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- PDB-8kdk: Crystal structure of CcbF in complex with PLP -

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Basic information

Entry
Database: PDB / ID: 8kdk
TitleCrystal structure of CcbF in complex with PLP
ComponentsCcbF
KeywordsLYASE / lincomycin / PLP / biosynthesis
Function / homology
Function and homology information


succinyldiaminopimelate transaminase / succinyldiaminopimelate transaminase activity / biosynthetic process / pyridoxal phosphate binding
Similarity search - Function
: / Aminotransferase, class I/classII / Aminotransferase class I and II / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase
Similarity search - Domain/homology
Biological speciesStreptomyces caelestis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsMori, T. / Lyu, S. / Kadlcik, S. / Abe, I.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Crystal structure of CcbF in complex with PLP
Authors: Mori, T. / Lyu, S. / Kadlcik, S. / Abe, I.
History
DepositionAug 9, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 14, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: CcbF
A: CcbF
B: CcbF
C: CcbF


Theoretical massNumber of molelcules
Total (without water)193,1804
Polymers193,1804
Non-polymers00
Water19,4561080
1
D: CcbF
A: CcbF


Theoretical massNumber of molelcules
Total (without water)96,5902
Polymers96,5902
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4850 Å2
ΔGint-18 kcal/mol
Surface area29090 Å2
MethodPISA
2
B: CcbF
C: CcbF


Theoretical massNumber of molelcules
Total (without water)96,5902
Polymers96,5902
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4890 Å2
ΔGint-17 kcal/mol
Surface area30470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.391, 102.700, 102.954
Angle α, β, γ (deg.)90.000, 92.440, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein
CcbF


Mass: 48295.023 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces caelestis (bacteria) / Gene: HDA41_002770 / Production host: Escherichia coli (E. coli) / References: UniProt: E9JES7
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1080 / 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: 2.06 Å3/Da / Density % sol: 40.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1M Tris-Cl pH 8.5, 31% PEG 4000, 0.16M NaOAc

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.1 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Nov 16, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.8→45.99 Å / Num. obs: 144884 / % possible obs: 100 % / Redundancy: 7.1 % / Biso Wilson estimate: 18.68 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.108 / Net I/σ(I): 11.2
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.794 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 7101 / CC1/2: 0.751 / % 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 / Resolution: 1.8→45.99 Å / SU ML: 0.212 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.8176
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2475 2008 1.39 %
Rwork0.2031 142814 -
obs0.2037 144822 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.51 Å2
Refinement stepCycle: LAST / Resolution: 1.8→45.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12704 0 0 1089 13793
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007513145
X-RAY DIFFRACTIONf_angle_d0.976217978
X-RAY DIFFRACTIONf_chiral_restr0.05891861
X-RAY DIFFRACTIONf_plane_restr0.01062378
X-RAY DIFFRACTIONf_dihedral_angle_d14.15884756
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.850.27291440.226110155X-RAY DIFFRACTION99.99
1.85-1.890.29211490.227610149X-RAY DIFFRACTION99.98
1.89-1.950.26391400.216810162X-RAY DIFFRACTION100
1.95-2.010.28161360.210610175X-RAY DIFFRACTION100
2.01-2.090.23971390.203310194X-RAY DIFFRACTION100
2.09-2.170.27641490.205310183X-RAY DIFFRACTION100
2.17-2.270.26281430.199710161X-RAY DIFFRACTION99.96
2.27-2.390.25951330.205910196X-RAY DIFFRACTION100
2.39-2.540.26841390.206910177X-RAY DIFFRACTION100
2.54-2.730.23241500.210410201X-RAY DIFFRACTION99.98
2.73-3.010.2711440.211210222X-RAY DIFFRACTION99.92
3.01-3.440.24161500.195610242X-RAY DIFFRACTION99.95
3.44-4.340.21411440.182910239X-RAY DIFFRACTION100
4.34-45.990.22771480.205410358X-RAY DIFFRACTION99.77

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