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- PDB-9cly: Crystal structure of the 3-ketoacyl-(acyl-carrier-protein) reduct... -

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Basic information

Entry
Database: PDB / ID: 9cly
TitleCrystal structure of the 3-ketoacyl-(acyl-carrier-protein) reductase, CylG, from Streptococcus agalactiae 2603V/R
ComponentsCylG protein
KeywordsOXIDOREDUCTASE / fatty acid and phospholipid metabolism / NAD(P)-dependent dehydrogenase / CSBID / Center for Structural Biology of Infectious Diseases / Structural Genomics / NAD(P)-binding domain-containing protein(
Function / homology
Function and homology information


oxidoreductase activity
Similarity search - Function
: / PKS_KR / Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / Enoyl-(Acyl carrier protein) reductase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
IMIDAZOLE / Chem-NDP / CylG protein
Similarity search - Component
Biological speciesStreptococcus agalactiae 2603V/R (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.16 Å
AuthorsMaltseva, N. / Kim, Y. / Endres, M. / Joachimiak, A. / Center for Structural Biology of Infectious Diseases (CSBID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: To be published
Title: Crystal structure of the 3-ketoacyl-(acyl-carrier-protein) reductase, CylG, from Streptococcus agalactiae 2603V/R
Authors: Maltseva, N. / Kim, Y. / Endres, M. / Joachimiak, A.
History
DepositionJul 12, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 24, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CylG protein
B: CylG protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,8305
Polymers53,2702
Non-polymers1,5603
Water2,774154
1
A: CylG protein
B: CylG protein
hetero molecules

A: CylG protein
B: CylG protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,66010
Polymers106,5404
Non-polymers3,1206
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation1
Unit cell
Length a, b, c (Å)111.518, 111.518, 102.561
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z
Components on special symmetry positions
IDModelComponents
11A-474-

HOH

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Components

#1: Protein CylG protein


Mass: 26635.037 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus agalactiae 2603V/R (bacteria)
Gene: cylG, SAG0664 / Plasmid: p53 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Gold / References: UniProt: Q8E0R2
#2: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H30N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 154 / Source method: isolated from a natural source / Formula: H2O
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: 3.46 Å3/Da / Density % sol: 64.41 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / Details: 60% Tacsimate, pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 10, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.16→50 Å / Num. obs: 39959 / % possible obs: 100 % / Redundancy: 19.8 % / Biso Wilson estimate: 32.39 Å2 / CC1/2: 0.988 / Net I/σ(I): 21.86
Reflection shellResolution: 2.16→2.2 Å / Num. unique obs: 1970 / CC1/2: 0.815 / Rpim(I) all: 0.253

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.16→48.29 Å / SU ML: 0.1857 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 19.8073
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2021 2040 5.11 %
Rwork0.1689 37881 -
obs0.1707 39921 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 40.27 Å2
Refinement stepCycle: LAST / Resolution: 2.16→48.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3699 0 101 154 3954
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00683962
X-RAY DIFFRACTIONf_angle_d0.81325356
X-RAY DIFFRACTIONf_chiral_restr0.0556617
X-RAY DIFFRACTIONf_plane_restr0.0066673
X-RAY DIFFRACTIONf_dihedral_angle_d15.14341551
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.16-2.210.26141290.20722484X-RAY DIFFRACTION99.5
2.21-2.270.24651190.19462508X-RAY DIFFRACTION99.96
2.27-2.330.19611240.18732525X-RAY DIFFRACTION100
2.33-2.390.21491460.18552477X-RAY DIFFRACTION100
2.39-2.470.21581370.18942492X-RAY DIFFRACTION100
2.47-2.560.22321220.18562533X-RAY DIFFRACTION100
2.56-2.660.25691380.19732505X-RAY DIFFRACTION100
2.66-2.780.23111400.19432485X-RAY DIFFRACTION99.92
2.78-2.930.2211440.1942523X-RAY DIFFRACTION100
2.93-3.110.20231350.19222510X-RAY DIFFRACTION100
3.12-3.350.19691540.17852500X-RAY DIFFRACTION99.96
3.36-3.690.1861190.14832547X-RAY DIFFRACTION99.96
3.69-4.230.1651140.13812583X-RAY DIFFRACTION100
4.23-5.320.17961580.13352557X-RAY DIFFRACTION100
5.33-48.290.20341610.17482652X-RAY DIFFRACTION99.86
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)
12.143230141960.6741201145550.7471930395241.27065504140.3282901820191.019845816770.146844920530.274415882892-0.4039351395290.02565813949790.0954194392849-0.4737334275540.1670705845850.293616502996-0.2331605582690.2475681242230.0575534691047-0.06379383977790.296060451624-0.08095750717820.41668282388855.9031983471-64.979074061820.0821152172
23.241640669580.3543585198980.2263579550652.84775460574-1.036034840385.499701361080.01875649183020.628706110526-0.202810140207-0.4504527781270.0974993242129-0.2403674503790.4146348686040.206153201364-0.1155535915440.2390896955360.003914432494410.008969443379360.297489047853-0.06838332312770.30531511529948.1154372424-53.017386645310.363374267
37.241407680860.3151905636370.3302155362344.84551835060.090800221193.64726268266-0.0661632291794-0.3987497297980.3902549876680.354931493151-0.0839458924532-0.270329697747-0.5079267639910.2437653713790.1195866865660.336081399742-0.0711317885299-0.05492654570340.203294803143-0.02122985656960.25687252348543.2641940687-25.628614719226.2266110636
42.846467024521.01576669456-0.7504375790042.28656177539-0.4402354075631.979844942840.0289460903126-0.0003195755882910.3093526602010.0113662098758-0.03454203857880.0716544579189-0.2894231337820.03496971974470.006097408605960.219213960903-0.00804050786208-0.02808760180.1831999219150.001939893773920.17427347986231.8218584219-33.791100568817.1780411326
52.977525966370.605076345684-0.2639254574814.00702792921-1.53476671346.18170433220.0796823831032-0.3636442855650.1238415598040.5403391935490.03846920675670.130124675611-0.254084545258-0.34428035389-0.1445624160940.1873316874490.0110655066831-0.01669242759530.233438419677-0.02327000667010.2583461477639.6354199937-45.054034853928.6922108665
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'B' and (resid -1 through 169 )BC-1 - 1691 - 171
22chain 'B' and (resid 170 through 240 )BC170 - 240172 - 242
33chain 'A' and (resid 1 through 58 )AA1 - 581 - 58
44chain 'A' and (resid 59 through 169 )AA59 - 16959 - 169
55chain 'A' and (resid 170 through 240 )AA170 - 240170 - 240

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