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- PDB-1l5a: Crystal Structure of VibH, an NRPS Condensation Enzyme -

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Basic information

Entry
Database: PDB / ID: 1l5a
TitleCrystal Structure of VibH, an NRPS Condensation Enzyme
Componentsamide synthase
KeywordsBIOSYNTHETIC PROTEIN / nonribosomal peptide synthetase / NRPS condensation domain / amide synthase / vibriobactin
Function / homology
Function and homology information


acid-ammonia (or amide) ligase activity / 2,3-dihydroxybenzoate-serine ligase activity / enterobactin synthetase complex / enterobactin biosynthetic process / siderophore biosynthetic process / amino acid activation for nonribosomal peptide biosynthetic process / secondary metabolite biosynthetic process / phosphopantetheine binding / cytoplasm / cytosol
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #80 / Nonribosomal peptide synthetase, condensation domain / Chloramphenicol Acetyltransferase / Chloramphenicol acetyltransferase-like domain / Condensation domain / Condensation domain / Chloramphenicol acetyltransferase-like domain superfamily / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Special ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #80 / Nonribosomal peptide synthetase, condensation domain / Chloramphenicol Acetyltransferase / Chloramphenicol acetyltransferase-like domain / Condensation domain / Condensation domain / Chloramphenicol acetyltransferase-like domain superfamily / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Special / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Vibriobactin synthesis protein, putative
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.55 Å
AuthorsKeating, T.A. / Marshall, C.G. / Walsh, C.T. / Keating, A.E.
CitationJournal: Nat.Struct.Biol. / Year: 2002
Title: The structure of VibH represents nonribosomal peptide synthetase condensation, cyclization and epimerization domains.
Authors: Keating, T.A. / Marshall, C.G. / Walsh, C.T. / Keating, A.E.
History
DepositionMar 6, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 26, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 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: amide synthase
B: amide synthase
C: amide synthase


Theoretical massNumber of molelcules
Total (without water)149,3853
Polymers149,3853
Non-polymers00
Water3,495194
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)132.595, 161.349, 115.602
Angle α, β, γ (deg.)90.00, 104.81, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein amide synthase / VibH


Mass: 49795.074 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Gene: vibH / Plasmid: pET29b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9KTV9
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 194 / 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: 2

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Sample preparation

CrystalDensity Matthews: 4 Å3/Da / Density % sol: 69 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG 8000, Tris, magnesium formate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 20 ℃ / Details: used microseeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
112 mg/mlprotein1drop
2200 mMTris1reservoirpH8.5
31 %(w/v)PEG80001reservoir
460 mMmagnesium formate1reservoir

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSLS X12C10.9788, 0.9785, 0.9633
SYNCHROTRONNSLS X12C20.9633
DetectorType: BRANDEIS - B4 / Detector: CCD / Date: May 21, 2001
RadiationMonochromator: double crystal, torroidal mirror / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97881
20.97851
30.96331
ReflectionResolution: 2.55→35 Å / Num. all: 78790 / Num. obs: 73969 / % possible obs: 93.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 2.6 % / Biso Wilson estimate: 55.5 Å2 / Rsym value: 0.046 / Net I/σ(I): 19.1
Reflection shellResolution: 2.55→2.64 Å / Num. unique all: 4581 / Rsym value: 0.321 / % possible all: 58.5
Reflection
*PLUS
Lowest resolution: 35 Å / Rmerge(I) obs: 0.046
Reflection shell
*PLUS
Rmerge(I) obs: 0.32

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Processing

Software
NameClassification
SOLVEphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.55→34.14 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 2053567.31 / Data cutoff high rms absF: 2053567.31 / Isotropic thermal model: restrained / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.259 7379 10.1 %random
Rwork0.214 ---
all0.214 72923 --
obs0.259 72923 95.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 33.7813 Å2 / ksol: 0.302009 e/Å3
Displacement parametersBiso mean: 47.6 Å2
Baniso -1Baniso -2Baniso -3
1-0.21 Å20 Å22.75 Å2
2---2.25 Å20 Å2
3---2.04 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.42 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.45 Å0.34 Å
Refinement stepCycle: LAST / Resolution: 2.55→34.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10121 0 0 194 10315
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d23
X-RAY DIFFRACTIONc_improper_angle_d0.96
LS refinement shellResolution: 2.55→2.71 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.377 970 10 %
Rwork0.314 873 -
obs--76.8 %
Refinement
*PLUS
% reflection Rfree: 10 % / Rfactor obs: 0.214 / Rfactor Rfree: 0.259 / Rfactor Rwork: 0.214
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.41
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.96
LS refinement shell
*PLUS
Rfactor Rfree: 0.377 / Rfactor Rwork: 0.314

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