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- PDB-7cxv: Crystal structure of CmnK -

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Basic information

Entry
Database: PDB / ID: 7cxv
TitleCrystal structure of CmnK
ComponentsCmnK
KeywordsBIOSYNTHETIC PROTEIN / CmnB / Lyase / capreomycin
Function / homology
Function and homology information


nucleotide binding / cytoplasm
Similarity search - Function
Ornithine cyclodeaminase/mu-crystallin / Ornithine cyclodeaminase, N-terminal / Ornithine cyclodeaminase/mu-crystallin family / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesSaccharothrix mutabilis subsp. capreolus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsChang, C.Y. / Hsu, S.H.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, Taiwan)107-2113-M-009-021-MY3 Taiwan
CitationJournal: Biochemistry / Year: 2021
Title: Characterization of Enzymes Catalyzing the Formation of the Nonproteinogenic Amino Acid l-Dap in Capreomycin Biosynthesis.
Authors: Hsu, S.H. / Zhang, S. / Huang, S.C. / Wu, T.K. / Xu, Z. / Chang, C.Y.
History
DepositionSep 2, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 14, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CmnK
B: CmnK


Theoretical massNumber of molelcules
Total (without water)74,4182
Polymers74,4182
Non-polymers00
Water1,00956
1
A: CmnK

B: CmnK


Theoretical massNumber of molelcules
Total (without water)74,4182
Polymers74,4182
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_645-x+1,y-1/2,-z+1/21
Buried area4190 Å2
ΔGint-34 kcal/mol
Surface area24760 Å2
Unit cell
Length a, b, c (Å)50.436, 87.264, 147.061
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121

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Components

#1: Protein CmnK


Mass: 37209.023 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharothrix mutabilis subsp. capreolus (bacteria)
Gene: cmnK / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A6YEI2
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 56 / 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: 2.31 Å3/Da / Density % sol: 46.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 50 mM MgCl2.6H2O, 30% w/v PEG-550, 1 mM L-Dap, and 100 mM HEPES

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 0.9732 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 30, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9732 Å / Relative weight: 1
ReflectionResolution: 2.35→30 Å / Num. obs: 24261 / % possible obs: 95.4 % / Redundancy: 5.8 % / CC1/2: 0.98 / Net I/σ(I): 26.42
Reflection shellResolution: 2.35→2.43 Å / Mean I/σ(I) obs: 4.68 / Num. unique obs: 2568 / CC1/2: 0.95

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Processing

Software
NameVersionClassification
REFMAC5.8.0232refinement
PDB_EXTRACT3.25data extraction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7CXS

7cxs


Resolution: 2.35→28.14 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.909 / SU B: 7.678 / SU ML: 0.184 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.504 / ESU R Free: 0.27 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2439 1237 4.9 %RANDOM
Rwork0.1987 ---
obs0.2009 24261 91.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 95.93 Å2 / Biso mean: 29.498 Å2 / Biso min: 13.69 Å2
Baniso -1Baniso -2Baniso -3
1-0.08 Å20 Å20 Å2
2---0.08 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 2.35→28.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4854 0 0 56 4910
Biso mean---26.71 -
Num. residues----653
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0134957
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174668
X-RAY DIFFRACTIONr_angle_refined_deg1.3711.6336765
X-RAY DIFFRACTIONr_angle_other_deg1.2181.5710700
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2165650
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.91319.844256
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.61515711
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.5121548
X-RAY DIFFRACTIONr_chiral_restr0.0560.2639
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025720
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021120
LS refinement shellResolution: 2.35→2.411 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.231 65 -
Rwork0.2 1581 -
all-1646 -
obs--80.73 %

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