[English] 日本語
Yorodumi
- PDB-8gum: Chitin-active AA10 LPMO (GbpA) from Vibrio campbellii -

+
Open data


ID or keywords:

Loading...

-
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 / homologyN-acetylglucosamine-binding protein A / 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 / chitin binding / Immunoglobulin E-set / extracellular region / GlcNAc-binding protein A
Function and homology information
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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 / Water


Mass: 18.015 Da / Num. of mol.: 112 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more