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- PDB-8gum: Chitin-active AA10 LPMO (GbpA) from Vibrio campbellii -

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Basic information

Entry
Database: PDB / ID: 8gum
TitleChitin-active AA10 LPMO (GbpA) 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
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
GlcNAc-binding protein A
Similarity search - Component
Biological speciesVibrio campbellii ATCC BAA-1116 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 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 1.1Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Item: _pdbx_initial_refinement_model.accession_code / _pdbx_initial_refinement_model.source_name / _pdbx_initial_refinement_model.type
Revision 1.2Nov 6, 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)102,3662
Polymers102,3662
Non-polymers00
Water2,018112
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6440 Å2
ΔGint-4 kcal/mol
Surface area35270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.612, 113.612, 215.750
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

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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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 112 / 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: 3.4 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 phosphate dibasic; 0.1M ADA buffer, pH 6.5
PH range: 6.0-6.9 / Temp details: Incubator

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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: 0.99764 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Apr 23, 2021
RadiationMonochromator: Cu filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99764 Å / Relative weight: 1
ReflectionResolution: 2.35→30 Å / Num. obs: 59698 / % possible obs: 99.9 % / Redundancy: 14.3 % / Biso Wilson estimate: 59.21 Å2 / Rmerge(I) obs: 0.092 / Rpim(I) all: 0.025 / Rrim(I) all: 0.096 / Net I/σ(I): 28
Reflection shellResolution: 2.35→2.39 Å / Redundancy: 10 % / Rmerge(I) obs: 1.595 / Mean I/σ(I) obs: 0.8 / Num. unique obs: 2937 / CC1/2: 0.586 / Rpim(I) all: 0.514 / Rrim(I) all: 1.68 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
Blu-Icedata collection
HKL-2000data scaling
PHENIXv 1.192model building
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2xwx

2xwx


Resolution: 2.35→25.1 Å / SU ML: 0.3645 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.0038
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.262 2918 4.92 %
Rwork0.2199 56359 -
obs0.222 59277 99.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 90.35 Å2
Refinement stepCycle: LAST / Resolution: 2.35→25.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6402 0 0 112 6514
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00896560
X-RAY DIFFRACTIONf_angle_d0.99478943
X-RAY DIFFRACTIONf_chiral_restr0.0569957
X-RAY DIFFRACTIONf_plane_restr0.00711199
X-RAY DIFFRACTIONf_dihedral_angle_d14.98562354
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.35-2.390.43241310.35722462X-RAY DIFFRACTION93.58
2.39-2.430.31471220.30752666X-RAY DIFFRACTION99.57
2.43-2.470.30971390.27412628X-RAY DIFFRACTION99.75
2.47-2.520.25591220.26472668X-RAY DIFFRACTION99.93
2.52-2.570.28661090.28772666X-RAY DIFFRACTION99.93
2.57-2.630.31731340.28722661X-RAY DIFFRACTION100
2.63-2.690.29541290.2932677X-RAY DIFFRACTION99.96
2.69-2.760.36541450.29592652X-RAY DIFFRACTION100
2.76-2.830.381370.2912660X-RAY DIFFRACTION100
2.83-2.910.33091330.28572678X-RAY DIFFRACTION100
2.91-3.010.33151340.28642662X-RAY DIFFRACTION99.89
3.01-3.120.32271430.29672668X-RAY DIFFRACTION100
3.12-3.240.33261350.28062699X-RAY DIFFRACTION100
3.24-3.390.28021370.24942678X-RAY DIFFRACTION100
3.39-3.570.27851420.23772692X-RAY DIFFRACTION100
3.57-3.790.28011490.22912712X-RAY DIFFRACTION100
3.79-4.080.29581620.20942678X-RAY DIFFRACTION100
4.08-4.490.23431520.18132712X-RAY DIFFRACTION100
4.49-5.130.20841520.16172744X-RAY DIFFRACTION100
5.13-6.450.2441700.18522762X-RAY DIFFRACTION99.97
6.45-25.10.17811410.17732934X-RAY DIFFRACTION99.71
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)
13.62665470827-0.0122957468317-0.09481141528741.741368155440.2031071374251.228974409450.05738877020080.278261599504-0.659047406311-0.0622226989504-0.3892521893250.4222325194210.135744792394-0.360991508277-0.05929836103330.06829602943060.01417679221270.09262463957111.413077637-0.6021046341760.86112893319221.028965104519.7144402898-40.5011026967
23.897172354560.588006269641-0.5205478739580.0722674977122-0.1961194105320.228036075681-0.2647803655160.590062324152-1.12063718038-0.02196204840090.0202558037496-0.04396396631310.0761705928227-0.0864617974419-0.04453320232770.435772729123-0.04260122779460.07790954851731.17314243784-0.4877792658370.997884921302-3.9870419128916.6846051019-32.4605428809
34.375965568790.8788195132881.097407262222.258896485063.134630952344.334655834680.355545786393-0.290366323046-0.1788194541730.9228048158960.28061657041-0.6849062513080.176202993970.09191785136120.002013544773340.6404468305060.0800649940913-0.1792788706441.02112544966-0.2370656645810.6957284997736.5309976294547.7305031088-7.72379318503
40.990126923123-0.2654486731380.4641136053750.6908899162680.2716495724560.467307159492-0.09114338443811.04500647678-0.341314720174-1.1743536073-0.01849033484240.467388371761-0.407447066897-0.308578999242-0.002627546359041.83873135659-0.212575355190.07885630309670.89466055782-0.04814035346210.76467841918124.272152026486.2562888602-9.42214941209
52.837718423081.316225282960.4389157500073.356666550641.53369709381.99491365963-0.4622909193240.7953334967710.0844781311666-0.6996600749250.403663619957-0.0746570020178-0.454178799855-0.08250532238770.0003694773483070.514371028242-0.0631589563557-0.02628159470951.0988439948-0.1192666655880.436084697777-5.2173917835642.8927297008-33.3610273468
63.89051054208-0.9946606196330.08489760845630.2556388177810.05295968034060.280064608227-0.286826027961-0.1648936643790.493407454406-0.01404467290390.335020839693-0.305047528501-0.0137868043884-0.0127651001372-0.004597784405870.4357250766210.0432727886191-0.01509252046751.20737308795-0.2951066607170.73956891146118.423698011941.3575561711-25.8182844693
72.73979158036-0.1615580815870.5288259264431.272258574911.191363368232.359031822330.0634859921683-0.3588028112750.575859635192-0.0918163526118-0.1783632345070.129154769456-0.219765041694-0.369173571396-0.02326369177830.2913924423110.160599169652-0.01148484901151.29948100639-0.4111558419410.89146169985722.617368991641.9094758498-26.1490366589
80.1394816941160.1327256852070.02414389147440.500598829927-0.3586839683870.3886608392340.192310889981-0.232056183683-0.4506381720380.0824529373281-0.440019968193-0.496875914079-0.0169957526308-1.066062057130.0002700445292041.08710872727-0.1936489718320.008008618564691.68052693801-0.06915084966111.5818658682110.51929671044.19138714372-22.1768049069
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 248 )BB164 - 248164 - 248
77chain 'B' and (resid 249 through 325 )BB249 - 325249 - 295
88chain 'B' and (resid 326 through 390 )BB326 - 390296 - 360

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