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- PDB-7yn3: Crystal structure of CcbD complex with CcbZ carrier protein domain -

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Basic information

Entry
Database: PDB / ID: 7yn3
TitleCrystal structure of CcbD complex with CcbZ carrier protein domain
Components
  • CcbD
  • CcbZ
KeywordsLYASE / lincomycin / celesticetin / amide bond forming enzyme
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
1,1'-ethane-1,2-diyldipyrrolidine-2,5-dione / 4'-PHOSPHOPANTETHEINE / CcbZ / CcbD
Similarity search - Component
Biological speciesStreptomyces caelestis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsMori, T. / Lyu, S. / Abe, I.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Crystal structure of CcbD complex with carrier protein
Authors: Mori, T. / Lyu, S. / Abe, I.
History
DepositionJul 29, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 2, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)99,7918
Polymers98,6264
Non-polymers1,1654
Water11,295627
1
A: CcbD
C: CcbZ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,8954
Polymers49,3132
Non-polymers5832
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: CcbD
D: CcbZ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,8954
Polymers49,3132
Non-polymers5832
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)89.572, 90.104, 124.411
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein CcbD


Mass: 40806.281 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: 8506.611 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-1N2 / 1,1'-ethane-1,2-diyldipyrrolidine-2,5-dione


Mass: 224.213 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H12N2O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-PNS / 4'-PHOSPHOPANTETHEINE


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


Mass: 18.015 Da / Num. of mol.: 627 / 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: 2.55 Å3/Da / Density % sol: 51.67 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.1 M MES (pH 6.7), 0.16 M magnesium chloride, 0.2 M sodium thiocyanate, 8% w/v PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.07 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: May 17, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07 Å / Relative weight: 1
ReflectionResolution: 2.1→44.79 Å / Num. obs: 59483 / % possible obs: 100 % / Redundancy: 7.6 % / Biso Wilson estimate: 27.53 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.098 / Net I/σ(I): 14.7
Reflection shellResolution: 2.1→2.16 Å / Redundancy: 7.9 % / Rmerge(I) obs: 0.677 / Mean I/σ(I) obs: 2.9 / Num. unique obs: 4565 / CC1/2: 0.848 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7YN1

7yn1


Resolution: 2.1→44.79 Å / SU ML: 0.2202 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.6361
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2264 1994 3.36 %
Rwork0.1754 57412 -
obs0.177 59406 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.56 Å2
Refinement stepCycle: LAST / Resolution: 2.1→44.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6525 0 74 627 7226
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00666779
X-RAY DIFFRACTIONf_angle_d0.8559251
X-RAY DIFFRACTIONf_chiral_restr0.04651034
X-RAY DIFFRACTIONf_plane_restr0.00881220
X-RAY DIFFRACTIONf_dihedral_angle_d15.64272503
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.150.25961400.21854050X-RAY DIFFRACTION99.98
2.15-2.210.30721390.20694032X-RAY DIFFRACTION99.98
2.21-2.280.24891410.19114045X-RAY DIFFRACTION99.93
2.28-2.350.25191450.18894055X-RAY DIFFRACTION100
2.35-2.430.24341400.19124090X-RAY DIFFRACTION99.95
2.43-2.530.25451430.18874026X-RAY DIFFRACTION100
2.53-2.650.2711430.19874102X-RAY DIFFRACTION99.95
2.65-2.790.2441410.20014054X-RAY DIFFRACTION99.98
2.79-2.960.27131420.19834102X-RAY DIFFRACTION99.91
2.96-3.190.23131370.18374099X-RAY DIFFRACTION99.93
3.19-3.510.22691430.18144089X-RAY DIFFRACTION99.98
3.51-4.020.18911440.15584145X-RAY DIFFRACTION100
4.02-5.060.2041440.1434182X-RAY DIFFRACTION100
5.06-44.790.18561520.15634341X-RAY DIFFRACTION99.73

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