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- PDB-9dkr: Crystal structure of CcbD complexed with PCP domain of CcbZ -

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Basic information

Entry
Database: PDB / ID: 9dkr
TitleCrystal structure of CcbD complexed with PCP domain of CcbZ
Components
  • CcbD
  • CcbZ
KeywordsBIOSYNTHETIC PROTEIN / carrier protein / sugar
Function / homology
Function and homology information


: / GFO/IDH/MocA C-terminal domain / Gfo/Idh/MocA-like oxidoreductase, N-terminal / Oxidoreductase family, NAD-binding Rossmann fold / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
ACETATE ION / 4'-PHOSPHOPANTETHEINE / CcbZ / CcbD
Similarity search - Component
Biological speciesStreptomyces caelestis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.66 Å
AuthorsHeberlig, G.W. / Podust, L.M. / Burkart, M.D.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM095970 United States
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)K12HL141956 United States
CitationJournal: To Be Published
Title: Crystal structure of CcbD complexed with PCP domain of CcbZ
Authors: Heberlig, G.W. / Podust, L.M. / Burkart, M.D.
History
DepositionSep 9, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 1, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CcbD
B: CcbD
C: CcbZ
D: CcbZ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,6358
Polymers100,8004
Non-polymers8354
Water11,205622
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10770 Å2
ΔGint-62 kcal/mol
Surface area32310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.140, 98.956, 123.312
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein CcbD


Mass: 39198.477 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces caelestis (bacteria) / Gene: HDA41_002772 / Production host: Escherichia coli (E. coli) / References: UniProt: E9JES9
#2: Protein CcbZ / Putative dehydrogenase/acyl carrier protein


Mass: 11201.400 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces caelestis (bacteria) / Gene: HDA41_002769 / Production host: Escherichia coli (E. coli) / References: UniProt: E9JES6
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-PNS / 4'-PHOSPHOPANTETHEINE


Mass: 358.348 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H23N2O7PS
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 622 / Source method: isolated from a natural source / Formula: H2O
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: 2.63 Å3/Da / Density % sol: 53.29 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.2 M sodium acetate trihydrate, 20% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11595 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 12, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11595 Å / Relative weight: 1
ReflectionResolution: 1.66→123.31 Å / Num. obs: 124814 / % possible obs: 100 % / Redundancy: 13.3 % / CC1/2: 1 / Rmerge(I) obs: 0.073 / Rpim(I) all: 0.03 / Rrim(I) all: 0.079 / Net I/σ(I): 20.2
Reflection shellResolution: 1.66→1.69 Å / Redundancy: 13.5 % / Rmerge(I) obs: 1.676 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 6099 / CC1/2: 0.677 / Rpim(I) all: 0.683 / Rrim(I) all: 1.812 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
SHELXphasing
RefinementMethod to determine structure: SIRAS / Resolution: 1.66→77.297 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.956 / SU B: 2.043 / SU ML: 0.067 / Cross valid method: FREE R-VALUE / ESU R: 0.088 / ESU R Free: 0.089
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2141 6410 5.139 %
Rwork0.1841 118312 -
all0.186 --
obs-124722 99.994 %
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: 31.71 Å2
Baniso -1Baniso -2Baniso -3
1-1.563 Å20 Å2-0 Å2
2---0.944 Å20 Å2
3----0.619 Å2
Refinement stepCycle: LAST / Resolution: 1.66→77.297 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6515 0 50 622 7187
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0136748
X-RAY DIFFRACTIONr_bond_other_d0.0030.0146392
X-RAY DIFFRACTIONr_angle_refined_deg1.6541.6419212
X-RAY DIFFRACTIONr_angle_other_deg1.51.57114633
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.915852
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.58919.788377
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.6151041
X-RAY DIFFRACTIONr_dihedral_angle_other_3_deg13.898152
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1141575
X-RAY DIFFRACTIONr_chiral_restr0.0860.2857
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.027690
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021580
X-RAY DIFFRACTIONr_nbd_refined0.2190.21443
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1810.26035
X-RAY DIFFRACTIONr_nbtor_refined0.1660.23269
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0810.23288
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1310.2460
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1790.25
X-RAY DIFFRACTIONr_nbd_other0.1750.237
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1040.216
X-RAY DIFFRACTIONr_mcbond_it3.0433.183407
X-RAY DIFFRACTIONr_mcbond_other3.0373.1793406
X-RAY DIFFRACTIONr_mcangle_it4.3124.7564255
X-RAY DIFFRACTIONr_mcangle_other4.3124.7574256
X-RAY DIFFRACTIONr_scbond_it3.7543.5113341
X-RAY DIFFRACTIONr_scbond_other3.7533.5123342
X-RAY DIFFRACTIONr_scangle_it5.5065.1364956
X-RAY DIFFRACTIONr_scangle_other5.5065.1374957
X-RAY DIFFRACTIONr_lrange_it7.56160.37828838
X-RAY DIFFRACTIONr_lrange_other7.54260.29828210
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.66-1.7030.3124980.298623X-RAY DIFFRACTION100
1.703-1.750.2834620.2628452X-RAY DIFFRACTION100
1.75-1.80.2694910.2388186X-RAY DIFFRACTION99.9885
1.8-1.8560.2724370.2267950X-RAY DIFFRACTION100
1.856-1.9170.2443960.2087770X-RAY DIFFRACTION100
1.917-1.9840.2293770.1987535X-RAY DIFFRACTION99.9874
1.984-2.0590.2214200.1897216X-RAY DIFFRACTION99.9869
2.059-2.1430.2363790.1896974X-RAY DIFFRACTION100
2.143-2.2380.2263580.1836668X-RAY DIFFRACTION100
2.238-2.3470.223340.1796450X-RAY DIFFRACTION100
2.347-2.4740.2273210.1756140X-RAY DIFFRACTION100
2.474-2.6240.1892980.1695783X-RAY DIFFRACTION99.9836
2.624-2.8050.2132850.1835462X-RAY DIFFRACTION100
2.805-3.030.2032870.1775066X-RAY DIFFRACTION99.9813
3.03-3.3190.2132320.1914736X-RAY DIFFRACTION100
3.319-3.7110.2212350.1954259X-RAY DIFFRACTION100
3.711-4.2840.1892190.1593781X-RAY DIFFRACTION99.975
4.284-5.2450.1721840.1573209X-RAY DIFFRACTION100
5.245-7.4110.2111360.1842545X-RAY DIFFRACTION99.9627
7.411-77.2970.19610.161509X-RAY DIFFRACTION99.9363

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