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- PDB-3hft: Crystal structure of a putative polysaccharide deacetylase involv... -

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Basic information

Entry
Database: PDB / ID: 3hft
TitleCrystal structure of a putative polysaccharide deacetylase involved in o-antigen biosynthesis (wbms, bb0128) from bordetella bronchiseptica at 1.90 A resolution
ComponentsWbmS, polysaccharide deacetylase involved in O-antigen biosynthesis
KeywordsHYDROLASE / Structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


: / Polysaccharide deacetylase / Glycoside hydrolase/deacetylase / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Unknown ligand / NodB homology domain-containing protein / Uncharacterized protein
Similarity search - Component
Biological speciesBordetella bronchiseptica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å
AuthorsJoint Center for Structural Genomics / Joint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of WbmS, polysaccharide deacetylase involved in O-antigen biosynthesis (NP_886680.1) from BORDETELLA BRONCHISEPTICA at 1.90 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionMay 12, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 23, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Feb 1, 2023Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 27, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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: WbmS, polysaccharide deacetylase involved in O-antigen biosynthesis
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6759
Polymers30,1811
Non-polymers4948
Water2,810156
1
A: WbmS, polysaccharide deacetylase involved in O-antigen biosynthesis
hetero molecules

A: WbmS, polysaccharide deacetylase involved in O-antigen biosynthesis
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,35018
Polymers60,3622
Non-polymers98816
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area5600 Å2
ΔGint-93 kcal/mol
Surface area18980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.724, 74.724, 142.692
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

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Protein , 1 types, 1 molecules A

#1: Protein WbmS, polysaccharide deacetylase involved in O-antigen biosynthesis


Mass: 30181.121 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bordetella bronchiseptica (bacteria) / Gene: BB0128, NP_886680.1, wbmS / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q7WR29, UniProt: A0A0H3LGE5*PLUS

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Non-polymers , 5 types, 164 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 1 / Source method: obtained synthetically
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 156 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Sequence detailsTHE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.

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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: 3.3 Å3/Da / Density % sol: 62.73 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 20.0000% MPD, 0.1M HEPES pH 7.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.91162,0.97985,0.97968
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Dec 7, 2008 / Details: Flat collimating mirror, toroid focusing mirror
RadiationMonochromator: Double crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.911621
20.979851
30.979681
ReflectionResolution: 1.9→29.566 Å / Num. obs: 32707 / % possible obs: 100 % / Redundancy: 7.2 % / Biso Wilson estimate: 29.568 Å2 / Rmerge(I) obs: 0.085 / Rrim(I) all: 0.091 / Rsym value: 0.085 / Net I/av σ(I): 5.93 / Net I/σ(I): 15.5 / Num. measured all: 236428
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRrim(I) allRsym valueNet I/σ(I) obs% possible all
1.9-1.957.30.9022.11736923650.9710.9022.1100
1.95-27.30.6992.71684623000.7530.6992.7100
2-2.067.30.513.81651422550.5490.513.8100
2.06-2.127.30.3884.91603221920.4180.3884.9100
2.12-2.197.30.31861563921290.3420.3186100
2.19-2.277.30.2617.31510920640.2810.2617.3100
2.27-2.367.30.2049.41439619660.2190.2049.4100
2.36-2.457.30.17211.11404919220.1860.17211.1100
2.45-2.567.30.15212.51350918480.1640.15212.5100
2.56-2.697.30.12614.71297017810.1360.12614.7100
2.69-2.837.30.10217.81215316720.1090.10217.8100
2.83-37.30.088221177416180.0950.08822100
3-3.217.20.0825.51082615020.0860.0825.5100
3.21-3.477.10.06930.81005914080.0750.06930.8100
3.47-3.87.10.05735.7940213260.0620.05735.7100
3.8-4.257.10.04938.5848611960.0530.04938.5100
4.25-4.9170.04540.7749710680.0480.04540.7100
4.91-6.016.90.04637.663449200.050.04637.6100
6.01-8.56.60.04835.449277410.0520.04835.499.8
8.5-29.575.80.04236.625274340.0460.04236.697.1

