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- PDB-9dks: Crystal structure of CcbD C19S mutant complexed with single PCP d... -

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Basic information

Entry
Database: PDB / ID: 9dks
TitleCrystal structure of CcbD C19S mutant complexed with single PCP domain of CcbZ
Components
  • CcbD
  • CcbZ
KeywordsBIOSYNTHETIC PROTEIN / complex / sugar / carrier protein
Function / homology
Function and homology information


oxidoreductase activity / nucleotide binding
Similarity search - Function
: / : / 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
MALONATE ION / 4'-PHOSPHOPANTETHEINE / CcbZ / CcbD
Similarity search - Component
Biological speciesStreptomyces caelestis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 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 1.0Sep 17, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)90,1296
Polymers89,5663
Non-polymers5623
Water11,890660
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)75.280, 89.079, 135.029
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: 39182.414 Da / Num. of mol.: 2 / Mutation: C19S
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.: 1
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-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H2O4
#4: Chemical ChemComp-PNS / 4'-PHOSPHOPANTETHEINE


Mass: 358.348 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H23N2O7PS / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 660 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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 % sol: 51.69 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.2 M sodium malonate, 20% w/v PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11588 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Apr 20, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11588 Å / Relative weight: 1
ReflectionResolution: 1.55→135.03 Å / Num. obs: 132094 / % possible obs: 100 % / Redundancy: 13 % / CC1/2: 1 / Rmerge(I) obs: 0.076 / Rpim(I) all: 0.032 / Rrim(I) all: 0.083 / Net I/σ(I): 18.7
Reflection shellResolution: 1.55→1.58 Å / Redundancy: 12.9 % / Rmerge(I) obs: 1.973 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 6507 / CC1/2: 0.649 / Rpim(I) all: 0.826 / Rrim(I) all: 2.141 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.55→74.467 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.961 / SU B: 1.863 / SU ML: 0.063 / Cross valid method: FREE R-VALUE / ESU R: 0.073 / ESU R Free: 0.075
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2051 6716 5.088 %
Rwork0.1769 125283 -
all0.178 --
obs-131999 99.988 %
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: 25.25 Å2
Baniso -1Baniso -2Baniso -3
1-2.254 Å20 Å2-0 Å2
2---1.342 Å20 Å2
3----0.912 Å2
Refinement stepCycle: LAST / Resolution: 1.55→74.467 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5949 0 18 660 6627
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0136162
X-RAY DIFFRACTIONr_bond_other_d0.0010.0145826
X-RAY DIFFRACTIONr_angle_refined_deg1.6741.648405
X-RAY DIFFRACTIONr_angle_other_deg1.5461.57313328
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9835779
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.8719.499359
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.71415962
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2981576
X-RAY DIFFRACTIONr_chiral_restr0.0910.2767
X-RAY DIFFRACTIONr_gen_planes_refined0.010.027074
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021490
X-RAY DIFFRACTIONr_nbd_refined0.2150.21318
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1810.25479
X-RAY DIFFRACTIONr_nbtor_refined0.1690.23007
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0830.22891
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1530.2481
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0530.24
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.0850.28
X-RAY DIFFRACTIONr_nbd_other0.1920.245
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1370.216
X-RAY DIFFRACTIONr_mcbond_it2.1432.4373107
X-RAY DIFFRACTIONr_mcbond_other2.1432.4353106
X-RAY DIFFRACTIONr_mcangle_it2.9623.6473889
X-RAY DIFFRACTIONr_mcangle_other2.9623.6483890
X-RAY DIFFRACTIONr_scbond_it3.3012.7993055
X-RAY DIFFRACTIONr_scbond_other3.3012.83056
X-RAY DIFFRACTIONr_scangle_it4.8284.0624516
X-RAY DIFFRACTIONr_scangle_other4.8274.0634517
X-RAY DIFFRACTIONr_lrange_it6.06247.37926821
X-RAY DIFFRACTIONr_lrange_other5.97247.08126150
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.55-1.590.314760.2999205X-RAY DIFFRACTION99.9897
1.59-1.6340.294620.2798960X-RAY DIFFRACTION100
1.634-1.6810.264750.2558707X-RAY DIFFRACTION100
1.681-1.7330.2674560.2318418X-RAY DIFFRACTION100
1.733-1.790.2474420.218211X-RAY DIFFRACTION99.9884
1.79-1.8530.254500.2057914X-RAY DIFFRACTION99.988
1.853-1.9220.2234400.1877616X-RAY DIFFRACTION99.9628
1.922-2.0010.2373690.1847424X-RAY DIFFRACTION99.9872
2.001-2.090.2063880.1727106X-RAY DIFFRACTION100
2.09-2.1920.213550.1656777X-RAY DIFFRACTION99.986
2.192-2.310.1843480.1566463X-RAY DIFFRACTION99.9853
2.31-2.4510.183400.1586128X-RAY DIFFRACTION99.9536
2.451-2.620.2142900.1695805X-RAY DIFFRACTION100
2.62-2.8290.1942900.1845363X-RAY DIFFRACTION99.9823
2.829-3.0990.2232780.1834964X-RAY DIFFRACTION100
3.099-3.4650.2072310.1814526X-RAY DIFFRACTION100
3.465-4.0010.1722180.1554012X-RAY DIFFRACTION99.9764
4.001-4.8990.1511750.1373425X-RAY DIFFRACTION99.9445
4.899-6.9230.1991550.1642689X-RAY DIFFRACTION100
6.923-74.4670.208780.1721570X-RAY DIFFRACTION100

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