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- PDB-7c7m: The structure of SAM-bound CntL, an aminobutyrate transferase in ... -

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Basic information

Entry
Database: PDB / ID: 7c7m
TitleThe structure of SAM-bound CntL, an aminobutyrate transferase in staphylopine biosysnthesis
ComponentsStaphylopine biosynthesis enzyme CntL
KeywordsTRANSFERASE / Metallophore / Biosynthesis / Substrate / Aminobutyrate
Function / homologynicotianamine synthase activity / nicotianamine biosynthetic process / Nicotianamine synthase / methyltransferase activity / methylation / S-adenosyl-L-methionine-dependent methyltransferase superfamily / S-ADENOSYLMETHIONINE / D-histidine (S)-2-aminobutanoyltransferase CntL
Function and homology information
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.81 Å
AuthorsLuo, Z. / Luo, S. / Zhou, H.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)81773636 China
CitationJournal: Faseb J. / Year: 2021
Title: Structural insights into the ligand recognition and catalysis of the key aminobutanoyltransferase CntL in staphylopine biosynthesis.
Authors: Luo, Z. / Luo, S. / Ju, Y. / Ding, P. / Xu, J. / Gu, Q. / Zhou, H.
History
DepositionMay 26, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 28, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Staphylopine biosynthesis enzyme CntL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,1064
Polymers32,5831
Non-polymers5233
Water2,756153
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area320 Å2
ΔGint4 kcal/mol
Surface area12540 Å2
Unit cell
Length a, b, c (Å)45.522, 92.142, 56.669
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-483-

HOH

21A-541-

HOH

31A-542-

HOH

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Components

#1: Protein Staphylopine biosynthesis enzyme CntL / rRNA methyltransferase FmrO


Mass: 32582.947 Da / Num. of mol.: 1 / Mutation: A119T
Source method: isolated from a genetically manipulated source
Details: M(INITIATING METHIONINE)GSSHHHHHHSS G(EXPRESSION TAG)
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: fmrO, cntL, DDL17_02690, M1K003_1012
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A391FC11
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C15H22N6O5S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 153 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 1.82 Å3/Da / Density % sol: 32.45 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Bis-Tris pH 5.5, 2.0 M Ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 10, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.81→48.27 Å / Num. obs: 22386 / % possible obs: 99.8 % / Redundancy: 12.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.088 / Net I/σ(I): 21.4
Reflection shellResolution: 1.81→1.85 Å / Rmerge(I) obs: 0.56 / Num. unique obs: 1292 / CC1/2: 0.958

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Processing

Software
NameVersionClassification
REFMAC5.8.0230refinement
HKL-2000data reduction
HKL-2000data scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 1.81→48.27 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.949 / SU B: 2.726 / SU ML: 0.083 / Cross valid method: THROUGHOUT / ESU R: 0.145 / ESU R Free: 0.123 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20696 1130 5.1 %RANDOM
Rwork0.1853 ---
obs0.1864 21220 99.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.593 Å2
Baniso -1Baniso -2Baniso -3
1--1.9 Å2-0 Å20 Å2
2--2.93 Å2-0 Å2
3----1.03 Å2
Refinement stepCycle: 1 / Resolution: 1.81→48.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1977 0 35 153 2165
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0142102
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171913
X-RAY DIFFRACTIONr_angle_refined_deg1.2731.6782859
X-RAY DIFFRACTIONr_angle_other_deg0.941.6814470
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0985263
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.43924.563103
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.01815355
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.502158
X-RAY DIFFRACTIONr_chiral_restr0.0680.2294
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022355
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02372
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2981.9671043
X-RAY DIFFRACTIONr_mcbond_other1.2961.9671043
X-RAY DIFFRACTIONr_mcangle_it2.0212.9321309
X-RAY DIFFRACTIONr_mcangle_other2.0212.9331310
X-RAY DIFFRACTIONr_scbond_it2.2852.211057
X-RAY DIFFRACTIONr_scbond_other2.2842.211058
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.3923.2121550
X-RAY DIFFRACTIONr_long_range_B_refined4.61623.6892333
X-RAY DIFFRACTIONr_long_range_B_other4.51323.4482310
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.81→1.857 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.306 71 -
Rwork0.234 1542 -
obs--99.94 %

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