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- PDB-3cbw: Crystal structure of the YdhT protein from Bacillus subtilis -

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Basic information

Entry
Database: PDB / ID: 3cbw
TitleCrystal structure of the YdhT protein from Bacillus subtilis
ComponentsYdhT protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homology
Function and homology information


substituted mannan metabolic process / mannan endo-1,4-beta-mannosidase / mannan endo-1,4-beta-mannosidase activity / polysaccharide catabolic process / extracellular region
Similarity search - Function
Mannan endo-1,4-beta-mannosidase B/E / Glycoside hydrolase family 26 / Glycosyl hydrolase family 26 / Glycosyl hydrolase family 26 domain / Glycosyl hydrolases family 26 (GH26) domain profile. / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
CITRIC ACID / Mannan endo-1,4-beta-mannosidase
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.269 Å
AuthorsBonanno, J.B. / Rutter, M. / Bain, K.T. / Iizuka, M. / Romero, R. / Smith, D. / Wasserman, S. / Sauder, J.M. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal structure of the YdhT protein from Bacillus subtilis.
Authors: Bonanno, J.B. / Rutter, M. / Bain, K.T. / Iizuka, M. / Romero, R. / Smith, D. / Wasserman, S. / Sauder, J.M. / Burley, S.K. / Almo, S.C.
History
DepositionFeb 23, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 11, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Nov 14, 2018Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.4Feb 3, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / struct_ref_seq_dif / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.6Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: YdhT protein
B: YdhT protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,6475
Polymers80,0712
Non-polymers5763
Water10,665592
1
A: YdhT protein


Theoretical massNumber of molelcules
Total (without water)40,0351
Polymers40,0351
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: YdhT protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,6124
Polymers40,0351
Non-polymers5763
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.728, 69.619, 72.505
Angle α, β, γ (deg.)90.000, 91.090, 90.000
Int Tables number4
Space group name H-MP1211
DetailsAUTHORS STATE THAT THE MONOMERIC ASSEMBLY OF THE BIOLOGICAL UNIT THAT IS SHOWN IN REMARK 350 IS PUTATIVE AT THE TIME OF DEPOSITION.

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Components

#1: Protein YdhT protein


Mass: 40035.445 Da / Num. of mol.: 2 / Fragment: Residues 21-362 / Mutation: N153K, A158S, A160V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: 168 / Gene: ydhT, BSU05880 / Plasmid: modified pET26 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O05512
#2: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H8O7
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 592 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 1.82 Å3/Da / Density % sol: 32.39 %
Crystal growTemperature: 294 K / Method: vapor diffusion / pH: 3.5
Details: 100mM Citric acid pH 3.5, 25% PEG 3350, VAPOR DIFFUSION, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97958 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Feb 16, 2008
RadiationMonochromator: Diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97958 Å / Relative weight: 1
ReflectionResolution: 1.269→72.548 Å / Num. all: 145644 / Num. obs: 145644 / % possible obs: 95.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.6 % / Biso Wilson estimate: 9.6 Å2 / Rmerge(I) obs: 0.095 / Rsym value: 0.095 / Net I/σ(I): 15.1
Reflection shellResolution: 1.269→1.33 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.439 / Mean I/σ(I) obs: 3.3 / Num. unique all: 19656 / Rsym value: 0.439 / % possible all: 88.5

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
REFMACrefinement
PDB_EXTRACT3.004data extraction
MAR345CCDdata collection
MOSFLMdata reduction
SHELXCDphasing
SHELXEmodel building
RefinementMethod to determine structure: SAD / Resolution: 1.269→20 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.963 / SU B: 1.339 / SU ML: 0.027 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.052 / ESU R Free: 0.047 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.172 7331 5 %RANDOM
Rwork0.149 ---
obs0.151 145624 96.26 %-
all-145624 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 14.12 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å20 Å20.09 Å2
2--0.24 Å20 Å2
3----0.29 Å2
Refinement stepCycle: LAST / Resolution: 1.269→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5381 0 39 592 6012
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0225587
X-RAY DIFFRACTIONr_angle_refined_deg1.1971.9357627
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8495686
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.97724.638276
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.90315871
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.231520
X-RAY DIFFRACTIONr_chiral_restr0.0810.2791
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024392
X-RAY DIFFRACTIONr_nbd_refined0.20.22643
X-RAY DIFFRACTIONr_nbtor_refined0.3090.23860
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1420.2534
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1320.2104
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1420.266
X-RAY DIFFRACTIONr_mcbond_it0.8731.53392
X-RAY DIFFRACTIONr_mcangle_it1.34625391
X-RAY DIFFRACTIONr_scbond_it1.82132541
X-RAY DIFFRACTIONr_scangle_it2.6084.52224
X-RAY DIFFRACTIONr_rigid_bond_restr1.06235933
X-RAY DIFFRACTIONr_sphericity_free3.143592
X-RAY DIFFRACTIONr_sphericity_bonded1.82935420
LS refinement shellResolution: 1.269→1.302 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.228 527 -
Rwork0.184 9735 -
all-10262 -
obs-9735 92.68 %

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