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- PDB-8cc5: Vibrio cholerae GbpA (LPMO domain) -

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Basic information

Entry
Database: PDB / ID: 8cc5
TitleVibrio cholerae GbpA (LPMO domain)
ComponentsGlcNAc-binding protein A
KeywordsCELL ADHESION / Adhesin / LPMO / redox enzyme / colonization factor
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
ACETATE ION / COPPER (II) ION / GlcNAc-binding protein A
Similarity search - Component
Biological speciesVibrio cholerae O1 biovar El Tor (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.62 Å
AuthorsMontserrat-Canals, M. / Sorensen, H.V. / Cordara, G. / Krengel, U.
Funding support Norway, 2items
OrganizationGrant numberCountry
Norwegian Research Council272201 Norway
Norwegian Research Council245828 Norway
Citation
Journal: Acs Omega / Year: 2023
Title: Perdeuterated GbpA Enables Neutron Scattering Experiments of a Lytic Polysaccharide Monooxygenase.
Authors: Sorensen, H.V. / Montserrat-Canals, M. / Loose, J.S.M. / Fisher, S.Z. / Moulin, M. / Blakeley, M.P. / Cordara, G. / Bjerregaard-Andersen, K. / Krengel, U.
#1: Journal: Biochemistry / Year: 2023
Title: Human 2'-Deoxynucleoside 5'-Phosphate N -Hydrolase 1: Mechanism of 2'-Deoxyuridine 5'-Monophosphate Hydrolysis.
Authors: Devi, S. / Carberry, A.E. / Zickuhr, G.M. / Dickson, A.L. / Harrison, D.J. / da Silva, R.G.
#2: Journal: Acs Omega / Year: 2023
Title: Perdeuterated GbpA Enables Neutron Scattering Experiments of a Lytic Polysaccharide Monooxygenase.
Authors: Sorensen, H.V. / Montserrat-Canals, M. / Loose, J.S.M. / Fisher, S.Z. / Moulin, M. / Blakeley, M.P. / Cordara, G. / Bjerregaard-Andersen, K. / Krengel, U.
History
DepositionJan 26, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 30, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 20, 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)40,43315
Polymers39,6422
Non-polymers79113
Water3,369187
1
A: GlcNAc-binding protein A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,3309
Polymers19,8211
Non-polymers5098
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: GlcNAc-binding protein A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,1046
Polymers19,8211
Non-polymers2835
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)75.333, 89.374, 47.497
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11B-303-

ZN

21B-482-

HOH

31B-483-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#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 biovar El Tor (bacteria)
Gene: gbpA, VCA0811 / Production host: Escherichia coli (E. coli) / References: UniProt: A6XA54

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Non-polymers , 5 types, 200 molecules

#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 187 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.02 Å3/Da / Density % sol: 39.01 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2 M Zinc Acetate 0.1 M Sodium Cacodylate pH 6.5 18% w/v PEG 8K

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.87313 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Nov 29, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87313 Å / Relative weight: 1
ReflectionResolution: 1.62→47.542 Å / Num. obs: 78744 / % possible obs: 99.94 % / Redundancy: 6.8 % / CC1/2: 0.998 / Net I/σ(I): 10.83
Reflection shellResolution: 1.62→1.68 Å / Num. unique obs: 4085 / CC1/2: 0.374

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Processing

Software
NameVersionClassification
REFMAC5.8.0403refinement
XDSdata reduction
XSCALEdata scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.62→47.542 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.959 / WRfactor Rfree: 0.208 / WRfactor Rwork: 0.172 / SU B: 2.11 / SU ML: 0.07 / Average fsc free: 0 / Average fsc work: 0 / Cross valid method: FREE R-VALUE / ESU R: 0.101 / ESU R Free: 0.101
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.213 2034 4.898 %
Rwork0.1763 39494 -
all0.178 --
obs-41528 99.966 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 25.413 Å2
Baniso -1Baniso -2Baniso -3
1--1.884 Å20 Å2-0 Å2
2--0.881 Å20 Å2
3---1.003 Å2
Refinement stepCycle: LAST / Resolution: 1.62→47.542 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2798 0 19 187 3004
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0123149
X-RAY DIFFRACTIONr_bond_other_d00.0162791
X-RAY DIFFRACTIONr_angle_refined_deg1.3411.6514335
X-RAY DIFFRACTIONr_angle_other_deg0.4611.5736462
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.2975409
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.085514
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.29510461
X-RAY DIFFRACTIONr_dihedral_angle_6_deg17.75610156
X-RAY DIFFRACTIONr_chiral_restr0.0710.2448
X-RAY DIFFRACTIONr_gen_planes_refined0.0160.023894
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02750
X-RAY DIFFRACTIONr_nbd_refined0.2280.2600
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2080.22532
X-RAY DIFFRACTIONr_nbtor_refined0.1790.21487
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0840.21543
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1670.2145
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0610.21
X-RAY DIFFRACTIONr_metal_ion_refined0.1260.218
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3540.231
X-RAY DIFFRACTIONr_nbd_other0.320.263
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1490.28
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.1250.24
X-RAY DIFFRACTIONr_mcbond_it3.4092.461581
X-RAY DIFFRACTIONr_mcbond_other3.3262.4541579
X-RAY DIFFRACTIONr_mcangle_it4.324.3982007
X-RAY DIFFRACTIONr_mcangle_other4.3194.4012008
X-RAY DIFFRACTIONr_scbond_it4.9982.8221568
X-RAY DIFFRACTIONr_scbond_other4.9972.8231569
X-RAY DIFFRACTIONr_scangle_it7.1994.9692328
X-RAY DIFFRACTIONr_scangle_other7.1984.972329
X-RAY DIFFRACTIONr_lrange_it8.78428.7343509
X-RAY DIFFRACTIONr_lrange_other8.79128.7313485
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection all% reflection obs (%)WRfactor Rwork
1.62-1.6620.4211510.39228620.394301499.96680.384
1.662-1.7080.4131570.31927960.32429531000.309
1.708-1.7570.3481300.28427520.28728821000.266
1.757-1.8110.2951350.25926410.2627761000.237
1.811-1.870.2471310.22325540.22526851000.198
1.87-1.9360.2451420.18724910.1926331000.164
1.936-2.0090.2041080.16924180.17125261000.149
2.009-2.0910.2181180.17123450.17324631000.152
2.091-2.1830.2221240.16722110.1723351000.15
2.183-2.290.2081110.17221500.17422611000.154
2.29-2.4130.2251050.16220220.16521271000.145
2.413-2.5590.237910.17419470.17620381000.161
2.559-2.7350.234810.17718330.1819141000.167
2.735-2.9540.203790.17717120.17817911000.172
2.954-3.2340.209820.16615800.16816621000.168
3.234-3.6140.189800.16514290.16715091000.174
3.614-4.1690.182710.14112690.14313401000.16
4.169-5.0960.148620.1310910.13111531000.154
5.096-7.1660.173470.168690.1619161000.184
7.166-47.5420.195290.25220.19956397.86860.245

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