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- PDB-9z38: Crystal Structure of CalO4 from Micromonospora echinospora -

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Basic information

Entry
Database: PDB / ID: 9z38
TitleCrystal Structure of CalO4 from Micromonospora echinospora
Components3-oxoacyl-[acyl-carrier-protein] synthase-3
KeywordsTRANSFERASE / Calicheamicin / Acyltransferase / Thiolase
Function / homology3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III / 3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III / 3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III, C-terminal / 3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III C terminal / secondary metabolite biosynthetic process / 3-oxoacyl-[acyl-carrier-protein] synthase activity / Thiolase-like / fatty acid biosynthetic process / 3-oxoacyl-[acyl-carrier-protein] synthase-3
Function and homology information
Biological speciesMicromonospora echinospora (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.64 Å
AuthorsPang, F. / Townsend, C.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)ES001670 United States
CitationJournal: To Be Published
Title: Crystal Structure of CalO4 from Micromonospora echinospora
Authors: Pang, F. / Peng, Y. / Thadkapally, S. / Townsend, A.C.
History
DepositionNov 5, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 5, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 3-oxoacyl-[acyl-carrier-protein] synthase-3
C: 3-oxoacyl-[acyl-carrier-protein] synthase-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,53617
Polymers77,0212
Non-polymers51515
Water7,332407
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.696, 95.635, 172.584
Angle α, β, γ (deg.)90, 95.63, 90
Int Tables number5
Space group name H-MI121
Components on special symmetry positions
IDModelComponents
11A-406-

CL

21C-703-

HOH

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Components

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Protein , 1 types, 2 molecules AC

#1: Protein 3-oxoacyl-[acyl-carrier-protein] synthase-3


Mass: 38510.723 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Micromonospora echinospora (bacteria) / Gene: GA0070606_5687 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1C6VYG5

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Non-polymers , 5 types, 422 molecules

#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: Cl
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C3H8O3
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Ca
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 407 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationN

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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: 2.55 Å3/Da / Density meas: 76740.53 Mg/m3 / Density % sol: 51.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 0.12 M MES, 1.2 M magnesium sulfate heptahydrate

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Data collection

DiffractionMean temperature: 110 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.919689 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 13, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.919689 Å / Relative weight: 1
ReflectionResolution: 1.64→29.24 Å / Num. obs: 94115 / % possible obs: 99.9 % / Redundancy: 3.5 % / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.04786 / Rpim(I) all: 0.04786 / Rrim(I) all: 0.06768 / Net I/σ(I): 7.36
Reflection shellResolution: 1.64→1.699 Å / Num. unique obs: 9328 / CC1/2: 0.705 / CC star: 0.909

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.64→29.24 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.953 / SU B: 1.784 / SU ML: 0.059 / Cross valid method: FREE R-VALUE / ESU R: 0.077 / ESU R Free: 0.08
Details: Hydrogens have been used if present in the input file
RfactorNum. reflection% reflection
Rfree0.1928 4745 5.042 %
Rwork0.163 89369 -
all0.164 --
obs-94114 99.908 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 17.2 Å2
Baniso -1Baniso -2Baniso -3
1--0.004 Å20 Å2-0.003 Å2
2--0.57 Å20 Å2
3----0.555 Å2
Refinement stepCycle: LAST / Resolution: 1.64→29.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4994 0 27 407 5428
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0125168
X-RAY DIFFRACTIONr_angle_refined_deg2.1551.8127055
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1535695
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.548524
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.22910755
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.67110198
X-RAY DIFFRACTIONr_chiral_restr0.1670.2806
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.023996
X-RAY DIFFRACTIONr_nbd_refined0.220.22465
X-RAY DIFFRACTIONr_nbtor_refined0.320.23578
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1450.2385
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2080.294
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2520.236
X-RAY DIFFRACTIONr_mcbond_it1.9331.4832762
X-RAY DIFFRACTIONr_mcangle_it2.6972.6523457
X-RAY DIFFRACTIONr_scbond_it3.0791.7262406
X-RAY DIFFRACTIONr_scangle_it4.4313.0373596
X-RAY DIFFRACTIONr_lrange_it5.6920.1488104
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.64-1.6820.2763380.25565140.25669150.950.95499.08890.253
1.682-1.7280.2573310.22964000.2367310.9530.9631000.222
1.728-1.7780.2293290.20962730.2166020.9650.9711000.199
1.778-1.8330.233270.19560390.19763660.9650.9741000.183
1.833-1.8930.2263100.17658450.17961550.9670.9791000.164
1.893-1.9590.2072940.16657050.16860000.9720.98299.98330.153
1.959-2.0320.1852800.16155110.16257910.9770.9841000.149
2.032-2.1150.1832740.15552890.15655630.9790.9861000.144
2.115-2.2090.192670.15650680.15853350.9770.9851000.145
2.209-2.3160.1972650.15748170.15950840.9750.98599.96070.149
2.316-2.440.1922600.15546110.15748710.9760.9851000.146
2.44-2.5870.182040.15744000.15846040.9790.9851000.15
2.587-2.7640.2032170.15540980.15743150.9770.9851000.151
2.764-2.9830.1932300.15538390.15740700.9770.98599.97540.154
2.983-3.2650.1861730.15634980.15736710.9770.9851000.161
3.265-3.6440.181670.14432540.14634210.980.9871000.155
3.644-4.1970.1551560.13328150.13429710.9850.991000.149
4.197-5.1140.1481320.13424080.13525400.9880.9891000.16
5.114-7.1250.1771170.18618800.18519970.9830.9811000.21
7.125-29.240.22740.17211050.17511790.9830.9861000.219

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