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- PDB-7nsn: Multi-domain GH92 alpha-1,2-mannosidase from Neobacillus novalis:... -

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Basic information

Entry
Database: PDB / ID: 7nsn
TitleMulti-domain GH92 alpha-1,2-mannosidase from Neobacillus novalis: mannoimidazole complex
ComponentsGH92 alpha-1,2-mannosidase
KeywordsHYDROLASE / glycans / alpha-mannosidase / glycoside hydrolase family 92 / carbohydrate-binding module family 32
Function / homologyChem-MVL
Function and homology information
Biological speciesNeobacillus novalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.29 Å
AuthorsKolaczkowski, B.M. / Moroz, O.V. / Blagova, E. / Davies, G.J. / Wilson, K.S. / Moeler, M.S. / Meyer, A.S. / Westh, P. / Jensen, K. / Krogh, K.B.R.M.
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2023
Title: Structural and functional characterization of a multi-domain GH92 alpha-1,2-mannosidase from Neobacillus novalis.
Authors: Kolaczkowski, B.M. / Moroz, O.V. / Blagova, E. / Davies, G.J. / Moller, M.S. / Meyer, A.S. / Westh, P. / Jensen, K. / Wilson, K.S. / Krogh, K.B.R.M.
History
DepositionMar 8, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 21, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.2Apr 10, 2024Group: Database references / Refinement description / Category: citation / citation_author / software
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GH92 alpha-1,2-mannosidase
B: GH92 alpha-1,2-mannosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)312,12616
Polymers310,6002
Non-polymers1,52614
Water10,106561
1
A: GH92 alpha-1,2-mannosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)156,1839
Polymers155,3001
Non-polymers8838
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: GH92 alpha-1,2-mannosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)155,9437
Polymers155,3001
Non-polymers6436
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)94.605, 151.937, 114.007
Angle α, β, γ (deg.)90.000, 94.630, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Ens-ID: 1 / End auth comp-ID: ARG / End label comp-ID: ARG

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LEULEUAA190 - 1410190 - 1410
22SERSERBB41 - 141041 - 1410

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

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Components

#1: Protein GH92 alpha-1,2-mannosidase


Mass: 155300.016 Da / Num. of mol.: 2
Fragment: The first CBM32 domain in subunit B is disordered and therefore residues B79 to B227 are missing from the model.
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neobacillus novalis (bacteria) / Production host: Bacillus subtilis (bacteria)
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-MVL / (5R,6R,7S,8R)-5-(HYDROXYMETHYL)-5,6,7,8-TETRAHYDROIMIDAZO[1,2-A]PYRIDINE-6,7,8-TRIOL / Mannoimidazole


Mass: 200.192 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H12N2O4
#4: Chemical ChemComp-B3P / 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL


Mass: 282.334 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H26N2O6 / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 561 / Source method: isolated from a natural source / Formula: H2O
Compound detailsThe first CBM32 domain in subunit B is disordered and therefore residues B79 to B227 are missing ...The first CBM32 domain in subunit B is disordered and therefore residues B79 to B227 are missing from the model.
Has ligand of interestN

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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: 2.63 Å3/Da / Density % sol: 53.22 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop
Details: 21% PEG 3350, 0.1 M bis-Tris-propane pH 6.6, 0.2M sodium citrate, MMS

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91587 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 28, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91587 Å / Relative weight: 1
ReflectionResolution: 2.29→47.923 Å / Num. obs: 141182 / % possible obs: 98.1 % / Redundancy: 2.9 % / CC1/2: 0.981 / Rmerge(I) obs: 0.132 / Rpim(I) all: 0.131 / Rrim(I) all: 0.186 / Net I/σ(I): 5.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
12.54-47.923.20.04615.58650.9930.0460.06493.9
2.29-2.3330.7771.171090.5050.7631.0999.5

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Processing

Software
NameVersionClassification
XDSdata reduction
XDSdata scaling
xia2data reduction
xia2data scaling
Aimlessdata scaling
MOLREPphasing
REFMAC5.8.0267refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2wzs

2wzs


Resolution: 2.29→47.923 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.917 / SU B: 10.034 / SU ML: 0.216 / Cross valid method: THROUGHOUT / ESU R: 0.307 / ESU R Free: 0.227 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rfree0.2458 6947 4.922 %
Rwork0.2053 134197 -
all0.207 --
obs-141144 97.987 %
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: 32.923 Å2
Baniso -1Baniso -2Baniso -3
1-1.719 Å20 Å2-4.093 Å2
2---0.854 Å2-0 Å2
3----0.199 Å2
Refinement stepCycle: LAST / Resolution: 2.29→47.923 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20140 0 89 561 20790
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01220765
X-RAY DIFFRACTIONr_angle_refined_deg1.5331.63928114
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.25452592
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.22224.061037
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.452153311
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6921571
X-RAY DIFFRACTIONr_chiral_restr0.1130.22710
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0215987
X-RAY DIFFRACTIONr_nbd_refined0.2160.29007
X-RAY DIFFRACTIONr_nbtor_refined0.3120.213994
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.130.2943
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1610.243
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2030.210
X-RAY DIFFRACTIONr_mcbond_it2.9273.24310407
X-RAY DIFFRACTIONr_mcangle_it4.3444.85312966
X-RAY DIFFRACTIONr_scbond_it3.5483.34510358
X-RAY DIFFRACTIONr_scangle_it5.1394.92115148
X-RAY DIFFRACTIONr_lrange_it9.70142.29630873
X-RAY DIFFRACTIONr_ncsr_local_group_10.0690.0540258
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.068990.05012
12BX-RAY DIFFRACTIONLocal ncs0.068990.05012
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 allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.29-2.3490.3535060.332100200.333105970.5360.56299.330.328
2.349-2.4140.3354790.31597480.316103170.6620.6899.12770.308
2.414-2.4830.3314940.30494920.305100810.7120.72899.05760.296
2.483-2.560.3514570.28291910.28597570.7460.77598.88290.271
2.56-2.6430.3275020.28687750.28894730.7650.78197.9310.272
2.643-2.7360.2964180.26184770.26391320.8180.83497.40470.247
2.736-2.8390.2874250.25682780.25888530.8440.84898.30570.24
2.839-2.9540.3133760.24780710.2585510.8360.86198.78380.233
2.954-3.0850.2784080.22976360.23281530.8710.88998.66310.216
3.085-3.2350.2463620.21173140.21278000.9080.9298.41030.2
3.235-3.4090.2733050.20969060.21273990.8950.92797.45910.201
3.409-3.6150.2383040.19864950.19970640.9280.94196.24860.193
3.615-3.8630.2383440.17961190.18366070.9350.95197.82050.176
3.863-4.170.1853200.14357350.14561850.9590.96997.89810.142
4.17-4.5640.1632960.12552410.12756860.9670.97497.37950.127
4.564-5.0970.1622560.11546830.11851400.970.97896.08950.117
5.097-5.8750.1952480.14241390.14545660.9580.96996.07970.142
5.875-7.1680.2031970.16835630.1738820.9580.96796.85730.168
7.168-10.0260.1851570.14227340.14530180.9670.97695.79190.15
10.026-47.9230.164930.16215810.16217680.9720.9794.68330.174

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