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- PDB-6x6m: Peptide-bound structure of Marinomonas primoryensis peptide-bindi... -

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Basic information

Entry
Database: PDB / ID: 6x6m
TitlePeptide-bound structure of Marinomonas primoryensis peptide-binding domain
Components
  • Antifreeze protein
  • peptide
KeywordsPROTEIN BINDING / peptide-binding domain / protein-binding domain
Function / homology
Function and homology information


Cadherin-like domain / : / Cadherin-like domain / Bacterial antifreeze protein repeat / : / : / Serralysin-like metalloprotease, C-terminal / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like ...Cadherin-like domain / : / Cadherin-like domain / Bacterial antifreeze protein repeat / : / : / Serralysin-like metalloprotease, C-terminal / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesMarinomonas primoryensis (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsGuo, S. / Davies, P.L.
Funding support1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)
CitationJournal: To Be Published
Title: Molecular basis for a bacterial adhesins peptide-binding module
Authors: Davies, P.L. / Guo, S.
History
DepositionMay 28, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 1, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Antifreeze protein
B: peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,27919
Polymers53,4002
Non-polymers88017
Water8,053447
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2020 Å2
ΔGint-144 kcal/mol
Surface area24540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.240, 60.868, 63.609
Angle α, β, γ (deg.)66.403, 72.742, 68.354
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

#1: Protein Antifreeze protein


Mass: 52963.352 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: Protein/peptide peptide


Mass: 436.372 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 447 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 1.54 Å3/Da / Density % sol: 20.14 %
Crystal growTemperature: 298 K / Method: microbatch / pH: 4.6
Details: ~0.1 M calcium chloride, ~0.1 M sodium acetate (pH 4.6), ~30% (w/v) PEG 400

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Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 7, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.9→57.42 Å / Num. obs: 48424 / % possible obs: 98 % / Redundancy: 6.9 % / Biso Wilson estimate: 23.98 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 12.8
Reflection shellResolution: 2→2.05 Å / Rmerge(I) obs: 1.697 / Num. unique obs: 20688

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
xia2data reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 58kg

58kg


Resolution: 1.9→57.39 Å / SU ML: 0.2053 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 24.9194
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2185 2453 5.07 %
Rwork0.1958 45924 -
obs0.197 48377 97.09 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.85 Å2
Refinement stepCycle: LAST / Resolution: 1.9→57.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3760 0 32 447 4239
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00453931
X-RAY DIFFRACTIONf_angle_d0.62345385
X-RAY DIFFRACTIONf_chiral_restr0.0514632
X-RAY DIFFRACTIONf_plane_restr0.0033731
X-RAY DIFFRACTIONf_dihedral_angle_d15.14571359
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.940.31541240.27422303X-RAY DIFFRACTION87.46
1.94-1.980.27911130.25092534X-RAY DIFFRACTION96.01
1.98-2.020.27221350.22732544X-RAY DIFFRACTION96.3
2.02-2.070.2741430.22142516X-RAY DIFFRACTION96.59
2.07-2.120.24781390.21292573X-RAY DIFFRACTION97.03
2.12-2.170.25481390.20792557X-RAY DIFFRACTION97.05
2.17-2.240.24531300.19842514X-RAY DIFFRACTION96.74
2.24-2.310.21411490.19652534X-RAY DIFFRACTION97.03
2.31-2.390.23021260.18452567X-RAY DIFFRACTION97.47
2.39-2.490.22391420.19692558X-RAY DIFFRACTION97.54
2.49-2.60.20491270.19542581X-RAY DIFFRACTION97.83
2.6-2.740.23951400.19322601X-RAY DIFFRACTION97.93
2.74-2.910.21861320.19362562X-RAY DIFFRACTION98.32
2.91-3.140.22871440.20042582X-RAY DIFFRACTION98.34
3.14-3.450.20291470.18542559X-RAY DIFFRACTION98.65
3.45-3.950.19521440.18852608X-RAY DIFFRACTION98.78
3.95-4.980.17731380.17112607X-RAY DIFFRACTION99.2
4.98-57.390.21821410.20022624X-RAY DIFFRACTION99.53

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