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- PDB-7qsj: Methylmannose polysaccharide hydrolase MmpH from M. hassiacum -

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Basic information

Entry
Database: PDB / ID: 7qsj
TitleMethylmannose polysaccharide hydrolase MmpH from M. hassiacum
ComponentsMethylmannose polysaccharide hydrolase (MmpH)
KeywordsHYDROLASE / Methylmannose polysaccharide / Mycobacterium hassiacum / endomannosidase
Function / homologySix-hairpin glycosidase-like superfamily / Six-hairpin glycosidase superfamily / carbohydrate metabolic process / NICKEL (II) ION / Prenyltransferase
Function and homology information
Biological speciesMycolicibacterium hassiacum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.35 Å
AuthorsRipoll-Rozada, J. / Manso, J.A. / Pereira, P.J.B.
Funding support Portugal, 1items
OrganizationGrant numberCountry
Fundacao para a Ciencia e a TecnologiaPTDC/BTM-TEC/29221/2017 Portugal
CitationJournal: Commun Biol / Year: 2023
Title: Self-recycling and partially conservative replication of mycobacterial methylmannose polysaccharides.
Authors: Maranha, A. / Costa, M. / Ripoll-Rozada, J. / Manso, J.A. / Miranda, V. / Mendes, V.M. / Manadas, B. / Macedo-Ribeiro, S. / Ventura, M.R. / Pereira, P.J.B. / Empadinhas, N.
History
DepositionJan 13, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 25, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 8, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _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
Revision 1.2Jun 19, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Methylmannose polysaccharide hydrolase (MmpH)
B: Methylmannose polysaccharide hydrolase (MmpH)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,17511
Polymers82,4802
Non-polymers6949
Water12,268681
1
A: Methylmannose polysaccharide hydrolase (MmpH)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,4154
Polymers41,2401
Non-polymers1753
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Methylmannose polysaccharide hydrolase (MmpH)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,7597
Polymers41,2401
Non-polymers5196
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.037, 51.807, 149.134
Angle α, β, γ (deg.)90.000, 95.100, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Methylmannose polysaccharide hydrolase (MmpH)


Mass: 41240.234 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycolicibacterium hassiacum (bacteria) / Strain: DSM 44199 / CIP 105218 / JCM 12690 / 3849 / Gene: MHAS_04404 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A3P4A4D3
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 681 / Source method: isolated from a natural source / Formula: H2O
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: 2.2 Å3/Da / Density % sol: 44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1 M Tris-HCl pH 8.5, 0.02 M MgCl2, 21% (w/v) polyacrylic acid

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.9809 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 29, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9809 Å / Relative weight: 1
ReflectionResolution: 1.35→49.51 Å / Num. obs: 156986 / % possible obs: 99.89 % / Redundancy: 2 % / Biso Wilson estimate: 16.27 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.0237 / Rpim(I) all: 0.0237 / Rrim(I) all: 0.03352 / Net I/σ(I): 16.42
Reflection shellResolution: 1.35→1.398 Å / Rmerge(I) obs: 0.6802 / Mean I/σ(I) obs: 1.17 / Num. unique obs: 15681 / CC1/2: 0.537 / Rpim(I) all: 0.6802 / Rrim(I) all: 0.9619

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Processing

Software
NameVersionClassification
PHENIX1.20_4459refinement
SCALAdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 1.35→49.51 Å / SU ML: 0.1824 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.5689
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1768 7714 4.92 %
Rwork0.1423 149209 -
obs0.144 156923 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.44 Å2
Refinement stepCycle: LAST / Resolution: 1.35→49.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5363 0 39 681 6083
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00465691
X-RAY DIFFRACTIONf_angle_d0.72577792
X-RAY DIFFRACTIONf_chiral_restr0.0741819
X-RAY DIFFRACTIONf_plane_restr0.00841035
X-RAY DIFFRACTIONf_dihedral_angle_d11.96942023
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.35-1.370.38932650.35044945X-RAY DIFFRACTION99.81
1.37-1.380.34162630.31494921X-RAY DIFFRACTION99.79
1.38-1.40.33432610.29765006X-RAY DIFFRACTION99.92
1.4-1.420.3492630.26534848X-RAY DIFFRACTION99.84
1.42-1.430.28532530.25044992X-RAY DIFFRACTION99.94
1.43-1.450.26812650.2164916X-RAY DIFFRACTION100
1.45-1.480.23472390.19565000X-RAY DIFFRACTION99.98
1.48-1.50.28022500.21254901X-RAY DIFFRACTION99.79
1.5-1.520.27492450.2185048X-RAY DIFFRACTION99.74
1.52-1.550.17332520.15944822X-RAY DIFFRACTION99.94
1.55-1.570.2422760.18924997X-RAY DIFFRACTION99.89
1.57-1.60.18482520.14974931X-RAY DIFFRACTION100
1.6-1.630.20472500.13875003X-RAY DIFFRACTION99.94
1.63-1.660.17432610.13564940X-RAY DIFFRACTION99.87
1.66-1.70.19282540.13544962X-RAY DIFFRACTION99.92
1.7-1.740.17422440.13674982X-RAY DIFFRACTION99.94
1.74-1.780.18172650.14284942X-RAY DIFFRACTION99.96
1.78-1.830.18242640.13624955X-RAY DIFFRACTION99.9
1.83-1.890.18062770.12834973X-RAY DIFFRACTION100
1.89-1.950.17462760.11854946X-RAY DIFFRACTION99.98
1.95-2.020.15622440.11914948X-RAY DIFFRACTION100
2.02-2.10.16752640.12714968X-RAY DIFFRACTION99.98
2.1-2.190.17072770.12675022X-RAY DIFFRACTION100
2.19-2.310.16922580.12154938X-RAY DIFFRACTION99.96
2.31-2.450.16622590.12715027X-RAY DIFFRACTION99.92
2.45-2.640.17462460.13464995X-RAY DIFFRACTION99.75
2.64-2.910.15982410.1375041X-RAY DIFFRACTION99.89
2.91-3.330.16942550.13245007X-RAY DIFFRACTION99.58
3.33-4.190.12912420.1225049X-RAY DIFFRACTION99.92
4.19-49.510.16012530.14085184X-RAY DIFFRACTION99.63

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