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- PDB-6knh: Crystal structure of SbnH in complex with citrate, a PLP-dependen... -

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Basic information

Entry
Database: PDB / ID: 6knh
TitleCrystal structure of SbnH in complex with citrate, 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 / L-lysine biosynthetic process via diaminopimelate
Similarity search - Function
Ornithine decarboxylase / 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
CITRIC ACID / PHOSPHATE ION / Probable diaminopimelate decarboxylase protein
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus Mu50 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.76 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 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine.pdbx_diffrn_id / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein

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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)140,6459
Polymers139,7833
Non-polymers8616
Water9,008500
1
A: Probable diaminopimelate decarboxylase protein
B: Probable diaminopimelate decarboxylase protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,7636
Polymers93,1892
Non-polymers5744
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7450 Å2
ΔGint-33 kcal/mol
Surface area27460 Å2
MethodPISA
2
C: Probable diaminopimelate decarboxylase protein
hetero molecules

C: Probable diaminopimelate decarboxylase protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,7636
Polymers93,1892
Non-polymers5744
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area7530 Å2
ΔGint-32 kcal/mol
Surface area27620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)175.291, 79.585, 111.656
Angle α, β, γ (deg.)90.00, 102.48, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11C-770-

HOH

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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-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H8O7 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 500 / 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: 2.89 Å3/Da / Density % sol: 57.39 %
Crystal growTemperature: 290 K / Method: evaporation / Details: 0.2 M NaAC, 50mM Bis-Tris pH6.0, 23% PEG 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9791 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 19, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.76→50 Å / Num. obs: 139539 / % possible obs: 95.1 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.088 / Net I/σ(I): 21.6
Reflection shellResolution: 1.76→1.82 Å / Rmerge(I) obs: 0.49 / Num. unique obs: 13626

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2J66

2j66


Resolution: 1.76→50.01 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.959 / SU B: 1.935 / SU ML: 0.061 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.1 / ESU R Free: 0.093 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.188 6986 5 %RANDOM
Rwork0.1687 ---
obs0.1697 132551 94.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 61.77 Å2 / Biso mean: 25.812 Å2 / Biso min: 15.65 Å2
Baniso -1Baniso -2Baniso -3
1-0.2 Å20 Å20.54 Å2
2--1.27 Å20 Å2
3----1.56 Å2
Refinement stepCycle: final / Resolution: 1.76→50.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9177 0 54 500 9731
Biso mean--38.39 31.25 -
Num. residues----1149
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.019493
X-RAY DIFFRACTIONr_bond_other_d0.0020.028757
X-RAY DIFFRACTIONr_angle_refined_deg1.2151.93212907
X-RAY DIFFRACTIONr_angle_other_deg0.892320106
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.16551149
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.00724.368467
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.493151523
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.0731534
X-RAY DIFFRACTIONr_chiral_restr0.0710.21410
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0210817
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022307
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_it1.0922.4824599
X-RAY DIFFRACTIONr_mcbond_other1.0912.4824598
X-RAY DIFFRACTIONr_mcangle_it1.7543.7155741
X-RAY DIFFRACTIONr_mcangle_other1.7543.7155742
X-RAY DIFFRACTIONr_scbond_it1.5352.6984894
X-RAY DIFFRACTIONr_scbond_other1.5242.6964880
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.4933.987146
X-RAY DIFFRACTIONr_long_range_B_refined3.83220.33710572
X-RAY DIFFRACTIONr_long_range_B_other3.83320.31910562
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.764→1.81 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.226 488 -
Rwork0.21 8791 -
all-9279 -
obs--85.17 %

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