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- PDB-4kdw: Crystal structure of a bacterial immunoglobulin-like domain from ... -

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Basic information

Entry
Database: PDB / ID: 4kdw
TitleCrystal structure of a bacterial immunoglobulin-like domain from the M. primoryensis ice-binding adhesin
ComponentsAntifreeze protein
KeywordsCELL ADHESION / Bacterial Ig-like domain / extender domain / Ca2+-dependent / Immunoglobulin-like Beta-sandwich / Extender / Outer membrane (cell surface)
Function / homology
Function and homology information


Cadherin-like domain / : / : / Cadherin-like domain / Bacterial antifreeze protein repeat / : / Serralysin-like metalloprotease, C-terminal / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like ...Cadherin-like domain / : / : / Cadherin-like domain / Bacterial antifreeze protein repeat / : / Serralysin-like metalloprotease, C-terminal / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesMarinomonas primoryensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsGuo, S. / Garnham, C.P. / Karunan, S.P. / Campbell, R.L. / Allingham, J.S. / Davies, P.L.
CitationJournal: Febs J. / Year: 2013
Title: Role of Ca(2+) in folding the tandem beta-sandwich extender domains of a bacterial ice-binding adhesin.
Authors: Guo, S. / Garnham, C.P. / Karunan Partha, S. / Campbell, R.L. / Allingham, J.S. / Davies, P.L.
History
DepositionApr 25, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 2, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2013Group: Database references
Revision 1.2May 7, 2014Group: Other
Revision 1.3Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
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_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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.value / _struct_conn.pdbx_dist_value / _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_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

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Assembly

Deposited unit
A: Antifreeze protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,5099
Polymers12,1371
Non-polymers3738
Water2,522140
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)25.640, 28.620, 32.250
Angle α, β, γ (deg.)97.02, 112.93, 96.88
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Antifreeze protein


Mass: 12136.631 Da / Num. of mol.: 1 / Fragment: Single domain of MpAFP_RII
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Marinomonas primoryensis (bacteria) / Strain: Antarctic / Gene: MpAFP / Plasmid: pET 28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: A1YIY3
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 140 / 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: 1.72 Å3/Da / Density % sol: 28.4 %
Crystal growTemperature: 298 K / Method: evaporation / pH: 8.5
Details: 20% PEG 4000, 0.2M CaCl2, 0.1M Tris-HCl, microbatch, pH 8.5, EVAPORATION, temperature 298.0K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 6, 2012
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.35→29.191 Å / Num. obs: 17224 / % possible obs: 95.1 % / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 7.4 Å2 / Rmerge(I) obs: 0.049 / Net I/σ(I): 10.33
Reflection shellResolution: 1.35→1.42 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.085 / Mean I/σ(I) obs: 10.7 / % possible all: 91.6

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Processing

Software
NameVersionClassification
JBluIce-EPICSdata collection
PHASERphasing
REFMAC5.7.0032refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4KDV

4kdv


Resolution: 1.35→29.19 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.96 / SU B: 0.657 / SU ML: 0.028 / Cross valid method: THROUGHOUT / ESU R: 0.047 / ESU R Free: 0.053 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.165 887 5.1 %RANDOM
Rwork0.13 ---
obs0.132 16337 95.1 %-
all-16337 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 9.71 Å2
Baniso -1Baniso -2Baniso -3
1-0.54 Å20.21 Å20.06 Å2
2--0.03 Å20.21 Å2
3----0.46 Å2
Refinement stepCycle: LAST / Resolution: 1.35→29.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms691 0 13 140 844
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.02711
X-RAY DIFFRACTIONr_bond_other_d0.0010.02616
X-RAY DIFFRACTIONr_angle_refined_deg2.2441.921983
X-RAY DIFFRACTIONr_angle_other_deg0.92731423
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2285105
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.98928.51927
X-RAY DIFFRACTIONr_dihedral_angle_3_deg8.7041588
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1280.2133
X-RAY DIFFRACTIONr_gen_planes_refined0.010.02858
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02132
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.35→1.42 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.194 --
Rwork0.135 1107 -
obs--90.74 %

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