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- PDB-3nyi: The crystal structure of a fat acid (stearic acid)-binding protei... -

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Basic information

Entry
Database: PDB / ID: 3nyi
TitleThe crystal structure of a fat acid (stearic acid)-binding protein from Eubacterium ventriosum ATCC 27560.
Componentsfat acid-binding protein
KeywordsLIPID BINDING PROTEIN / stearic acid / DegV family protein / structural genomics / PSI-2 / protein structure initiative / midwest center for structural genomics / MCSG
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
STEARIC ACID / EDD domain protein, DegV family
Similarity search - Component
Biological speciesEubacterium ventriosum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsZhang, R. / Tan, K. / Li, H. / Keigher, L. / Babnigg, G. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: TO BE PUBLISHED
Title: The crystal structure of a fat acid (stearic acid)-binding protein from Eubacterium ventriosum ATCC 27560.
Authors: Zhang, R. / Tan, K. / Li, H. / Keigher, L. / Babnigg, G. / Joachimiak, A.
History
DepositionJul 15, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 22, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 21, 2016Group: Structure summary

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: fat acid-binding protein
B: fat acid-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,7084
Polymers66,1392
Non-polymers5692
Water6,630368
1
A: fat acid-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,3542
Polymers33,0691
Non-polymers2841
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: fat acid-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,3542
Polymers33,0691
Non-polymers2841
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)56.725, 110.221, 57.127
Angle α, β, γ (deg.)90.00, 108.62, 90.00
Int Tables number4
Space group name H-MP1211
DetailsExperimentally unknown. It is likely monomeric.

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Components

#1: Protein fat acid-binding protein


Mass: 33069.355 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Eubacterium ventriosum (bacteria) / Strain: ATCC 27560 / Gene: EUBVEN_01190 / Plasmid: MCSG19 / Production host: Escherichia coli (E. coli) / Strain (production host): pPK1037 / References: UniProt: A5Z657
#2: Chemical ChemComp-STE / STEARIC ACID / Stearic acid


Mass: 284.477 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H36O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 368 / 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: 2.54 Å3/Da / Density % sol: 51.54 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.2M MgCl2, 0.1M Bis-Tris, 25% PEG3350, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97929 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Jul 15, 2009 / Details: mirror
RadiationMonochromator: Si 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97929 Å / Relative weight: 1
ReflectionResolution: 1.9→43 Å / Num. all: 51716 / Num. obs: 51716 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.9 % / Rmerge(I) obs: 0.098 / Net I/σ(I): 19.8
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 1.4 / Num. unique all: 2556 / % possible all: 99.6

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
SHELXDphasing
MLPHAREphasing
DMmodel building
ARPmodel building
WARPmodel building
HKL-3000phasing
PHENIX(phenix.refine: 1.5_2)refinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing
RefinementMethod to determine structure: SAD / Resolution: 1.9→42.634 Å / SU ML: 0.23 / σ(F): 0.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2203 2559 5.09 %random
Rwork0.1682 ---
all0.1708 50313 --
obs0.1708 50313 96.21 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.423 Å2 / ksol: 0.4 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.4789 Å2-0 Å24.1424 Å2
2---0.5285 Å2-0 Å2
3---2.0075 Å2
Refinement stepCycle: LAST / Resolution: 1.9→42.634 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4561 0 40 368 4969
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084701
X-RAY DIFFRACTIONf_angle_d1.0816342
X-RAY DIFFRACTIONf_dihedral_angle_d16.9921744
X-RAY DIFFRACTIONf_chiral_restr0.072723
X-RAY DIFFRACTIONf_plane_restr0.004811
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9002-1.96820.28772160.21054282X-RAY DIFFRACTION86
1.9682-2.0470.28482760.20024551X-RAY DIFFRACTION93
2.047-2.14010.24232550.18164739X-RAY DIFFRACTION96
2.1401-2.25290.23552500.17584841X-RAY DIFFRACTION97
2.2529-2.39410.23732650.16544862X-RAY DIFFRACTION98
2.3941-2.57890.21942560.16594923X-RAY DIFFRACTION99
2.5789-2.83840.24412670.17414915X-RAY DIFFRACTION100
2.8384-3.2490.21332670.17544945X-RAY DIFFRACTION100
3.249-4.09290.20682820.15934926X-RAY DIFFRACTION99
4.0929-42.6450.18642250.15084770X-RAY DIFFRACTION94
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.58370.070.18561.13980.23420.7881-0.008-0.24030.11060.07580.0054-0.08740.0932-0.070400.1683-0.0133-0.01330.1863-0.01220.151246.39548.556926.276
20.86290.1734-0.5551.10540.0742.519-0.07260.02680.0546-0.10640.02270.03410.0959-0.2354-00.1484-0.0065-0.01870.1696-0.01230.150128.83454.18581.2782
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B

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