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- PDB-7qos: Cyclopropane fatty acid synthase from Aquifex aeolicous with boun... -

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Basic information

Entry
Database: PDB / ID: 7qos
TitleCyclopropane fatty acid synthase from Aquifex aeolicous with bound ligands
ComponentsCyclopropane-fatty-acyl-phospholipid synthase
KeywordsTRANSFERASE / phospholipid / complex / cyclopropane fatty acid synthase / methyl transferase / SAM
Function / homology
Function and homology information


lipid biosynthetic process / transferase activity
Similarity search - Function
Mycolic acid cyclopropane synthase / : / Mycolic acid cyclopropane synthetase / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
CARBONATE ION / Chem-E8Q / S-ADENOSYL-L-HOMOCYSTEINE / S-ADENOSYLMETHIONINE / Cyclopropane-fatty-acyl-phospholipid synthase
Similarity search - Component
Biological speciesAquifex aeolicus VF5 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.6 Å
AuthorsLukk, T. / Cronan, J.E. / Nair, S.K.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI15650 United States
Citation
Journal: To Be Published
Title: Structure of cyclopropane fatty acid synthase from Aquifex aeolicus
Authors: Cronan, J.E. / Nair, S.K. / Lukk, T.
#1: Journal: Microbiol. Mol. Biol. Rev. / Year: 2022
Title: Advances in the Structural Biology, Mechanism, and Physiology of Cyclopropane Fatty Acid Modifications of Bacterial Membranes
Authors: Cronan, J.E. / Lukk, T.
History
DepositionDec 28, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 2, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 30, 2022Group: Database references / Category: citation / citation_author
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cyclopropane-fatty-acyl-phospholipid synthase
B: Cyclopropane-fatty-acyl-phospholipid synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,2308
Polymers94,9752
Non-polymers2,2556
Water10,359575
1
A: Cyclopropane-fatty-acyl-phospholipid synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,6084
Polymers47,4881
Non-polymers1,1203
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cyclopropane-fatty-acyl-phospholipid synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,6224
Polymers47,4881
Non-polymers1,1343
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.740, 77.280, 86.360
Angle α, β, γ (deg.)90.000, 96.620, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Cyclopropane-fatty-acyl-phospholipid synthase


Mass: 47487.590 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus VF5 (bacteria) / Strain: VF5 / Gene: cfa, aq_1737 / Plasmid: pET28 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O67624

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Non-polymers , 5 types, 581 molecules

#2: Chemical ChemComp-E8Q / 2-azanylethyl-[(2~{S})-2,3-di(hexadecanoyloxy)propoxy]phosphinic acid


Mass: 675.960 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C37H74NO7P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CO3 / CARBONATE ION


Mass: 60.009 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CO3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N6O5S / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H22N6O5S / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 575 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.36 Å3/Da / Density % sol: 47.97 %
Crystal growTemperature: 282 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.2M L-pro, 10% PEG 3350, 0.1M HEPES 7.5, 5 mM S-adenosyl-L-Methionine; protein concentration 8 mg/mL, 1:1 ratio of protein to mother liquor. Protein storage buffer: 20 mM Tris pH 8.5, 0.5M ...Details: 0.2M L-pro, 10% PEG 3350, 0.1M HEPES 7.5, 5 mM S-adenosyl-L-Methionine; protein concentration 8 mg/mL, 1:1 ratio of protein to mother liquor. Protein storage buffer: 20 mM Tris pH 8.5, 0.5M NaCl. 30% PEG 3350 cryoprotectant.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97857 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 13, 2011
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 1.6→19.855 Å / Num. obs: 114947 / % possible obs: 98.6 % / Redundancy: 5.931 % / Biso Wilson estimate: 18.93 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.07 / Rrim(I) all: 0.077 / Χ2: 1.001 / Net I/σ(I): 14.13 / Num. measured all: 681759 / Scaling rejects: 6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.6-1.643.9510.7121.7474270.7020.8286.4
1.64-1.694.440.5862.380140.7740.66495.5
1.69-1.745.3770.4493.3881370.8930.49899.9
1.74-1.796.090.3434.7678950.9360.37599.9
1.79-1.856.2710.276.0576470.960.294100
1.85-1.916.2720.2087.8774150.9740.227100
1.91-1.986.2770.15910.3372000.9840.173100
1.98-2.076.2910.12612.7568980.9890.13799.9
2.07-2.166.3060.10714.8965970.9910.117100
2.16-2.266.3010.09216.8163470.9930.10199.9
2.26-2.396.3070.08218.8559920.9940.089100
2.39-2.536.3140.07420.7957220.9950.08199.8
2.53-2.76.3040.06822.7753630.9950.074100
2.7-2.926.3230.06225.0849740.9960.06799.9
2.92-3.26.3030.05827.0446170.9960.06399.9
3.2-3.586.2970.05329.441710.9960.05899.9
3.58-4.136.3120.0530.9736910.9970.05599.9
4.13-5.066.290.04931.9131110.9970.05499.8
5.06-7.166.2510.0530.9224350.9970.05599.9
7.16-19.8555.9730.05131.5212940.9930.05794.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.19.2-4158refinement
XSCALEdata scaling
PHASERphasing
PDB_EXTRACT3.27data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1KPG

1kpg


Resolution: 1.6→19.855 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 2 / Phase error: 21.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2072 5747 5 %
Rwork0.1815 109187 -
obs0.1828 114934 98.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 80.04 Å2 / Biso mean: 27.0563 Å2 / Biso min: 10.36 Å2
Refinement stepCycle: final / Resolution: 1.6→19.855 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5842 0 153 577 6572
Biso mean--29.82 36.09 -
Num. residues----701
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.6-1.61810.3191640.2748310684
1.6181-1.63710.2791680.2586320588
1.6371-1.65710.29721810.2501343092
1.6571-1.67810.27011850.2421352497
1.6781-1.70010.25131920.2321364099
1.7001-1.72340.25231940.21873684100
1.7234-1.7480.24211920.21363643100
1.748-1.77410.23371940.20663693100
1.7741-1.80180.22821930.20613665100
1.8018-1.83130.2431950.21383707100
1.8313-1.86290.25081910.20353632100
1.8629-1.89670.23531950.20033706100
1.8967-1.93320.22621950.19583697100
1.9332-1.97260.23991910.19663632100
1.9726-2.01540.22991950.18733703100
2.0154-2.06230.2281950.18823695100
2.0623-2.11380.21471940.18773686100
2.1138-2.17090.22031920.18663658100
2.1709-2.23470.2071940.18713692100
2.2347-2.30670.2081940.18423676100
2.3067-2.3890.20911940.18513692100
2.389-2.48450.21431950.18623691100
2.4845-2.59730.19321930.18363680100
2.5973-2.73390.22291950.18163699100
2.7339-2.90470.21811950.18493704100
2.9047-3.12820.21571950.18443703100
3.1282-3.44160.18671950.17873714100
3.4416-3.93620.19991960.15883716100
3.9362-4.94650.14781960.13893730100
4.9465-19.8550.18661990.17053784100

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