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- PDB-2o16: Crystal structure of a putative acetoin utilization protein (AcuB... -

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Basic information

Entry
Database: PDB / ID: 2o16
TitleCrystal structure of a putative acetoin utilization protein (AcuB) from Vibrio cholerae
ComponentsAcetoin utilization protein AcuB, putative
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homology
Function and homology information


: / CBS-domain / CBS-domain / Domain in cystathionine beta-synthase and other proteins. / CBS domain superfamily / CBS domain / CBS domain / CBS domain profile. / Roll / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Acetoin utilization protein AcuB, putative
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsPatskovsky, Y. / Bonanno, J.B. / Rutter, M. / Bain, K.T. / Powell, A. / Slocombe, A. / 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 a putative acetoin utilization protein (AcuB) from Vibrio cholerae
Authors: Patskovsky, Y. / Bonanno, J.B. / Rutter, M. / Bain, K.T. / Powell, A. / Slocombe, A. / Sauder, J.M. / Burley, S.K. / Almo, S.C.
History
DepositionNov 28, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 12, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 24, 2012Group: Database references / Structure summary
Revision 1.4Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.5Nov 14, 2018Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.6Feb 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 1.7Aug 30, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _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: Acetoin utilization protein AcuB, putative
B: Acetoin utilization protein AcuB, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,5829
Polymers35,9172
Non-polymers6657
Water4,053225
1
A: Acetoin utilization protein AcuB, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,2434
Polymers17,9581
Non-polymers2853
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: Acetoin utilization protein AcuB, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,3385
Polymers17,9581
Non-polymers3804
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
B: Acetoin utilization protein AcuB, putative
hetero molecules

A: Acetoin utilization protein AcuB, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,5829
Polymers35,9172
Non-polymers6657
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y+1/2,-z1
Buried area4670 Å2
ΔGint-72 kcal/mol
Surface area14120 Å2
MethodPISA
4


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3280 Å2
ΔGint-48 kcal/mol
Surface area15520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.677, 58.006, 53.561
Angle α, β, γ (deg.)90.000, 108.850, 90.000
Int Tables number4
Space group name H-MP1211
Detailsprobable monomer

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Components

#1: Protein Acetoin utilization protein AcuB, putative


Mass: 17958.482 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Gene: VC0737 / Plasmid: modified pET26 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9KTZ3
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 225 / Source method: isolated from a natural source / Formula: H2O

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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: 2.03 Å3/Da / Density % sol: 39.49 %
Crystal growTemperature: 294 K / Method: vapor diffusion / pH: 8.5
Details: 100mM Tris pH 8.5, 2M ammonium phosphate, VAPOR DIFFUSION, temperature 294K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Aug 26, 2006 / Details: Osmic mirrors
RadiationMonochromator: Osmic mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. all: 22818 / Num. obs: 22430 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.8 % / Rmerge(I) obs: 0.073 / Rsym value: 0.073 / Χ2: 0.791 / Net I/σ(I): 23.8
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.481 / Mean I/σ(I) obs: 2.8 / Num. unique all: 1913 / Rsym value: 0.481 / Χ2: 0.719 / % possible all: 84.8

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT2data extraction
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1XKF

1xkf


Resolution: 1.9→20 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.924 / SU B: 2.821 / SU ML: 0.087 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.147 / ESU R Free: 0.149 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.234 722 3.2 %RANDOM
Rwork0.174 ---
obs0.176 22408 98.21 %-
all-22816 --
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: 26.349 Å2
Baniso -1Baniso -2Baniso -3
1--0.59 Å20 Å20.61 Å2
2--0.26 Å20 Å2
3---0.73 Å2
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2078 0 35 225 2338
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0222157
X-RAY DIFFRACTIONr_angle_refined_deg1.361.9962929
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.065269
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.63325.40287
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.29315407
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.106159
X-RAY DIFFRACTIONr_chiral_restr0.0920.2360
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021519
X-RAY DIFFRACTIONr_nbd_refined0.2120.21006
X-RAY DIFFRACTIONr_nbtor_refined0.3010.21499
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1710.2195
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1960.286
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2590.225
X-RAY DIFFRACTIONr_mcbond_it1.1891.51409
X-RAY DIFFRACTIONr_mcangle_it1.77122192
X-RAY DIFFRACTIONr_scbond_it2.6633839
X-RAY DIFFRACTIONr_scangle_it4.1194.5734
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.275 47 -
Rwork0.209 1294 -
obs-1341 81.47 %

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