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- PDB-7a9i: Crystal structure of Coronafacic Acid Ligase from Pectobacterium ... -

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Basic information

Entry
Database: PDB / ID: 7a9i
TitleCrystal structure of Coronafacic Acid Ligase from Pectobacterium brasiliense
ComponentsCfl
KeywordsLIGASE
Function / homology
Function and homology information


medium-chain fatty acid-CoA ligase activity / fatty acid metabolic process
Similarity search - Function
ANL, N-terminal domain / AMP-binding enzyme C-terminal domain / AMP-binding enzyme, C-terminal domain / AMP-binding, conserved site / Putative AMP-binding domain signature. / AMP-dependent synthetase/ligase / AMP-binding enzyme / AMP-binding enzyme, C-terminal domain superfamily
Similarity search - Domain/homology
PHOSPHATE ION / 6-ethyl-1-oxidanylidene-indene-4-carboxylic acid / Cfl
Similarity search - Component
Biological speciesPectobacterium brasiliense (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsLevy, C.W.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/K002341/1 United Kingdom
Citation
Journal: Nature / Year: 2021
Title: Discovery, characterization and engineering of ligases for amide synthesis.
Authors: Winn, M. / Rowlinson, M. / Wang, F. / Bering, L. / Francis, D. / Levy, C. / Micklefield, J.
#1: Journal: Acta Crystallogr., Sect. D: Biol. Crystallogr. / Year: 2012
Title: Towards automated crystallographic structure refinement with phenix.refine.
Authors: Afonine, P.V.
History
DepositionSep 2, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 5, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 2, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2May 1, 2024Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cfl
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,8945
Polymers60,4061
Non-polymers4874
Water3,531196
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area660 Å2
ΔGint-18 kcal/mol
Surface area22930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.828, 115.293, 70.942
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z

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Components

#1: Protein Cfl / Ligase


Mass: 60406.453 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pectobacterium brasiliense (bacteria) / Gene: cfl, KCO_08370, KU74_07105 / Production host: Escherichia coli (E. coli) / References: UniProt: M4GWN4
#2: Chemical ChemComp-R4Z / 6-ethyl-1-oxidanylidene-indene-4-carboxylic acid


Mass: 202.206 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H10O3
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 196 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.63 Å3/Da / Density % sol: 53.31 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 2M ammonium sulfate, 0.1M sodium Hepes pH 7.5, 2% v/v Peg 400
Temp details: Cold room

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9159 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 11, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9159 Å / Relative weight: 1
ReflectionResolution: 2.1→64.51 Å / Num. obs: 37973 / % possible obs: 99.82 % / Redundancy: 6.4 % / Biso Wilson estimate: 42.68 Å2 / CC1/2: 0.998 / CC star: 1 / Rmerge(I) obs: 0.1 / Rpim(I) all: 0.043 / Net I/σ(I): 8.07
Reflection shellResolution: 2.1→2.175 Å / Redundancy: 6.7 % / Rmerge(I) obs: 1.252 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 3717 / CC1/2: 0.742 / CC star: 0.923 / Rpim(I) all: 0.5237 / % possible all: 99.38

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
DIALSdata reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: inhouse

Resolution: 2.1→64.51 Å / SU ML: 0.239 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.0074
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2293 1998 5.26 %
Rwork0.1947 35969 -
obs0.1966 37967 99.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 55.88 Å2
Refinement stepCycle: LAST / Resolution: 2.1→64.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3989 0 30 196 4215
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00854148
X-RAY DIFFRACTIONf_angle_d1.07555633
X-RAY DIFFRACTIONf_chiral_restr0.064637
X-RAY DIFFRACTIONf_plane_restr0.0072713
X-RAY DIFFRACTIONf_dihedral_angle_d16.4866547
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.150.33311370.28292485X-RAY DIFFRACTION97.4
2.15-2.210.3391400.26832503X-RAY DIFFRACTION99.77
2.21-2.270.30581400.27592517X-RAY DIFFRACTION99.55
2.27-2.350.30421420.24562560X-RAY DIFFRACTION99.67
2.35-2.430.2921420.23022535X-RAY DIFFRACTION99.89
2.43-2.530.27071420.22122549X-RAY DIFFRACTION99.81
2.53-2.640.27041410.2092547X-RAY DIFFRACTION99.89
2.64-2.780.25811410.212555X-RAY DIFFRACTION99.78
2.78-2.960.25261420.22262566X-RAY DIFFRACTION99.96
2.96-3.190.24721430.21582565X-RAY DIFFRACTION99.93
3.19-3.510.24231440.19752588X-RAY DIFFRACTION100
3.51-4.010.1931440.17142599X-RAY DIFFRACTION100
4.01-5.060.18721460.15042640X-RAY DIFFRACTION99.96
5.06-64.510.20521540.18712760X-RAY DIFFRACTION99.97
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)
12.847363666520.3751357144190.4722923293531.650796865990.1123623789552.849672787320.0358188056562-0.200943776370.4604404177320.240726793653-0.0516561121889-0.0635909881308-0.4208882501320.1081171836930.01261622996610.315014991977-0.03959773577790.01704185301060.268563913053-0.01647026660550.30652949564310.021750983931.894284443925.6037392976
21.889078524980.7731256051550.5304487253171.319593980361.043679754973.00817184183-0.01803074744360.272289734636-0.167969721635-0.1778563246620.15544349992-0.1159190760250.1695158063170.149854366668-0.1250914067380.305345183019-0.05299862125930.00700982152820.3245680790270.01236322719860.3148884682676.8971785744113.62354701386.01516319764
32.364449310820.77855326084-2.236521908710.474183686469-0.4282836007282.35674411904-0.447827471381-0.135718008246-0.877565761006-0.2694783493020.169001868735-0.4766713824030.68453564575-0.04355911231560.2183231651780.539704012123-0.06899575586810.03820234452310.4102891118850.02857127192880.64885372565920.14981562288.67946932784-16.4260698972
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A

IDRefine TLS-IDSelection detailsLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 22 through 197 )A22 - 19724 - 193
22chain 'A' and (resid 198 through 417 )A198 - 417194 - 410
33chain 'A' and (resid 418 through 537 )A - B418 - 580411

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