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- PDB-5gjo: Crystal structure of SrLDC mutant (A225C/T302C) in complex with PLP -

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Basic information

Entry
Database: PDB / ID: 5gjo
TitleCrystal structure of SrLDC mutant (A225C/T302C) in complex with PLP
ComponentsLysine/ornithine decarboxylase
KeywordsLYASE / barrel domain
Function / homology
Function and homology information


ornithine decarboxylase / putrescine biosynthetic process from ornithine / lysine decarboxylase / lysine decarboxylase activity / ornithine decarboxylase activity / spermidine biosynthetic process / cytoplasm
Similarity search - Function
Ornithine decarboxylase / Orn/DAP/Arg decarboxylase 2, conserved site / Orn/DAP/Arg decarboxylase 2, pyridoxal-phosphate binding site / Orn/DAP/Arg decarboxylases family 2 pyridoxal-P attachment site. / Orn/DAP/Arg decarboxylases family 2 signature 2. / 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 ...Ornithine decarboxylase / Orn/DAP/Arg decarboxylase 2, conserved site / Orn/DAP/Arg decarboxylase 2, pyridoxal-phosphate binding site / Orn/DAP/Arg decarboxylases family 2 pyridoxal-P attachment site. / Orn/DAP/Arg decarboxylases family 2 signature 2. / 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 / Lyase, Ornithine Decarboxylase; Chain A, domain 1 / Lyase, Ornithine Decarboxylase; Chain A, domain 1 / Alanine racemase / Alanine racemase/group IV decarboxylase, C-terminal / PLP-binding barrel / TIM Barrel / Alpha-Beta Barrel / Beta Barrel / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
PYRIDOXAL-5'-PHOSPHATE / Lysine/ornithine decarboxylase
Similarity search - Component
Biological speciesSelenomonas ruminantium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsSagong, H.-Y. / Kim, K.-J.
CitationJournal: PLoS ONE / Year: 2017
Title: Lysine Decarboxylase with an Enhanced Affinity for Pyridoxal 5-Phosphate by Disulfide Bond-Mediated Spatial Reconstitution
Authors: Sagong, H.-Y. / Kim, K.-J.
History
DepositionJul 1, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 10, 2017Provider: repository / Type: Initial release
Revision 1.1May 17, 2017Group: Database references
Revision 1.2Sep 9, 2020Group: Derived calculations / Structure summary / Category: struct / struct_conn
Item: _struct.title / _struct_conn.pdbx_dist_value ..._struct.title / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry
Revision 1.3Nov 8, 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: Lysine/ornithine decarboxylase
B: Lysine/ornithine decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,08416
Polymers86,7372
Non-polymers1,34714
Water14,484804
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8110 Å2
ΔGint-106 kcal/mol
Surface area28450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.917, 122.859, 136.853
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Lysine/ornithine decarboxylase / LDC / PLP binding barrel domain


Mass: 43368.578 Da / Num. of mol.: 2 / Mutation: A225C, T302C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Selenomonas ruminantium (bacteria) / Strain: ATCC12561 / Gene: ldc / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21T1R / References: UniProt: O50657, lysine decarboxylase

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Non-polymers , 5 types, 818 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10NO6P
#5: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 804 / Source method: isolated from a natural source / Formula: H2O

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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: 2.71 Å3/Da / Density % sol: 54.69 % / Mosaicity: 0.43 °
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: Ammonium sulfate, Sodium cacodylate, NaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97934 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Nov 13, 2015
RadiationMonochromator: Double Crystal Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 87717 / % possible obs: 99.3 % / Redundancy: 11.5 % / Rmerge(I) obs: 0.077 / Net I/av σ(I): 48.829 / Net I/σ(I): 12.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
1.8-1.8390.2980.959198.3
1.83-1.869.20.2750.968198.3
1.86-1.99.50.2510.973198.2
1.9-1.949.80.2270.977198.9
1.94-1.9810.30.20.985198.8
1.98-2.0310.50.1840.989199.2
2.03-2.0810.80.1680.988199.2
2.08-2.1311.20.150.992199.8
2.13-2.211.30.1370.993198.9
2.2-2.2711.40.1250.994199.5
2.27-2.3511.60.1150.995199.5
2.35-2.4411.80.1090.995199.5
2.44-2.55120.1020.996199.7
2.55-2.6912.30.0930.997199.5
2.69-2.8612.70.0830.997199.8
2.86-3.0813.20.0750.998199.9
3.08-3.3913.60.0650.998199.9
3.39-3.8813.80.0580.998199.9
3.88-4.8813.70.0510.999199.6
4.88-5012.70.0530.998199

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Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-2000data scaling
REFMAC5.8.0135refinement
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5GJN

5gjn


Resolution: 1.8→50 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.95 / SU B: 2.046 / SU ML: 0.063 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.095 / ESU R Free: 0.099
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1967 4404 5 %RANDOM
Rwork0.1615 ---
obs0.1771 83265 99.05 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 96.82 Å2 / Biso mean: 22.488 Å2 / Biso min: 9.73 Å2
Baniso -1Baniso -2Baniso -3
1-0.27 Å20 Å20 Å2
2--1.51 Å2-0 Å2
3----1.79 Å2
Refinement stepCycle: final / Resolution: 1.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5941 0 78 804 6823
Biso mean--36.73 32.42 -
Num. residues----769
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0196182
X-RAY DIFFRACTIONr_bond_other_d0.0020.025838
X-RAY DIFFRACTIONr_angle_refined_deg2.0551.9828368
X-RAY DIFFRACTIONr_angle_other_deg1.093313458
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5835771
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.71524270
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.921151020
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7321537
X-RAY DIFFRACTIONr_chiral_restr0.1320.2917
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0216948
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021369
X-RAY DIFFRACTIONr_mcbond_it2.0691.9323084
X-RAY DIFFRACTIONr_mcbond_other2.0591.9313083
X-RAY DIFFRACTIONr_mcangle_it2.8562.8873855
LS refinement shellResolution: 1.798→1.844 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.234 316 -
Rwork0.201 5800 -
all-6116 -
obs--94.76 %

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