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- PDB-8gul: Chitin-active AA10 LPMO (GbpA) complexed with Cu(II) from Vibrio ... -

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Basic information

Entry
Database: PDB / ID: 8gul
TitleChitin-active AA10 LPMO (GbpA) complexed with Cu(II) from Vibrio campbellii
ComponentsGlcNAc-binding protein A
KeywordsMETAL BINDING PROTEIN / LPMO / Chitin degradation / Cu(II)-dependent enzyme.
Function / homology
Function and homology information


chitin binding / extracellular region
Similarity search - Function
Immunoglobulin-like - #2550 / Alpha-Beta Plaits - #2150 / N-acetylglucosamine-binding protein A / : / GlcNAc-binding protein A, third domain / N-acetylglucosamine binding protein A domain 2 / N-acetylglucosamine binding protein domain 2 / chitin-binding protein cbp21 / : / Cellulose/chitin-binding protein, N-terminal ...Immunoglobulin-like - #2550 / Alpha-Beta Plaits - #2150 / N-acetylglucosamine-binding protein A / : / GlcNAc-binding protein A, third domain / N-acetylglucosamine binding protein A domain 2 / N-acetylglucosamine binding protein domain 2 / chitin-binding protein cbp21 / : / Cellulose/chitin-binding protein, N-terminal / Lytic polysaccharide mono-oxygenase, cellulose-degrading / Coagulation Factor XIII; Chain A, domain 1 / Distorted Sandwich / Immunoglobulin E-set / Alpha-Beta Plaits / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
COPPER (II) ION / GlcNAc-binding protein A
Similarity search - Component
Biological speciesVibrio campbellii ATCC BAA-1116 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.44 Å
AuthorsZhou, Y. / Robinson, R.C. / Suginta, W.
Funding support Thailand, 1items
OrganizationGrant numberCountry
Vidyasirimedhi Institute of Science and Technology (VISTEC) Thailand
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2023
Title: Structural and binding studies of a new chitin-active AA10 lytic polysaccharide monooxygenase from the marine bacterium Vibrio campbellii.
Authors: Zhou, Y. / Wannapaiboon, S. / Prongjit, M. / Pornsuwan, S. / Sucharitakul, J. / Kamonsutthipaijit, N. / Robinson, R.C. / Suginta, W.
History
DepositionSep 12, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 21, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)102,5895
Polymers102,3662
Non-polymers2233
Water3,765209
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry, Apo-LPMO titrated with CuSO4 solution by ITC
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6950 Å2
ΔGint-37 kcal/mol
Surface area35250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.433, 113.433, 213.761
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 289 through 291 or resid 321 through 390))
d_2ens_1(chain "B" and resid 289 through 390)

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ILEILESERSERAA289 - 291289 - 291
d_12GLUGLULEULEUAA321 - 390321 - 390
d_21ILEILELEULEUBB289 - 390289 - 390

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Components

#1: Protein GlcNAc-binding protein A


Mass: 51182.844 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio campbellii ATCC BAA-1116 (bacteria)
Strain: ATCC BAA-1116 / Gene: gbpA, VIBHAR_04739 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A7N3J0
#2: 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
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 209 / 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: 3.36 Å3/Da / Density meas: 0.012 Mg/m3 / Density % sol: 66.64 %
Crystal growTemperature: 292.15 K / Method: vapor diffusion, sitting drop / Details: 1.0M Ammonium sulfate, 0.1M ADA buffer, pH 7.0 / PH range: 6.5-7.5 / Temp details: Incubater

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: Cold nitrogen gas stream / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 0.99984 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Jun 21, 2022
RadiationMonochromator: Cu filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99984 Å / Relative weight: 1
ReflectionResolution: 2.44→30 Å / Num. obs: 52161 / % possible obs: 99 % / Redundancy: 26.2 % / Biso Wilson estimate: 52.35 Å2 / Rmerge(I) obs: 0.125 / Rpim(I) all: 0.024 / Rrim(I) all: 0.127 / Net I/σ(I): 29.1
Reflection shellResolution: 2.44→2.48 Å / Rmerge(I) obs: 1.19 / Mean I/σ(I) obs: 0.72 / Num. unique obs: 2166 / CC1/2: 0.454 / Rpim(I) all: 0.518 / Rrim(I) all: 1.31 / % possible all: 84.1

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
Blu-Icedata collection
HKL-2000data scaling
PHENIXv 1.19.2model building
PHENIXphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Alphafold2

