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- PDB-4x9x: Biochemical Roles for Conserved Residues in the Bacterial Fatty A... -

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Basic information

Entry
Database: PDB / ID: 4x9x
TitleBiochemical Roles for Conserved Residues in the Bacterial Fatty Acid Binding Protein Family
ComponentsDegV domain-containing protein MW1315
KeywordsTRANSFERASE / Fatty Acid / Kinase / FakB / DegV
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
OLEIC ACID / DegV domain-containing protein MW1315
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.199 Å
AuthorsBroussard, T.C. / Miller, D.J. / Jackson, P. / Nourse, A. / Rock, C.O.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM034496 United States
Cancer Center Support GrantCA21765 United States
American Lebanese Syrian Associated Charities United States
CitationJournal: J.Biol.Chem. / Year: 2016
Title: Biochemical Roles for Conserved Residues in the Bacterial Fatty Acid-binding Protein Family.
Authors: Broussard, T.C. / Miller, D.J. / Jackson, P. / Nourse, A. / White, S.W. / Rock, C.O.
History
DepositionDec 11, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 27, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 3, 2016Group: Database references
Revision 1.2Mar 30, 2016Group: Database references
Revision 1.3Sep 20, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Feb 28, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DegV domain-containing protein MW1315
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,3215
Polymers32,8521
Non-polymers4694
Water5,134285
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1680 Å2
ΔGint15 kcal/mol
Surface area12250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)167.343, 41.872, 38.573
Angle α, β, γ (deg.)90.00, 94.49, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein DegV domain-containing protein MW1315


Mass: 32852.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (strain MW2) (bacteria)
Strain: MW2 / Gene: MW1315 / Plasmid: pET15B / Production host: Escherichia coli (E. coli) / References: UniProt: Q8NWR0
#2: Chemical ChemComp-OLA / OLEIC ACID


Mass: 282.461 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H34O2
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 285 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.05 Å3/Da / Density % sol: 40.01 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 0.1 M Citrate pH 5.5, 20% PEG 3000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 6, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.2→26.1 Å / Num. obs: 78877 / % possible obs: 94.5 % / Redundancy: 4 % / Biso Wilson estimate: 8.9 Å2 / Rsym value: 0.059 / Net I/σ(I): 27.4
Reflection shellResolution: 1.2→1.24 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.357 / Mean I/σ(I) obs: 2.4 / % possible all: 77

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementResolution: 1.199→26.094 Å / SU ML: 0.09 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 12.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.144 1998 2.53 %Random selection
Rwork0.1182 ---
obs0.1189 78842 94.22 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.199→26.094 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2065 0 32 285 2382
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082243
X-RAY DIFFRACTIONf_angle_d1.223053
X-RAY DIFFRACTIONf_dihedral_angle_d13.669864
X-RAY DIFFRACTIONf_chiral_restr0.073365
X-RAY DIFFRACTIONf_plane_restr0.006392
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.1986-1.22850.21381040.2014107X-RAY DIFFRACTION71
1.2285-1.26170.21941330.17224836X-RAY DIFFRACTION84
1.2617-1.29890.18431200.14645198X-RAY DIFFRACTION89
1.2989-1.34080.16121560.13055403X-RAY DIFFRACTION94
1.3408-1.38870.1681450.11735564X-RAY DIFFRACTION96
1.3887-1.44430.14971450.11055580X-RAY DIFFRACTION97
1.4443-1.510.12191530.09075652X-RAY DIFFRACTION97
1.51-1.58960.09831450.08315682X-RAY DIFFRACTION98
1.5896-1.68920.11971460.08875695X-RAY DIFFRACTION98
1.6892-1.81960.12761460.0965718X-RAY DIFFRACTION98
1.8196-2.00270.13721440.10315761X-RAY DIFFRACTION99
2.0027-2.29230.12321540.10315838X-RAY DIFFRACTION100
2.2923-2.88750.14781510.12365830X-RAY DIFFRACTION100
2.8875-26.10050.15481560.13765980X-RAY DIFFRACTION99

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