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- PDB-4ir7: Crystal Structure of Mtb FadD10 in Complex with Dodecanoyl-AMP -

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Basic information

Entry
Database: PDB / ID: 4ir7
TitleCrystal Structure of Mtb FadD10 in Complex with Dodecanoyl-AMP
ComponentsLong chain fatty acid CoA ligase FadD10
KeywordsTRANSFERASE / open conformation / Structural Genomics / TB Structural Genomics Consortium / TBSGC
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 / Chem-1ZZ / :
Function and homology information
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 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 14, 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
Revision 1.3Feb 28, 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: Long chain fatty acid CoA ligase FadD10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,2813
Polymers56,7271
Non-polymers5542
Water57632
1
A: Long chain fatty acid CoA ligase FadD10
hetero molecules

A: Long chain fatty acid CoA ligase FadD10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,5636
Polymers113,4552
Non-polymers1,1084
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+2/31
Buried area3710 Å2
ΔGint-36 kcal/mol
Surface area39780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)138.212, 138.212, 82.582
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Long chain fatty acid CoA ligase FadD10


Mass: 56727.488 Da / Num. of mol.: 1
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): BL21 (DE3) plys / References: UniProt: I6WXG2, fatty-acyl-CoA synthase system
#2: Chemical ChemComp-1ZZ / 5'-O-[(S)-(dodecanoyloxy)(hydroxy)phosphoryl]adenosine


Mass: 529.524 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H36N5O8P
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 32 / 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: 4.01 Å3/Da / Density % sol: 69.36 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PEG 6000, LiSO4, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: ROTATING ANODE / Type: Cu FINE FOCUS / Wavelength: 1.542 Å
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Oct 1, 2007
RadiationMonochromator: Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.542 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 24707 / % possible obs: 99.9 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.109 / Χ2: 1.603 / Net I/σ(I): 6.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.75-2.897.20.8933581.3161100
2.89-3.077.20.55834141.3871100
3.07-3.317.20.29934001.3911100
3.31-3.647.20.17334121.4371100
3.64-4.177.20.11334211.4671100
4017-50257.20.07634521.5291100
5.25-506.90.04235291.705198.9

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.7.3_928refinement
PDB_EXTRACT3.11data extraction
CrystalCleardata collection
HKL-2000data reduction
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→39.034 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7788 / SU ML: 0.4 / σ(F): 1.34 / Phase error: 28.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2795 1147 5.07 %Random
Rwork0.2261 ---
obs0.2286 22632 99.7 %-
all-22632 --
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 32.369 Å2 / ksol: 0.327 e/Å3
Displacement parametersBiso max: 141.69 Å2 / Biso mean: 63.6413 Å2 / Biso min: 28.3 Å2
Baniso -1Baniso -2Baniso -3
1-2.8617 Å20 Å20 Å2
2--2.8617 Å2-0 Å2
3----5.7234 Å2
Refinement stepCycle: LAST / Resolution: 2.8→39.034 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3733 0 37 32 3802
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023835
X-RAY DIFFRACTIONf_angle_d0.6045232
X-RAY DIFFRACTIONf_chiral_restr0.04626
X-RAY DIFFRACTIONf_plane_restr0.003675
X-RAY DIFFRACTIONf_dihedral_angle_d10.6661376
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.8-2.92740.36411300.331426632793100
2.9274-3.08170.3641560.313126572813100
3.0817-3.27470.34921520.299826392791100
3.2747-3.52740.36751480.27226522800100
3.5274-3.88210.29161480.233326812829100
3.8821-4.44310.24131510.179926882839100
4.4431-5.59520.19681310.179227272858100
5.5952-39.03750.25861310.21042778290998

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