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- PDB-1uxo: The crystal structure of the ydeN gene product from B. subtilis -

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Basic information

Entry
Database: PDB / ID: 1uxo
TitleThe crystal structure of the ydeN gene product from B. subtilis
ComponentsPutative hydrolase YdeN
KeywordsHYDROLASE / A/B HYDROLASE / ESTERASE / PSI / PROTEIN STRUCTURE INITIATIVE / MCSG / MIDWEST CENTER FOR STRUCTURAL GENOMICS
Function / homology
Function and homology information


Hydrolases / hydrolase activity
Similarity search - Function
Putative hydrolase RBBP9/YdeN / Serine hydrolase / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Putative hydrolase YdeN
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 1.8 Å
AuthorsJanda, I.K. / Devedjiev, Y. / Cooper, D.R. / Chruszcz, M. / Derewenda, U. / Gabrys, A. / Minor, W. / Joachimiak, A. / Derewenda, Z.S. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: Acta Crystallogr. D Biol. Crystallogr. / Year: 2004
Title: Harvesting the high-hanging fruit: the structure of the YdeN gene product from Bacillus subtilis at 1.8 angstroms resolution.
Authors: Janda, I. / Devedjiev, Y. / Cooper, D. / Chruszcz, M. / Derewenda, U. / Gabrys, A. / Minor, W. / Joachimiak, A. / Derewenda, Z.S.
History
DepositionFeb 27, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 27, 2004Provider: repository / Type: Initial release
Revision 1.1Jul 4, 2012Group: Database references / Structure summary / Version format compliance
Revision 1.2Nov 21, 2018Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Source and taxonomy / Structure summary
Category: citation / citation_author ...citation / citation_author / entity / entity_src_gen / entity_src_nat / pdbx_struct_mod_residue / struct_ref
Item: _citation.journal_abbrev / _citation.page_last ..._citation.journal_abbrev / _citation.page_last / _citation.title / _citation_author.name / _entity.pdbx_description / _entity.pdbx_ec / _entity.pdbx_mutation / _entity.src_method / _pdbx_struct_mod_residue.details / _struct_ref.db_code / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_seq_one_letter_code
Revision 1.3Aug 21, 2019Group: Data collection / Database references / Derived calculations
Category: pdbx_database_related / struct_conn
Item: _pdbx_database_related.db_name / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Sep 25, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_status / reflns
Item: _exptl_crystal_grow.method / _pdbx_database_status.status_code_sf / _reflns.pdbx_Rmerge_I_obs
Revision 1.5May 4, 2022Group: Database references / Structure summary / Category: audit_author / database_2
Item: _audit_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative hydrolase YdeN


Theoretical massNumber of molelcules
Total (without water)21,8681
Polymers21,8681
Non-polymers00
Water5,224290
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)36.128, 53.971, 93.151
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Putative hydrolase YdeN


Mass: 21867.555 Da / Num. of mol.: 1 / Fragment: RESIDUES 2-190 / Mutation: K88A,Q89A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: 168 / Gene: ydeN, BSU05260 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P96671, Hydrolases
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 290 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED MUTATION LYS 88 ALA AND GLN 89 ALA IN CHAIN A
Sequence detailsALA A 88, MUTAGENESIS FOR CRYSTALLIZATION ALA A 89, MUTAGENESIS FOR CRYSTALLIZATION

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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: 2.1 Å3/Da / Density % sol: 40.7 %
Crystal growMethod: vapor diffusion, sitting drop / pH: 4.6 / Details: 20% PEG 8000, 0.05 M KH2PO4, PH 4.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.97920,0.97931,0.97546
DetectorDate: Oct 15, 2003
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97921
20.979311
30.975461
ReflectionResolution: 1.7→50 Å / Num. obs: 31784 / % possible obs: 99.8 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.082 / Net I/σ(I): 13.9
Reflection shellResolution: 1.83→1.91 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.22 / Mean I/σ(I) obs: 4.3 / % possible all: 65.8

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Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
SHELXDphasing
SHARPphasing
REFMAC5.1.24refinement
RefinementMethod to determine structure: OTHER / Resolution: 1.8→46.62 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.951 / SU B: 2.196 / SU ML: 0.068 / Cross valid method: THROUGHOUT / ESU R: 0.375 / ESU R Free: 0.116 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.181 1038 6.3 %RANDOM
Rwork0.125 ---
obs-15495 94.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 12.41 Å2
Baniso -1Baniso -2Baniso -3
1--0.71 Å20 Å20 Å2
2--1.03 Å20 Å2
3----0.33 Å2
Refinement stepCycle: LAST / Resolution: 1.8→46.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1493 0 0 290 1783
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0211553
X-RAY DIFFRACTIONr_bond_other_d0.0020.021382
X-RAY DIFFRACTIONr_angle_refined_deg1.6211.942109
X-RAY DIFFRACTIONr_angle_other_deg1.90433230
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2715185
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1080.2233
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021713
X-RAY DIFFRACTIONr_gen_planes_other0.0130.02314
X-RAY DIFFRACTIONr_nbd_refined0.3240.2330
X-RAY DIFFRACTIONr_nbd_other0.2520.21588
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0870.2860
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.3030.2230
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0460.26
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3040.245
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2290.230
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3951.5928
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.1421503
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.1153625
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.6194.5606
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.85 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.263 43
Rwork0.158 707

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