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- PDB-5hm3: 2.25 Angstrom Resolution Crystal Structure of Long-chain-fatty-ac... -

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Basic information

Entry
Database: PDB / ID: 5hm3
Title2.25 Angstrom Resolution Crystal Structure of Long-chain-fatty-acid-AMP Ligase FadD32 from Mycobacterium tuberculosis in complex with Inhibitor 5'-O-[(11-phenoxyundecanoyl)sulfamoyl]adenosine
ComponentsLong-chain-fatty-acid--AMP ligase FadD32
KeywordsLIGASE/LIGASE INHIBITOR / long-chain-fatty-acid--AMP ligase / FadD32 / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / LIGASE-LIGASE INHIBITOR complex
Function / homology
Function and homology information


long-chain-fatty-acid-[acyl-carrier-protein] ligase / long-chain fatty acid [acyl-carrier-protein] ligase activity / adenylyltransferase activity / Actinobacterium-type cell wall biogenesis / mycolate cell wall layer assembly / lipid biosynthetic process / ligase activity / peptidoglycan-based cell wall / fatty acid biosynthetic process / ATP binding / plasma membrane
Similarity search - Function
: / Fatty acyl-AMP ligase /fatty acyl-CoA ligase / ANL, N-terminal domain / AMP-dependent synthetase/ligase / AMP-binding enzyme / AMP-binding enzyme, C-terminal domain superfamily
Similarity search - Domain/homology
5'-O-[(11-phenoxyundecanoyl)sulfamoyl]adenosine / DI(HYDROXYETHYL)ETHER / PHOSPHATE ION / Long-chain-fatty-acid--AMP ligase FadD32
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.25 Å
AuthorsMinasov, G. / Warwrzak, Z. / Kuhn, M.L. / Shuvalova, L. / Flores, K.J. / Wilson, D.J. / Grimes, K.D. / Aldrich, C.C. / Anderson, W.A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: Acs Infect Dis. / Year: 2016
Title: Structure of the Essential Mtb FadD32 Enzyme: A Promising Drug Target for Treating Tuberculosis.
Authors: Kuhn, M.L. / Alexander, E. / Minasov, G. / Page, H.J. / Warwrzak, Z. / Shuvalova, L. / Flores, K.J. / Wilson, D.J. / Shi, C. / Aldrich, C.C. / Anderson, W.F.
History
DepositionJan 15, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 3, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 7, 2016Group: Database references
Revision 1.2Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Long-chain-fatty-acid--AMP ligase FadD32
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,14010
Polymers71,8881
Non-polymers1,2539
Water2,360131
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1460 Å2
ΔGint-21 kcal/mol
Surface area26130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.779, 74.558, 127.762
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Long-chain-fatty-acid--AMP ligase FadD32 / FAAL / Acyl-AMP synthetase


Mass: 71887.539 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: fadD32, Rv3801c / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: O53580, Ligases; Forming carbon-sulfur bonds; Acid-thiol ligases

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Non-polymers , 6 types, 140 molecules

#2: Chemical ChemComp-649 / 5'-O-[(11-phenoxyundecanoyl)sulfamoyl]adenosine


Mass: 606.691 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H38N6O8S
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 131 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.02 Å3/Da / Density % sol: 39 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.6
Details: Protein: 6.0 mG/mL, 0.1M Pottasium chloride, 0.01 M Tris-HCL buffer pH 8.3, 5% glycerol, and 0.5 mM TCEP; Screen: Cubic Phase I (F10), 2.4 M Na/K phosphate pH 7.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.97875 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 20, 2014 / Details: Si(111)
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97875 Å / Relative weight: 1
ReflectionResolution: 2.25→30 Å / Num. obs: 29261 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 4.9 % / Biso Wilson estimate: 49.5 Å2 / Rmerge(I) obs: 0.074 / Rsym value: 0.074 / Net I/σ(I): 18.4
Reflection shellResolution: 2.25→2.29 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.583 / Mean I/σ(I) obs: 2.8 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.25→29.36 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.94 / SU B: 13.796 / SU ML: 0.173 / Cross valid method: THROUGHOUT / ESU R: 0.376 / ESU R Free: 0.238 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23875 1478 5.1 %RANDOM
Rwork0.18484 ---
obs0.18761 27630 99.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 62.991 Å2
Baniso -1Baniso -2Baniso -3
1-0.18 Å2-0 Å2-0 Å2
2--2.45 Å20 Å2
3----2.62 Å2
Refinement stepCycle: 1 / Resolution: 2.25→29.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4804 0 78 131 5013
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0195230
X-RAY DIFFRACTIONr_bond_other_d0.0010.024922
X-RAY DIFFRACTIONr_angle_refined_deg1.5211.9647138
X-RAY DIFFRACTIONr_angle_other_deg0.731311295
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.5725664
X-RAY DIFFRACTIONr_dihedral_angle_2_deg24.54423.096239
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.30915787
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.5751548
X-RAY DIFFRACTIONr_chiral_restr0.0840.2789
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0216042
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021241
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.5183.6642620
X-RAY DIFFRACTIONr_mcbond_other2.5113.6632619
X-RAY DIFFRACTIONr_mcangle_it3.8775.4813296
X-RAY DIFFRACTIONr_mcangle_other3.8775.4823297
X-RAY DIFFRACTIONr_scbond_it2.7424.0442610
X-RAY DIFFRACTIONr_scbond_other2.7424.0442610
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.265.9213843
X-RAY DIFFRACTIONr_long_range_B_refined7.10429.7635891
X-RAY DIFFRACTIONr_long_range_B_other7.10429.7735892
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.25→2.308 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.311 95 -
Rwork0.255 1999 -
obs--99.29 %
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)
12.88490.9229-0.06412.00521.07943.6394-0.1652-0.47030.4727-0.07-0.07090.3609-0.3684-0.67620.23610.09610.087-0.0680.295-0.09120.1474-0.01721.39375.0025
23.5122-0.31690.46362.3759-0.40654.5557-0.0403-0.31560.49110.0087-0.0418-0.2002-0.32020.29120.0820.1491-0.0385-0.05540.1517-0.11320.211815.77816.95946.6581
32.75870.4312-0.03261.9109-0.35462.1755-0.09770.0072-0.0941-0.06610.05630.11050.1406-0.24820.04140.0438-0.0428-0.01190.06170.01750.02732.8352-11.3719-9.3492
41.9163-0.2696-0.43322.01490.04652.9164-0.11230.32470.2305-0.30430.0097-0.36850.02320.47370.10260.1503-0.08620.01370.23030.11390.164219.613-2.0336-24.5003
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 106
2X-RAY DIFFRACTION2A107 - 201
3X-RAY DIFFRACTION3A202 - 346
4X-RAY DIFFRACTION4A347 - 636

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