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- PDB-3fys: Crystal Structure of DegV, a fatty acid binding protein from Baci... -

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Basic information

Entry
Database: PDB / ID: 3fys
TitleCrystal Structure of DegV, a fatty acid binding protein from Bacillus subtilis
ComponentsProtein degV
KeywordsFATTY ACID-BINDING PROTEIN / FATTY ACID-BINDING / EDD fold
Function / homology
Function and homology information


Hypothetical Protein Tm841; Chain: A;domain 3 - #10 / Rossmann fold - #10170 / DegV / DegV, C-terminal domain / Uncharacterised protein, DegV family COG1307 / DegV domain profile. / Hypothetical Protein Tm841; Chain: A;domain 3 / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
BROMIDE ION / PALMITIC ACID / Protein DegV
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SAD / Resolution: 2.5 Å
AuthorsNan, J. / Zhou, Y.F. / Yang, C.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2009
Title: Structure of a fatty acid-binding protein from Bacillus subtilis determined by sulfur-SAD phasing using in-house chromium radiation
Authors: Nan, J. / Zhou, Y.F. / Yang, C. / Brostromer, E. / Kristensen, O. / Su, X.-D.
History
DepositionJan 23, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 12, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein degV
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,05110
Polymers35,1731
Non-polymers8789
Water2,378132
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.1, 84.7, 42.2
Angle α, β, γ (deg.)90.0, 94.1, 90.0
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Protein degV


Mass: 35173.074 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: BSU35480, degV, yviA / Plasmid: PET28A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P32436
#2: Chemical ChemComp-PLM / PALMITIC ACID / Palmitic acid


Mass: 256.424 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H32O2
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-BR / BROMIDE ION / Bromide


Mass: 79.904 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Br
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 132 / 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: 2.13 Å3/Da / Density % sol: 42.35 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.15M potassium bromide, 30% w/v polyethylene glycol monomethyl ether 2000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 2.2909 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Sep 3, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 2.2909 Å / Relative weight: 1
ReflectionResolution: 2.5→24.9 Å / Num. all: 9588 / Num. obs: 9588 / % possible obs: 93.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 23.2 Å2 / Rsym value: 0.037 / Net I/σ(I): 60.25
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 2.2 % / Mean I/σ(I) obs: 31.6 / Num. unique all: 721 / Rsym value: 0.08 / % possible all: 65.3

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Processing

Software
NameVersionClassification
HKL-2000data collection
SOLVEphasing
PHENIX(phenix.refine)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.5→11.953 Å / Occupancy max: 1 / Occupancy min: 0.24 / FOM work R set: 0.837 / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.4 / Phase error: 23.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2246 461 4.85 %RANDOM
Rwork0.1485 9038 --
all0.1523 9499 --
obs0.1523 9499 93.45 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 48.696 Å2 / ksol: 0.408 e/Å3
Displacement parametersBiso max: 87.03 Å2 / Biso mean: 23.831 Å2 / Biso min: 6.91 Å2
Baniso -1Baniso -2Baniso -3
1--1.545 Å20 Å2-0.454 Å2
2--3.322 Å20 Å2
3----1.777 Å2
Refinement stepCycle: LAST / Resolution: 2.5→11.953 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2230 0 29 132 2391
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062297
X-RAY DIFFRACTIONf_angle_d0.9983095
X-RAY DIFFRACTIONf_chiral_restr0.069341
X-RAY DIFFRACTIONf_plane_restr0.004395
X-RAY DIFFRACTIONf_dihedral_angle_d16.784853
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
2.5003-2.85780.2971270.16652678280583
2.8578-3.58440.25651780.15273110328897
3.5844-11.95360.17441560.13013250340699

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