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- PDB-3lnv: The crystal structure of fatty acyl-adenylate ligase from L. pneu... -

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Basic information

Entry
Database: PDB / ID: 3lnv
TitleThe crystal structure of fatty acyl-adenylate ligase from L. pneumophila in complex with acyl adenylate and pyrophosphate
ComponentsSaframycin Mx1 synthetase B
KeywordsBIOSYNTHETIC PROTEIN / Structural Genomics / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homology
Function and homology information


lipid biosynthetic process
Similarity search - Function
Fatty acyl-AMP ligase /fatty acyl-CoA ligase / ANL, C-terminal domain / ANL, N-terminal domain / GMP Synthetase; Chain A, domain 3 / AMP-dependent synthetase/ligase / AMP-binding enzyme, C-terminal domain superfamily / AMP-binding enzyme / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-1ZZ / PYROPHOSPHATE 2- / Saframycin Mx1 synthetase B
Similarity search - Component
Biological speciesLegionella pneumophila subsp. pneumophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsZhang, Z. / Burley, S.K. / Swaminathan, S. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: J.Mol.Biol. / Year: 2011
Title: Structural and Functional Studies of Fatty Acyl Adenylate Ligases from E. coli and L. pneumophila.
Authors: Zhang, Z. / Zhou, R. / Sauder, J.M. / Tonge, P.J. / Burley, S.K. / Swaminathan, S.
History
DepositionFeb 3, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 7, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 10, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / struct_conn / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Sep 6, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Nov 22, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Saframycin Mx1 synthetase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,5703
Polymers67,8651
Non-polymers7052
Water6,990388
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)70.193, 78.243, 108.395
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Saframycin Mx1 synthetase B / fatty acyl-adenylate ligase


Mass: 67864.523 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila subsp. pneumophila (bacteria)
Strain: Philadelphia 1 / ATCC 33152 / DSM 7513 / Gene: 11191l2, lpg2229 / Plasmid: BC-pSGX3(BC) / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(de3)codon+ril Stratagene / References: UniProt: Q5ZTD3
#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-POP / PYROPHOSPHATE 2- / Pyrophosphate


Mass: 175.959 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H2O7P2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 388 / 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: 2.19 Å3/Da / Density % sol: 43.91 %
Crystal growMethod: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2 M Magnesium chloride hexahydrate 0.1 M Bis Tris pH 6.5, 25% PEG 3350, VAPOR DIFFUSION, SITTING DROP

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 12, 2009 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2→78.24 Å / Num. obs: 41113 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 12.9 % / Biso Wilson estimate: 21.98 Å2 / Rmerge(I) obs: 0.141 / Net I/σ(I): 20.8
Reflection shellResolution: 2→2.11 Å / Redundancy: 13 % / Rmerge(I) obs: 0.73 / Mean I/σ(I) obs: 3.7 / Num. unique all: 5897 / % possible all: 100

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Processing

Software
NameVersionClassification
CBASSdata collection
PHASERphasing
PHENIX(phenix.refine)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KXW

3kxw


Resolution: 2→44.553 Å / SU ML: 0.28 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 1.3 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2443 2077 5.06 %random
Rwork0.1934 ---
obs0.1959 41038 99.97 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 37.207 Å2 / ksol: 0.334 e/Å3
Displacement parametersBiso mean: 22.82 Å2
Baniso -1Baniso -2Baniso -3
1--5.0131 Å20 Å20 Å2
2--0.4888 Å2-0 Å2
3---4.5243 Å2
Refinement stepCycle: LAST / Resolution: 2→44.553 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4513 0 45 388 4946
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014683
X-RAY DIFFRACTIONf_angle_d1.276346
X-RAY DIFFRACTIONf_dihedral_angle_d19.1141725
X-RAY DIFFRACTIONf_chiral_restr0.093701
X-RAY DIFFRACTIONf_plane_restr0.007800
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.04660.30031350.21662555X-RAY DIFFRACTION100
2.0466-2.09770.24171500.20482537X-RAY DIFFRACTION100
2.0977-2.15440.25391350.20022577X-RAY DIFFRACTION100
2.1544-2.21780.26931320.19642556X-RAY DIFFRACTION100
2.2178-2.28940.271450.19952564X-RAY DIFFRACTION100
2.2894-2.37120.25921380.19462567X-RAY DIFFRACTION100
2.3712-2.46620.2271140.18982595X-RAY DIFFRACTION100
2.4662-2.57840.24041350.18782586X-RAY DIFFRACTION100
2.5784-2.71430.28681510.19692562X-RAY DIFFRACTION100
2.7143-2.88440.27421600.20162568X-RAY DIFFRACTION100
2.8844-3.1070.26711330.20412612X-RAY DIFFRACTION100
3.107-3.41960.25751210.19362627X-RAY DIFFRACTION100
3.4196-3.91420.22871390.17932635X-RAY DIFFRACTION100
3.9142-4.93040.17711330.16782655X-RAY DIFFRACTION100
4.9304-44.5640.23791560.20442765X-RAY DIFFRACTION100

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