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- PDB-7pb7: Structure of LPMO domain of colonization factor GbpA from Vibrio ... -

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Basic information

Entry
Database: PDB / ID: 7pb7
TitleStructure of LPMO domain of colonization factor GbpA from Vibrio cholerae in the presence of calcium
ComponentsGlcNAc-binding protein A
KeywordsCELL ADHESION / Colonization factor / LPMO / metalloenzyme
Function / homology
Function and homology information


chitin binding / extracellular region
Similarity search - Function
N-acetylglucosamine-binding protein A / : / GlcNAc-binding protein A, third domain / N-acetylglucosamine binding protein A domain 2 / N-acetylglucosamine binding protein domain 2 / : / Cellulose/chitin-binding protein, N-terminal / Lytic polysaccharide mono-oxygenase, cellulose-degrading / Immunoglobulin E-set
Similarity search - Domain/homology
COPPER (II) ION / GlcNAc-binding protein A
Similarity search - Component
Biological speciesVibrio cholerae O1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsBjerregaard-Andersen, K. / Krengel, U.
Funding support Norway, 1items
OrganizationGrant numberCountry
Norwegian Research Council247730 Norway
CitationJournal: To Be Published
Title: Structure of LPMO domain of colonization factor GbpA from Vibrio cholerae in the presence of calcium
Authors: Bjerregaard-Andersen, K. / Krengel, U.
History
DepositionJul 31, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 10, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GlcNAc-binding protein A
B: GlcNAc-binding protein A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,8496
Polymers39,6422
Non-polymers2074
Water9,224512
1
A: GlcNAc-binding protein A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,9253
Polymers19,8211
Non-polymers1042
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: GlcNAc-binding protein A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,9253
Polymers19,8211
Non-polymers1042
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.610, 45.200, 99.590
Angle α, β, γ (deg.)90.000, 101.055, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein GlcNAc-binding protein A


Mass: 19820.988 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae O1 (bacteria) / Gene: gbpA, VC_A0811 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9KLD5
#2: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 512 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 45.65 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Calcium chloride dihydrate, 0.1 M HEPES pH 7.0, 20 % w/v PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.979655 Å
DetectorType: MAR CCD 130 mm / Detector: CCD / Date: Sep 16, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979655 Å / Relative weight: 1
ReflectionResolution: 1.8→34.27 Å / Num. obs: 33236 / % possible obs: 99.48 % / Redundancy: 4.1 % / Biso Wilson estimate: 12.5 Å2 / CC1/2: 0.993 / Net I/σ(I): 7.78
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 4.1 % / Mean I/σ(I) obs: 1.75 / Num. unique obs: 5267 / CC1/2: 0.705 / % possible all: 98.5

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Processing

Software
NameVersionClassification
Coot1.13_2998model building
PHENIX1.13_2998refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2xwx

2xwx


Resolution: 1.8→32.58 Å / SU ML: 0.2085 / Cross valid method: FREE R-VALUE / σ(F): 0.89 / Phase error: 23.5718 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.2282 3231 5.02 %
Rwork0.1788 61147 -
obs0.1813 33236 99.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 16.3 Å2
Refinement stepCycle: LAST / Resolution: 1.8→32.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2798 0 4 512 3314
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00492882
X-RAY DIFFRACTIONf_angle_d0.71913940
X-RAY DIFFRACTIONf_chiral_restr0.0517414
X-RAY DIFFRACTIONf_plane_restr0.0046528
X-RAY DIFFRACTIONf_dihedral_angle_d18.1651038
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.820.32491320.31812459X-RAY DIFFRACTION92.04
1.82-1.850.35431390.28562708X-RAY DIFFRACTION99.55
1.85-1.880.30091380.29012627X-RAY DIFFRACTION99.53
1.88-1.910.25211430.26122678X-RAY DIFFRACTION99.33
1.91-1.950.29031420.23862667X-RAY DIFFRACTION99.47
1.95-1.990.31421390.22672627X-RAY DIFFRACTION99.68
1.99-2.030.23451460.20812731X-RAY DIFFRACTION99.83
2.03-2.070.27221390.21172638X-RAY DIFFRACTION99.78
2.07-2.120.26571400.21662638X-RAY DIFFRACTION99.61
2.12-2.170.22061430.192696X-RAY DIFFRACTION99.68
2.17-2.230.2751390.18492653X-RAY DIFFRACTION99.86
2.23-2.30.25341410.17132654X-RAY DIFFRACTION99.64
2.3-2.370.23741430.18472743X-RAY DIFFRACTION99.69
2.37-2.460.24691390.18232601X-RAY DIFFRACTION99.89
2.46-2.550.23531430.16962710X-RAY DIFFRACTION99.76
2.55-2.670.24231440.17342686X-RAY DIFFRACTION99.68
2.67-2.810.27591380.16752662X-RAY DIFFRACTION99.68
2.81-2.990.17991400.16342638X-RAY DIFFRACTION99.75
2.99-3.220.21631420.15712703X-RAY DIFFRACTION99.68
3.22-3.540.17521390.14522654X-RAY DIFFRACTION99.75
3.54-4.050.21931420.13172687X-RAY DIFFRACTION99.4
4.05-5.10.14791400.11812646X-RAY DIFFRACTION99.54
5.1-34.270.16441400.15612641X-RAY DIFFRACTION98.83

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