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- PDB-6x5w: Peptide-bound structure of Marinomonas primoryensis peptide-bindi... -

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Basic information

Entry
Database: PDB / ID: 6x5w
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: 1.8 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 27, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 1, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: 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)55,23227
Polymers53,4892
Non-polymers1,74325
Water9,332518
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.163, 58.922, 63.249
Angle α, β, γ (deg.)62.513, 85.814, 65.932
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AB

#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: 525.510 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 4 types, 543 molecules

#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#5: Chemical
ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 518 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 1.45 Å3/Da / Density % sol: 56.78 %
Crystal growTemperature: 293 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: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Sep 26, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.8→55.54 Å / Num. obs: 138852 / % possible obs: 97.7 % / Redundancy: 6.9 % / Biso Wilson estimate: 19.6 Å2 / Rmerge(I) obs: 0.146 / Net I/σ(I): 16.22
Reflection shellResolution: 1.8→1.83 Å / Rmerge(I) obs: 0.809 / Num. unique obs: 51767 / % possible all: 94.4

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
DIALSdata reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5k8g

5k8g


Resolution: 1.8→55.54 Å / SU ML: 0.2103 / Cross valid method: FREE R-VALUE / σ(F): 2.24 / Phase error: 23.6832
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2281 2669 4.97 %
Rwork0.1902 51010 -
obs0.1921 53679 97.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.08 Å2
Refinement stepCycle: LAST / Resolution: 1.8→55.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3762 0 85 518 4365
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00663981
X-RAY DIFFRACTIONf_angle_d0.82835430
X-RAY DIFFRACTIONf_chiral_restr0.0544628
X-RAY DIFFRACTIONf_plane_restr0.0051732
X-RAY DIFFRACTIONf_dihedral_angle_d21.06871387
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.830.30821350.28332699X-RAY DIFFRACTION96.39
1.83-1.870.29221440.25762615X-RAY DIFFRACTION96.13
1.87-1.910.28831290.24342678X-RAY DIFFRACTION96.79
1.91-1.950.25561370.23512637X-RAY DIFFRACTION96.76
1.95-1.990.25181530.21972618X-RAY DIFFRACTION96.69
1.99-2.040.26131410.20882706X-RAY DIFFRACTION97.13
2.04-2.10.21561450.19422634X-RAY DIFFRACTION97.24
2.1-2.160.23121520.19682683X-RAY DIFFRACTION97.36
2.16-2.230.26551300.19662670X-RAY DIFFRACTION97.49
2.23-2.310.2631370.19482668X-RAY DIFFRACTION97.57
2.31-2.40.27621280.19162702X-RAY DIFFRACTION97.96
2.4-2.510.2151310.18772731X-RAY DIFFRACTION97.95
2.51-2.640.23651500.18722681X-RAY DIFFRACTION98.09
2.64-2.810.25321300.18962700X-RAY DIFFRACTION98.47
2.81-3.030.23731550.19552705X-RAY DIFFRACTION98.59
3.03-3.330.22481520.17692692X-RAY DIFFRACTION98.85
3.33-3.810.20741470.17672713X-RAY DIFFRACTION99.13
3.81-4.80.19731250.15552736X-RAY DIFFRACTION99.24
4.8-55.540.181480.18622742X-RAY DIFFRACTION99.52

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