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- PDB-8if7: Crystal structure of CmnB -

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Basic information

Entry
Database: PDB / ID: 8if7
TitleCrystal structure of CmnB
ComponentsCmnB
KeywordsBIOSYNTHETIC PROTEIN / PLP-dependent enzyme / CmnB / capreomycin / L-Dap
Function / homologycysteine synthase activity / : / cysteine biosynthetic process from serine / Pyridoxal-phosphate dependent enzyme / Pyridoxal-phosphate dependent enzyme / Tryptophan synthase beta subunit-like PLP-dependent enzyme / cytoplasm / Chem-P1T / CmnB
Function and homology information
Biological speciesSaccharothrix mutabilis subsp. capreolus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsChang, C.Y. / Toh, S.I. / Lo, C.L.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, Taiwan)110-2113-M-A49-026-MY3 Taiwan
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2023
Title: Crystal structure of CmnB involved in the biosynthesis of the nonproteinogenic amino acid L-2,3-diaminopropionic acid.
Authors: Toh, S.I. / Lo, C.L. / Chang, C.Y.
History
DepositionFeb 17, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 26, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CmnB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,7662
Polymers40,4481
Non-polymers3181
Water1,08160
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.649, 64.649, 84.189
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

#1: Protein CmnB


Mass: 40447.848 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharothrix mutabilis subsp. capreolus (bacteria)
Gene: cmnB / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A6YEH3
#2: Chemical ChemComp-P1T / 2-[({3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYL)AMINO]ACRYLIC ACID


Mass: 318.220 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C11H15N2O7P / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 60 / 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: 2.31 Å3/Da / Density % sol: 46.66 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: 20 mM Tris pH8.0

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 5, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→30 Å / Num. obs: 17474 / % possible obs: 99 % / Redundancy: 8.3 % / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.039 / Rpim(I) all: 0.015 / Rrim(I) all: 0.042 / Χ2: 0.889 / Net I/σ(I): 21
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.2-2.2880.41117170.9730.9930.1530.4390.87598.3
2.28-2.378.50.32717500.9850.9960.1190.3480.84199
2.37-2.488.50.23417290.9930.9980.0850.2490.89698.4
2.48-2.618.50.17217360.9950.9990.0620.1830.95599.1
2.61-2.778.40.12417390.9960.9990.0450.1321.01299
2.77-2.998.40.0817400.99810.0290.0851.02299.2
2.99-3.298.30.05317540.99910.0190.0561.01299.1
3.29-3.768.20.03517590.99910.0130.0370.94599.5
3.76-4.7380.02617560.99910.010.0280.76699.4
4.73-307.70.02217940.99910.0080.0230.53598.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
SCALAdata scaling
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→28.91 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.933 / Cross valid method: THROUGHOUT / ESU R: 0.296 / ESU R Free: 0.211 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22532 851 5.2 %RANDOM
Rwork0.18112 ---
obs0.18345 15620 93.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.208 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å20 Å20 Å2
2---0 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 2.2→28.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2538 0 21 60 2619
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0122605
X-RAY DIFFRACTIONr_bond_other_d0.0020.0162443
X-RAY DIFFRACTIONr_angle_refined_deg1.3661.6493556
X-RAY DIFFRACTIONr_angle_other_deg0.7281.5565636
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9815341
X-RAY DIFFRACTIONr_dihedral_angle_2_deg14.89535
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.88410390
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0570.2424
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023090
X-RAY DIFFRACTIONr_gen_planes_other0.0070.02521
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_it2.5183.3611370
X-RAY DIFFRACTIONr_mcbond_other2.513.3611367
X-RAY DIFFRACTIONr_mcangle_it3.8385.0361709
X-RAY DIFFRACTIONr_mcangle_other3.8365.0371708
X-RAY DIFFRACTIONr_scbond_it3.1033.81235
X-RAY DIFFRACTIONr_scbond_other3.13.81235
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.785.5411848
X-RAY DIFFRACTIONr_long_range_B_refined6.61143.5632854
X-RAY DIFFRACTIONr_long_range_B_other6.60843.5712849
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.201→2.258 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.254 47 -
Rwork0.227 712 -
obs--57.37 %

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