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- PDB-6knk: Crystal structure of SbnH in complex with citryl-diaminoethane -

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Basic information

Entry
Database: PDB / ID: 6knk
TitleCrystal structure of SbnH in complex with citryl-diaminoethane
ComponentsProbable diaminopimelate decarboxylase protein
KeywordsBIOSYNTHETIC PROTEIN / PLP-dependent decarboxylase / Staphyloferrin B
Function / homology
Function and homology information


diaminopimelate decarboxylase activity / polyamine biosynthetic process / L-lysine biosynthetic process via diaminopimelate
Similarity search - Function
Ornithine decarboxylase / Ornithine/DAP/Arg decarboxylase / Orn/DAP/Arg decarboxylase 2, C-terminal / Pyridoxal-dependent decarboxylase, C-terminal sheet domain / Orn/DAP/Arg decarboxylase 2, N-terminal / Pyridoxal-dependent decarboxylase, pyridoxal binding domain / Alanine racemase/group IV decarboxylase, C-terminal / PLP-binding barrel / Lipocalin family conserved site / Lipocalin signature.
Similarity search - Domain/homology
Chem-DN9 / PHOSPHATE ION / Chem-X3J / Probable diaminopimelate decarboxylase protein
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus Mu50 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsTang, J. / Ju, Y. / Zhou, H.
Funding support China, 2items
OrganizationGrant numberCountry
Ministry of Science and Technology (China)2017YFE0109900 China
National Natural Science Foundation of ChinaNo. 81773636 China
CitationJournal: J.Mol.Biol. / Year: 2019
Title: Structural Insights into Substrate Recognition and Activity Regulation of the Key Decarboxylase SbnH in Staphyloferrin B Biosynthesis.
Authors: Tang, J. / Ju, Y. / Gu, Q. / Xu, J. / Zhou, H.
History
DepositionAug 5, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 13, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Nov 22, 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 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.d_res_low

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Probable diaminopimelate decarboxylase protein
B: Probable diaminopimelate decarboxylase protein
C: Probable diaminopimelate decarboxylase protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)140,4987
Polymers139,6093
Non-polymers8894
Water4,936274
1
A: Probable diaminopimelate decarboxylase protein
B: Probable diaminopimelate decarboxylase protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,8675
Polymers93,0732
Non-polymers7953
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6400 Å2
ΔGint-32 kcal/mol
Surface area27740 Å2
MethodPISA
2
C: Probable diaminopimelate decarboxylase protein
hetero molecules

C: Probable diaminopimelate decarboxylase protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,2634
Polymers93,0732
Non-polymers1902
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area6340 Å2
ΔGint-39 kcal/mol
Surface area28560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)176.299, 80.325, 111.524
Angle α, β, γ (deg.)90.00, 102.07, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Probable diaminopimelate decarboxylase protein


Mass: 46536.312 Da / Num. of mol.: 3 / Mutation: K50A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus Mu50 (bacteria)
Strain: Mu50 / Gene: SAV0123 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0H3JPF2
#2: Chemical ChemComp-DN9 / (2~{S})-2-[2-[2-[[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]methylamino]ethylamino]-2-oxidanylidene-ethyl]-2-oxidanyl-butanedioic acid


Mass: 465.349 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H24N3O11P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-X3J / (2S)-2-{2-[(2-AMINOETHYL)AMINO]-2-OXOETHYL}-2-HYDROXYBUTANEDIOIC ACID / 5,6-DIHYDRO-BENZO[H]CINNOLIN-3-YLAMINE


Mass: 234.207 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H14N2O6 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 274 / 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: 2.94 Å3/Da / Density % sol: 58.14 %
Crystal growTemperature: 290 K / Method: evaporation
Details: 0.2 M Na Citrate, 50 mM Bis-Tris pH 6.0, 23% PEG 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 16, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.3→46.74 Å / Num. obs: 65898 / % possible obs: 97.3 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.047 / Net I/σ(I): 15.1
Reflection shellResolution: 2.3→2.35 Å / Rmerge(I) obs: 0.367 / Num. unique obs: 4430

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2J66

2j66


Resolution: 2.3→46.74 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.932 / SU B: 9.466 / SU ML: 0.211 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.327 / ESU R Free: 0.227 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALL
RfactorNum. reflection% reflectionSelection details
Rfree0.2455 3242 4.9 %RANDOM
Rwork0.2208 ---
obs0.222 62570 96.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 75.6 Å2 / Biso mean: 41.074 Å2 / Biso min: 22.1 Å2
Baniso -1Baniso -2Baniso -3
1-0.92 Å20 Å2-0.51 Å2
2--5.29 Å20 Å2
3----5.5 Å2
Refinement stepCycle: final / Resolution: 2.3→46.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9187 0 57 274 9518
Biso mean--55.36 36.98 -
Num. residues----1148
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0199524
X-RAY DIFFRACTIONr_bond_other_d0.0020.028763
X-RAY DIFFRACTIONr_angle_refined_deg1.0871.92712952
X-RAY DIFFRACTIONr_angle_other_deg0.879320124
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.83451150
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.924.54478
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.532151522
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.1311533
X-RAY DIFFRACTIONr_chiral_restr0.0620.21407
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0210945
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022322
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_it0.7574.1414606
X-RAY DIFFRACTIONr_mcbond_other0.7584.144605
X-RAY DIFFRACTIONr_mcangle_it1.3336.2085754
X-RAY DIFFRACTIONr_mcangle_other1.3336.2085755
X-RAY DIFFRACTIONr_scbond_it0.6344.2214918
X-RAY DIFFRACTIONr_scbond_other0.6334.2214917
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.1436.3117199
X-RAY DIFFRACTIONr_long_range_B_refined2.47132.53910349
X-RAY DIFFRACTIONr_long_range_B_other2.47132.54110350
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.353 208 -
Rwork0.32 4681 -
all-4889 -
obs--98.35 %

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