0771
Non-polymers68110
Water5,459303
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area960 Å2
ΔGint-72 kcal/mol
Surface area8570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.220, 50.550, 79.420
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 Antifreeze protein /


Mass: 20077.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Marinomonas primoryensis (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: A1YIY3
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#3: Sugar ChemComp-GLC / alpha-D-glucopyranose / alpha-D-glucose / D-glucose / glucose / Glucose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-glucopyranoseCOMMON NAMEGMML 1.0
a-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Sugar ChemComp-BGC / beta-D-glucopyranose / beta-D-glucose / D-glucose / glucose / Glucose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranoseCOMMON NAMEGMML 1.0
b-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 303 / 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: 2.26 Å3/Da / Density % sol: 45.59 %
Crystal growTemperature: 293 K / Method: microbatch
Details: 20% PEG 3350, 0.2 M Calcium Chloride, Glucose, HEPES pH7

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97934 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Sep 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 1.03→45.22 Å / Num. obs: 74600 / % possible obs: 83.2 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.042 / Net I/σ(I): 23.9
Reflection shellResolution: 1.03→1.05 Å

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementResolution: 1.03→39.71 Å / SU ML: 0.06 / Cross valid method: THROUGHOUT / σ(F): 1.4 / Phase error: 15.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.164 3725 5 %RANDOM
Rwork0.155 ---
obs0.156 74502 83.2 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.03→39.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1418 0 32 303 1753
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081537
X-RAY DIFFRACTIONf_angle_d1.3062116
X-RAY DIFFRACTIONf_dihedral_angle_d12.182531
X-RAY DIFFRACTIONf_chiral_restr0.31239
X-RAY DIFFRACTIONf_plane_restr0.007282
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.0342-1.04730.5165130.4683237X-RAY DIFFRACTION8
1.0473-1.06110.3744350.314675X-RAY DIFFRACTION22
1.0611-1.07560.2207550.25761027X-RAY DIFFRACTION33
1.0756-1.0910.2416680.22611309X-RAY DIFFRACTION43
1.091-1.10730.2183870.21011647X-RAY DIFFRACTION53
1.1073-1.12460.20271030.18931940X-RAY DIFFRACTION62
1.1246-1.1430.1791150.17862183X-RAY DIFFRACTION71
1.143-1.16270.19091300.17272479X-RAY DIFFRACTION79
1.1627-1.18390.1871410.17212695X-RAY DIFFRACTION87
1.1839-1.20660.16991490.16462852X-RAY DIFFRACTION90
1.2066-1.23130.17371570.15412978X-RAY DIFFRACTION96
1.2313-1.25810.15291650.14963136X-RAY DIFFRACTION100
1.2581-1.28730.16041640.14683113X-RAY DIFFRACTION100
1.2873-1.31950.16051640.14623120X-RAY DIFFRACTION100
1.3195-1.35520.17441650.14923135X-RAY DIFFRACTION100
1.3552-1.39510.13961650.14573133X-RAY DIFFRACTION100
1.3951-1.44010.16771650.14883132X-RAY DIFFRACTION100
1.4401-1.49160.15211660.14123151X-RAY DIFFRACTION100
1.4916-1.55130.14761650.13993143X-RAY DIFFRACTION100
1.5513-1.62190.15971670.13613165X-RAY DIFFRACTION100
1.6219-1.70740.16141650.14363140X-RAY DIFFRACTION100
1.7074-1.81440.15581680.14573187X-RAY DIFFRACTION100
1.8144-1.95450.13981670.14953169X-RAY DIFFRACTION100
1.9545-2.15120.13571680.14343190X-RAY DIFFRACTION100
2.1512-2.46240.15751680.15423204X-RAY DIFFRACTION100
2.4624-3.10220.18261710.16663238X-RAY DIFFRACTION100
3.1022-39.73930.17121790.1583399X-RAY DIFFRACTION100

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