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- PDB-5juh: Crystal structure of C-terminal domain (RV) of MpAFP -

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Basic information

Entry
Database: PDB / ID: 5juh
TitleCrystal structure of C-terminal domain (RV) of MpAFP
ComponentsAntifreeze protein
KeywordsCELL ADHESION / RTX / Antifreeze protein / Type I Secretion
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
Biological speciesMarinomonas primoryensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.35 Å
AuthorsGuo, S.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR) Canada
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
DepositionMay 10, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 19, 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 1.2Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry

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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)21,5119
Polymers21,1911
Non-polymers3218
Water3,261181
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area580 Å2
ΔGint-72 kcal/mol
Surface area7140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.960, 43.340, 78.840
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: 21190.785 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 181 / 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: 1.41 Å3/Da / Density % sol: 12.72 %
Crystal growTemperature: 298 K / Method: microbatch / pH: 4.6 / Details: Calcium chloride, Sodium acetate, PEG 400

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Feb 12, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.23→43.35 Å / Num. obs: 27687 / % possible obs: 78 % / Redundancy: 8.2 % / Net I/σ(I): 10.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementResolution: 1.35→39.42 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.972 / SU B: 2.703 / SU ML: 0.045 / Cross valid method: THROUGHOUT / ESU R: 0.055 / ESU R Free: 0.057 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17709 1254 5 %RANDOM
Rwork0.12531 ---
obs0.12795 23810 92.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 18.322 Å2
Baniso -1Baniso -2Baniso -3
1-1.11 Å20 Å20 Å2
2---0.96 Å20 Å2
3----0.15 Å2
Refinement stepCycle: 1 / Resolution: 1.35→39.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 8 181 1190
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0290.021036
X-RAY DIFFRACTIONr_bond_other_d0.0020.02945
X-RAY DIFFRACTIONr_angle_refined_deg2.3571.9631421
X-RAY DIFFRACTIONr_angle_other_deg1.20732186
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8795144
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.328.250
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.94715160
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.180.2177
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021244
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02206
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_it2.2771.505558
X-RAY DIFFRACTIONr_mcbond_other2.2411.503557
X-RAY DIFFRACTIONr_mcangle_it2.7892.269699
X-RAY DIFFRACTIONr_mcangle_other2.7882.27700
X-RAY DIFFRACTIONr_scbond_it3.621.766478
X-RAY DIFFRACTIONr_scbond_other3.6141.767478
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.182.541719
X-RAY DIFFRACTIONr_long_range_B_refined4.89916.0754840
X-RAY DIFFRACTIONr_long_range_B_other4.18315.1264591
X-RAY DIFFRACTIONr_rigid_bond_restr4.90831981
X-RAY DIFFRACTIONr_sphericity_free32.917513
X-RAY DIFFRACTIONr_sphericity_bonded11.84152164
LS refinement shellResolution: 1.35→1.385 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.383 59 -
Rwork0.357 1127 -
obs--60.7 %

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