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- PDB-3juu: Crystal structure of porphyranase B (PorB) from Zobellia galactan... -

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Basic information

Entry
Database: PDB / ID: 3juu
TitleCrystal structure of porphyranase B (PorB) from Zobellia galactanivorans
Componentsporphyranase B
KeywordsHYDROLASE/CARBOHYDRATE / GLYCOSIDE HYDROLASE FAMILY GH16 / BETA-SANDWICH FOLD / JELLY ROLL / SUGAR BINDING PROTEIN / HYDROLASE-CARBOHYDRATE COMPLEX
Function / homology
Function and homology information


beta-porphyranase / hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate metabolic process / periplasmic space
Similarity search - Function
Glycosyl hydrolases family 16 / Glycoside hydrolase family 16 / Glycosyl hydrolases family 16 (GH16) domain profile. / Jelly Rolls - #200 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesZobellia galactanivorans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsHehemann, J.H. / Correc, G. / Barbeyron, T. / Michel, G. / Czjzek, M.
CitationJournal: Nature / Year: 2010
Title: Transfer of carbohydrate-active enzymes from marine bacteria to Japanese gut microbiota.
Authors: Hehemann, J.H. / Correc, G. / Barbeyron, T. / Helbert, W. / Czjzek, M. / Michel, G.
History
DepositionSep 15, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 7, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 27, 2013Group: Database references
Revision 1.3Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 9, 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

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Assembly

Deposited unit
A: porphyranase B
B: porphyranase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,09116
Polymers64,5642
Non-polymers1,52714
Water7,945441
1
A: porphyranase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,0468
Polymers32,2821
Non-polymers7647
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: porphyranase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,0468
Polymers32,2821
Non-polymers7647
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)86.131, 120.892, 67.919
Angle α, β, γ (deg.)90.00, 101.50, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein porphyranase B


Mass: 32281.943 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zobellia galactanivorans (bacteria) / Gene: ZG1017 / Plasmid: pFO4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: D7GXF9*PLUS
#2: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 441 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsA SEQUENCE DATABASE REFERENCE FOR THIS PROTEIN DOES NOT CURRENTLY EXIST.

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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: 2.68 Å3/Da / Density % sol: 54.16 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 33-35% PEG 1000, 0.4M Lithiumsulfate, 0.1M Mes pH 6.0, 10% Glycero, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Feb 4, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.8→69.2 Å / Num. all: 62925 / Num. obs: 62907 / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.7 % / Rmerge(I) obs: 0.089 / Net I/σ(I): 11
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.395 / Mean I/σ(I) obs: 3.7 / Num. unique all: 9191 / % possible all: 100

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Processing

Software
NameVersionClassification
MxCuBEdata collection
PHASER(CCP4)phasing
REFMAC5.5.0072refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ILF

3ilf


Resolution: 1.8→44.7 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.935 / SU B: 1.948 / SU ML: 0.062 / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R: 0.101 / ESU R Free: 0.104 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19856 3192 5.1 %RANDOM
Rwork0.15717 ---
all0.15965 62907 --
obs0.15924 59714 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.439 Å2
Baniso -1Baniso -2Baniso -3
1-0.35 Å20 Å2-0.05 Å2
2---0.51 Å20 Å2
3---0.14 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.104 Å0.101 Å
Refinement stepCycle: LAST / Resolution: 1.8→44.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4340 0 88 441 4869
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.0224555
X-RAY DIFFRACTIONr_angle_refined_deg2.2171.9526152
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8165539
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.34625.088226
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.44815786
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.8681518
X-RAY DIFFRACTIONr_chiral_restr0.1990.2603
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0213472
X-RAY DIFFRACTIONr_mcbond_it1.3581.52661
X-RAY DIFFRACTIONr_mcangle_it2.29224290
X-RAY DIFFRACTIONr_scbond_it3.58931894
X-RAY DIFFRACTIONr_scangle_it5.6034.51860
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.267 247 -
Rwork0.221 4376 -
obs--100 %

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