Resolution: 2.44→29.78 Å / SU ML: 0.3364 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.7911
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2397 2598 4.99 %
Rwork0.2045 49444 -
obs0.2063 52042 99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 73.82 Å2
Refinement stepCycle: LAST / Resolution: 2.44→29.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6408 0 7 209 6624
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00196570
X-RAY DIFFRACTIONf_angle_d0.47068957
X-RAY DIFFRACTIONf_chiral_restr0.0423958
X-RAY DIFFRACTIONf_plane_restr0.00391200
X-RAY DIFFRACTIONf_dihedral_angle_d11.13222356
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.312887558753 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.44-2.490.39531320.34732140X-RAY DIFFRACTION83.78
2.49-2.530.2971480.29182511X-RAY DIFFRACTION97.69
2.53-2.590.33971350.26722580X-RAY DIFFRACTION99.31
2.59-2.640.32211430.25972585X-RAY DIFFRACTION99.93
2.64-2.70.27271410.23862573X-RAY DIFFRACTION100
2.7-2.770.29011560.24672555X-RAY DIFFRACTION100
2.77-2.840.28461320.24772606X-RAY DIFFRACTION100
2.85-2.930.3011040.25082612X-RAY DIFFRACTION100
2.93-3.020.24331390.24692602X-RAY DIFFRACTION100
3.02-3.130.29091270.23642626X-RAY DIFFRACTION100
3.13-3.260.29471200.22952626X-RAY DIFFRACTION100
3.26-3.40.23721380.22172600X-RAY DIFFRACTION100
3.4-3.580.27661290.21322633X-RAY DIFFRACTION100
3.58-3.810.24251400.19492637X-RAY DIFFRACTION100
3.81-4.10.25081450.18822649X-RAY DIFFRACTION100
4.1-4.510.18141380.16482644X-RAY DIFFRACTION100
4.51-5.160.18961320.15832688X-RAY DIFFRACTION100
5.16-6.490.19521400.18282726X-RAY DIFFRACTION99.97
6.49-29.780.21741590.19252851X-RAY DIFFRACTION99.9
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.99398079776-0.430271135758-0.185283328161.85870157197-0.04139466871692.137648887160.05880281691330.356806397398-0.658207363947-0.089784766623-0.1924804677320.2447688970140.0934772474006-0.188037452655-0.03906011573760.179954166777-0.0200255912887-0.006027669399220.900923233033-0.359334520490.62107365655221.105849298219.73636173-40.4261526843
24.149767619270.62114569987-0.699207484166-0.0755284738711-0.2576852318530.487479184653-0.1634489463850.528313502745-0.8903888397130.002802955561920.0241973664778-0.1032169745220.0930451576408-0.118303404967-0.01157865193940.373496770697-0.007685983830470.04210441604690.839504391966-0.3063141689410.763733111777-3.9199629852716.6520971398-32.2046389419
33.842663489631.858027426191.992329097122.769590519533.873319933624.664484726580.361796153056-0.218513017574-0.1797639356450.8735015238120.286354928541-0.5969923144120.1700187839760.1390929932380.002876619394660.5853013114660.05795042046-0.1441095358420.797381538728-0.1763526246010.5876736351496.6374267594747.8654067517-7.68405116001
40.983731873062-0.920029299490.3145444721130.9128128781470.2590263076170.6087510144120.04267495112890.957132723849-0.101350668777-1.03251161668-0.07805853018960.369423118365-0.377825673576-0.2599724934648.70014751263E-51.6733369143-0.08539609098450.04802492497890.780084433496-0.06348044810250.62805318916524.26443374186.3698197571-9.62210276703
51.879650443080.5974442137830.7513176230192.78608814521.437763277592.01783625856-0.2214199195360.4426017482180.103073523792-0.5219266684940.1627773697180.00263015935598-0.414036655597-0.04186844404170.0001414956234770.370282081764-0.0157325464712-0.02147481757280.807924830457-0.07827310954080.402521033641-5.2677751258842.9608139943-33.1265824713
64.89311855796-0.8849074988950.3926888735450.00183594075518-0.09627751524220.290612152704-0.1368583872-0.07738636752990.6418226985010.001279125895310.141196930275-0.181783007162-0.0790356716429-0.0779308867336-0.003175726223020.3425958508330.0316286356185-0.007587990880.883452086537-0.2279067324710.61592403030219.857485184542.9039300858-26.5031445667
70.05605315852350.629628396157-0.3935799455630.751813364605-0.5377094892270.4482256630890.4357781034-0.418608787936-0.7998252463010.733121272403-0.193617615885-0.4789328165710.605066279174-0.3826860835077.45682453754E-51.10585786414-0.158610591284-0.05574894111861.610534717860.007851334478371.4825341536211.78452334135.20967498013-21.2252334169
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 163 )AA1 - 1631 - 163
22chain 'A' and (resid 164 through 296 )AA164 - 296164 - 296
33chain 'A' and (resid 297 through 391 )AA297 - 391297 - 391
44chain 'A' and (resid 392 through 464 )AA392 - 464392 - 464
55chain 'B' and (resid 1 through 163 )BB1 - 1631 - 163
66chain 'B' and (resid 164 through 288 )BB164 - 288164 - 288
77chain 'B' and (resid 289 through 390 )BB289 - 390289 - 361

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