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- PDB-6kni: Crystal structure of SbnH in complex with the cofactor PLP, a PLP... -

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Basic information

Entry
Database: PDB / ID: 6kni
TitleCrystal structure of SbnH in complex with the cofactor PLP, a PLP-dependent decarboxylase in Staphyloferrin B biothesynthesis
ComponentsProbable diaminopimelate decarboxylase protein
KeywordsBIOSYNTHETIC PROTEIN / PLP-dependent decarboxylase / Staphyloferrin B
Function / homology
Function and homology information


diaminopimelate decarboxylase activity / polyamine biosynthetic process / lysine biosynthetic process via diaminopimelate
Similarity search - Function
Ornithine decarboxylase / Orn/DAP/Arg decarboxylase 2, C-terminal / Pyridoxal-dependent decarboxylase, C-terminal sheet domain / Ornithine/DAP/Arg decarboxylase / 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
PYRIDOXAL-5'-PHOSPHATE / Probable diaminopimelate decarboxylase protein
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus Mu50 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 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
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: Probable diaminopimelate decarboxylase protein
B: Probable diaminopimelate decarboxylase protein
C: Probable diaminopimelate decarboxylase protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)140,5256
Polymers139,7833
Non-polymers7413
Water10,647591
1
A: Probable diaminopimelate decarboxylase protein
B: Probable diaminopimelate decarboxylase protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,6834
Polymers93,1892
Non-polymers4942
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7050 Å2
ΔGint-20 kcal/mol
Surface area27640 Å2
MethodPISA
2
C: Probable diaminopimelate decarboxylase protein
hetero molecules

C: Probable diaminopimelate decarboxylase protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,6834
Polymers93,1892
Non-polymers4942
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area7110 Å2
ΔGint-21 kcal/mol
Surface area28120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)176.608, 80.311, 111.826
Angle α, β, γ (deg.)90.00, 102.15, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Probable diaminopimelate decarboxylase protein


Mass: 46594.414 Da / Num. of mol.: 3
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-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 591 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.96 Å3/Da / Density % sol: 58.39 %
Crystal growTemperature: 290 K / Method: evaporation / Details: 0.2 M NaAC, 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: BL17U1 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 28, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.97→109.32 Å / Num. obs: 105438 / % possible obs: 97.7 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.097 / Net I/σ(I): 9.1
Reflection shellResolution: 1.97→2.08 Å / Rmerge(I) obs: 0.443 / Num. unique obs: 15457

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
Aimlessdata scaling
MERLOTphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2j66

2j66


Resolution: 1.97→50 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.23672 5226 -
Rwork0.20466 --
obs-100190 97.45 %
Refinement stepCycle: LAST / Resolution: 1.97→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9182 0 45 591 9818
LS refinement shellResolution: 1.97→2.021 Å
RfactorNum. reflection% reflection
Rfree0.299 383 -
Rwork0.285 7481 -
obs--98.36 %

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