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- PDB-4isb: Crystal Structure of Apo Mtb FadD10 -

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Basic information

Entry
Database: PDB / ID: 4isb
TitleCrystal Structure of Apo Mtb FadD10
ComponentsLong chain fatty acid CoA ligase FadD10
KeywordsTRANSFERASE / LIGASE / Structural Genomics / TB Structural Genomics Consortium / TBSGC / Fatty acyl-acyl carrier protein synthetase
Function / homologyANL, C-terminal domain / ANL, N-terminal domain / GMP Synthetase; Chain A, domain 3 / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta / :
Function and homology information
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å
AuthorsLiu, Z. / Wang, F. / Sacchettini, J.C. / TB Structural Genomics Consortium (TBSGC)
CitationJournal: J.Biol.Chem. / Year: 2013
Title: Structures of Mycobacterium tuberculosis FadD10 protein reveal a new type of adenylate-forming enzyme.
Authors: Liu, Z. / Ioerger, T.R. / Wang, F. / Sacchettini, J.C.
History
DepositionJan 16, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 8, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 20, 2014Group: Database references
Revision 1.2Nov 15, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Long chain fatty acid CoA ligase FadD10
B: Long chain fatty acid CoA ligase FadD10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,7776
Polymers114,3932
Non-polymers3844
Water1,06359
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4050 Å2
ΔGint-77 kcal/mol
Surface area40690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.318, 107.913, 85.689
Angle α, β, γ (deg.)90.000, 106.920, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Long chain fatty acid CoA ligase FadD10


Mass: 57196.434 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: Rv0099 / Plasmid: pDEST17 / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) plys / References: UniProt: I6WXG2, fatty-acyl-CoA synthase system
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 59 / 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: 2.22 Å3/Da / Density % sol: 44.5 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: PEG 6000, LiSO4, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 7, 2007
RadiationMonochromator: Double-crystal, Si(111) liquid N2 cooled / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionRedundancy: 3.6 % / Av σ(I) over netI: 17.2 / Number: 182548 / Rmerge(I) obs: 0.12 / Χ2: 2.32 / D res high: 2.2 Å / D res low: 50 Å / Num. obs: 50192 / % possible obs: 99.4
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
5.975098.310.0597.0083.7
4.745.9799.610.0644.4383.8
4.144.7499.410.0613.7793.6
3.764.1499.510.073.3063.6
3.493.7699.210.0833.1733.7
3.293.4999.610.0972.7843.7
3.123.2999.510.1162.5363.7
2.993.1299.810.1422.0593.8
2.872.9999.710.1641.7593.8
2.772.8799.710.1941.6143.8
2.692.7799.610.231.4773.8
2.612.6999.510.2731.4883.8
2.542.6199.610.3251.2813.8
2.482.5499.610.3931.3193.8
2.422.4899.410.4341.2683.7
2.372.4299.310.5061.3653.6
2.322.3799.610.4691.2613.5
2.282.329910.5091.1483.3
2.242.2898.910.551.4363.2
2.22.2499.110.6061.2313.1
ReflectionResolution: 2.2→50 Å / Num. all: 50192 / Num. obs: 50192 / % possible obs: 99.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.6 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 9.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.2-2.243.10.606199.1
2.24-2.283.20.55198.9
2.28-2.323.30.509199
2.32-2.373.50.469199.6
2.37-2.423.60.506199.3
2.42-2.483.70.434199.4
2.48-2.543.80.393199.6
2.54-2.613.80.325199.6
2.61-2.693.80.273199.5
2.69-2.773.80.23199.6
2.77-2.873.80.194199.7
2.87-2.993.80.164199.7
2.99-3.123.80.142199.8
3.12-3.293.70.116199.5
3.29-3.493.70.097199.6
3.49-3.763.70.083199.2
3.76-4.143.60.07199.5
4.14-4.743.60.061199.4
4.74-5.973.80.064199.6
5.97-503.70.059198.3

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Phasing

Phasing dmFOM : 0.63 / FOM acentric: 0.64 / FOM centric: 0.59 / Reflection: 50158 / Reflection acentric: 48768 / Reflection centric: 1390
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
6.3-500.920.930.8321802001179
3.9-6.30.910.910.7867436471272
3.1-3.90.830.840.6884318173258
2.8-3.10.680.690.5485108304206
2.4-2.80.50.50.411512214795327
2.2-2.40.360.360.2791729024148

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
RESOLVE2.15phasing
PHENIX1.7.3_928refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.2→48.886 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.27 / σ(F): 0 / Phase error: 28.62 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2728 1968 4.02 %
Rwork0.2269 --
obs0.2288 49014 96.87 %
all-49014 -
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 27.648 Å2 / ksol: 0.367 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.0757 Å20 Å20.2534 Å2
2--1.603 Å2-0 Å2
3----1.6787 Å2
Refinement stepCycle: LAST / Resolution: 2.2→48.886 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7422 0 20 59 7501
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.017565
X-RAY DIFFRACTIONf_angle_d1.25510316
X-RAY DIFFRACTIONf_dihedral_angle_d13.9222698
X-RAY DIFFRACTIONf_chiral_restr0.0781236
X-RAY DIFFRACTIONf_plane_restr0.0051332
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.25510.33011390.26873048X-RAY DIFFRACTION89
2.2551-2.3160.3141280.2553235X-RAY DIFFRACTION93
2.316-2.38420.29471190.24883319X-RAY DIFFRACTION95
2.3842-2.46110.33331450.25843273X-RAY DIFFRACTION95
2.4611-2.54910.32361450.25913291X-RAY DIFFRACTION96
2.5491-2.65110.30581360.26343353X-RAY DIFFRACTION97
2.6511-2.77180.29781460.26893389X-RAY DIFFRACTION97
2.7718-2.91790.35211320.26293423X-RAY DIFFRACTION99
2.9179-3.10070.30131440.26053420X-RAY DIFFRACTION99
3.1007-3.34010.29111500.23193431X-RAY DIFFRACTION99
3.3401-3.67610.24961360.21383458X-RAY DIFFRACTION99
3.6761-4.20780.22831460.1913445X-RAY DIFFRACTION99
4.2078-5.30030.21271490.18293484X-RAY DIFFRACTION99
5.3003-48.89820.25381530.20983477X-RAY DIFFRACTION99

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