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- PDB-8cc3: Vibrio cholerae GbpA (LPMO domain) -

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Basic information

Entry
Database: PDB / ID: 8cc3
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: 1.128 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)40,36814
Polymers39,6422
Non-polymers72612
Water4,540252
1
A: GlcNAc-binding protein A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,2648
Polymers19,8211
Non-polymers4437
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)74.911, 89.103, 47.135
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
11A-305-

ZN

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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, 264 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.: 7 / 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.: 252 / 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: 1.98 Å3/Da / Density % sol: 38.01 %
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: 0.97626 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 11, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97626 Å / Relative weight: 1
ReflectionResolution: 1.128→47.14 Å / Num. obs: 221328 / % possible obs: 98.74 % / Redundancy: 2.2 % / CC1/2: 0.995 / Net I/σ(I): 6.13
Reflection shellResolution: 1.13→1.17 Å / Num. unique obs: 11391 / CC1/2: 0.219

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Processing

Software
NameVersionClassification
REFMAC5.8.0403refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.128→47.135 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.961 / WRfactor Rfree: 0.206 / WRfactor Rwork: 0.176 / SU B: 1.332 / SU ML: 0.028 / Average fsc free: 0 / Average fsc work: 0 / Cross valid method: FREE R-VALUE / ESU R: 0.042 / ESU R Free: 0.041
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2007 5893 5.017 %
Rwork0.1735 111562 -
all0.175 --
obs-117455 98.558 %
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: 11.934 Å2
Baniso -1Baniso -2Baniso -3
1--1.256 Å20 Å20 Å2
2---1.578 Å20 Å2
3---2.834 Å2
Refinement stepCycle: LAST / Resolution: 1.128→47.135 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2798 0 18 252 3068
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0123386
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163005
X-RAY DIFFRACTIONr_angle_refined_deg1.5041.6514674
X-RAY DIFFRACTIONr_angle_other_deg0.5081.5756963
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.695447
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.286517
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.2710500
X-RAY DIFFRACTIONr_dihedral_angle_6_deg17.03810170
X-RAY DIFFRACTIONr_chiral_restr0.0750.2474
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.024264
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02816
X-RAY DIFFRACTIONr_nbd_refined0.220.2679
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2130.22814
X-RAY DIFFRACTIONr_nbtor_refined0.1830.21544
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0880.21613
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1690.2206
X-RAY DIFFRACTIONr_metal_ion_refined0.0860.218
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.4320.252
X-RAY DIFFRACTIONr_nbd_other0.2420.2116
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2960.223
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0520.22
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.0750.27
X-RAY DIFFRACTIONr_mcbond_it1.1051.1641703
X-RAY DIFFRACTIONr_mcbond_other1.071.1621700
X-RAY DIFFRACTIONr_mcangle_it1.4712.0912177
X-RAY DIFFRACTIONr_mcangle_other1.4712.0932178
X-RAY DIFFRACTIONr_scbond_it1.2771.3051683
X-RAY DIFFRACTIONr_scbond_other1.2761.3051684
X-RAY DIFFRACTIONr_scangle_it1.692.3262497
X-RAY DIFFRACTIONr_scangle_other1.6892.3262498
X-RAY DIFFRACTIONr_lrange_it2.3714.3733836
X-RAY DIFFRACTIONr_lrange_other2.26713.8213790
X-RAY DIFFRACTIONr_rigid_bond_restr5.63936391
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
1.128-1.1570.2834140.27976380.279873892.14920.254
1.157-1.1890.2884070.25378930.255849597.70450.224
1.189-1.2240.2623800.23976970.24824397.98620.211
1.224-1.2610.2554200.22274480.224802598.04360.194
1.261-1.3030.2494090.20872970.21780898.69360.18
1.303-1.3480.2123850.18870920.189756598.83670.161
1.348-1.3990.2183620.18468240.185727398.80380.158
1.399-1.4560.23810.16465780.166701799.17340.144
1.456-1.5210.2043520.1663630.162674799.52570.141
1.521-1.5950.1753110.1661100.161645699.45790.145
1.595-1.6810.1933130.15458220.156615899.62650.144
1.681-1.7830.1992780.15255210.154581799.69060.147
1.783-1.9060.1922670.15652070.158549899.56350.158
1.906-2.0580.1842360.15548880.156513499.80520.163
2.058-2.2540.1712200.15244990.153472099.97880.169
2.254-2.520.1832140.16440890.16543031000.191
2.52-2.9080.2161870.17536100.177381899.450.207
2.908-3.5580.1791580.16631130.16732711000.201
3.558-5.0180.1561320.14424360.145257199.88330.185
5.018-47.1350.244670.21114370.213151699.20840.27

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