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
SCALA3.2.5data scaling
PDB_EXTRACT3.006data extraction
MOSFLMdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.9→29.566 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.961 / Occupancy max: 1 / Occupancy min: 0.37 / SU B: 4.639 / SU ML: 0.069 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.099 / ESU R Free: 0.095
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1.HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2.ATOM RECORD CONTAINS RESIDUAL B FUNLORS ONLY. 3.A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN ...Details: 1.HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2.ATOM RECORD CONTAINS RESIDUAL B FUNLORS ONLY. 3.A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4.A ZINC ION WITH 40% OCCUPANCY IS MODELED. THE PRESENCE OF ZINC AT THIS SITE IS SUPPORTED BY X-RAY FLUORESCENCE, BINDING GEOMETRY AND ANOMALOUS DIFFERENCE FOURIERS ABOVE AND BELOW THE ZINC ABSORPTION EDGE. THE OCCUPANCY WAS LOWERED TO 40% TO BETTER FIT THE OBSERVED DENSITY. 5.MPD AND ETHYLENE GLYCOL MOLECULES FROM AND CRYSTALLIZATION ARE MODELED IN THE STRUCTURE. AN ACETATE-LIKE UNKNOWN LIGAND(UNL) IS MODELED NEAR THE METAL BINDING SITE ACCORDING TO THE POSSIBLE BIOLOGICAL FUNCTION OF THIS PROTEIN, A METAL-ION DEPENDENT DEACETYLASE.
RfactorNum. reflection% reflectionSelection details
Rfree0.184 1654 5.1 %RANDOM
Rwork0.162 30985 --
obs0.163 32639 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 77.84 Å2 / Biso mean: 38.386 Å2 / Biso min: 23.44 Å2
Baniso -1Baniso -2Baniso -3
1-0.6 Å20 Å20 Å2
2--0.6 Å20 Å2
3----1.2 Å2
Refinement stepCycle: LAST / Resolution: 1.9→29.566 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1971 0 33 156 2160
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0212117
X-RAY DIFFRACTIONr_bond_other_d0.0020.021413
X-RAY DIFFRACTIONr_angle_refined_deg1.4371.9322894
X-RAY DIFFRACTIONr_angle_other_deg0.91833398
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.5645255
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.32923.056108
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.13115317
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.9651518
X-RAY DIFFRACTIONr_chiral_restr0.0920.2308
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022402
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02474
X-RAY DIFFRACTIONr_nbd_refined0.2150.3464
X-RAY DIFFRACTIONr_nbd_other0.2130.31588
X-RAY DIFFRACTIONr_nbtor_refined0.1880.51060
X-RAY DIFFRACTIONr_nbtor_other0.0910.51047
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1720.5263
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2660.310
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2960.333
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2170.517
X-RAY DIFFRACTIONr_mcbond_it1.79131296
X-RAY DIFFRACTIONr_mcbond_other0.4553497
X-RAY DIFFRACTIONr_mcangle_it2.58452041
X-RAY DIFFRACTIONr_scbond_it4.4588969
X-RAY DIFFRACTIONr_scangle_it5.92911853
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.274 117 -
Rwork0.216 2237 -
all-2354 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 5.502 Å / Origin y: 1.355 Å / Origin z: 15.413 Å
111213212223313233
T-0.0764 Å20.0382 Å20.0198 Å2--0.0751 Å20.0459 Å2---0.0838 Å2
L1.1136 °2-0.4288 °20.731 °2-1.8193 °2-1.199 °2--2.0699 °2
S-0.0128 Å °-0.2073 Å °-0.1344 Å °0.2659 Å °0.2332 Å °0.1583 Å °-0.1494 Å °-0.2808 Å °-0.2204 Å °

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