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- PDB-2plj: Crystal structure of lysine/ornithine decarboxylase complexed wit... -

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Basic information

Entry
Database: PDB / ID: 2plj
TitleCrystal structure of lysine/ornithine decarboxylase complexed with putrescine from Vibrio vulnificus
Componentslysine/ornithine decarboxylase
KeywordsLYASE / TYPE IV DECARBOXYLASE / BETA/ALPHA BARREL / BETA BARREL
Function / homology
Function and homology information


ornithine decarboxylase / putrescine biosynthetic process from ornithine / ornithine decarboxylase activity / polyamine biosynthetic process / cytoplasm
Similarity search - Function
Ornithine decarboxylase / Orn/DAP/Arg decarboxylase 2, conserved 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 ...Ornithine decarboxylase / Orn/DAP/Arg decarboxylase 2, conserved 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
Chem-P3T / Ornithine decarboxylase / Ornithine decarboxylase
Similarity search - Component
Biological speciesVibrio vulnificus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsLee, J. / Goldsmith, E.J. / Phillips, M.A.
CitationJournal: J.Biol.Chem. / Year: 2007
Title: Phylogenetic diversity and the structural basis of substrate specificity in the beta/alpha-barrel fold basic amino acid decarboxylases.
Authors: Lee, J. / Michael, A.J. / Martynowski, D. / Goldsmith, E.J. / Phillips, M.A.
History
DepositionApr 19, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 10, 2007Provider: repository / Type: Initial release
Revision 1.1Oct 24, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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.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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: lysine/ornithine decarboxylase
B: lysine/ornithine decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,5015
Polymers91,8382
Non-polymers6633
Water11,061614
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6470 Å2
ΔGint-32 kcal/mol
Surface area28580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.074, 88.683, 111.843
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein lysine/ornithine decarboxylase


Mass: 45919.051 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio vulnificus (bacteria) / Strain: CMCP6 / Gene: LysA / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q8D594, UniProt: A0A3Q0KZG4*PLUS, lysine decarboxylase, ornithine decarboxylase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-P3T / (4-{[(4-AMINOBUTYL)AMINO]METHYL}-5-HYDROXY-6-METHYLPYRIDIN-3-YL)METHYL DIHYDROGEN PHOSPHATE / PHOSPHORIC ACID MONO-{4-[(4-AMINO-BUTYLAMINO)-METHYL]-5-HYDROXY-6-METHYL-PYRIDIN-3-YLMETHYL} ESTER


Mass: 319.294 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H22N3O5P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 614 / 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: 2.21 Å3/Da / Density % sol: 44.47 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.4
Details: 35% PEG-4000, 0.1M Tris HCl pH8.4, 0.2M Magnesium chloride, 0.5% w/v n-octyl-b-D-glucoside , VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.979269 Å
DetectorType: SBC-3 / Detector: CCD / Date: Dec 15, 2006
RadiationMonochromator: Double-Crystal Monochromator Si-111, Si-220 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979269 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 90404 / % possible obs: 99.9 % / Observed criterion σ(F): 1.4 / Observed criterion σ(I): 2 / Redundancy: 7 % / Biso Wilson estimate: 25.4 Å2 / Rmerge(I) obs: 0.074 / Rsym value: 0.074 / Net I/σ(I): 35.9
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.633 / Mean I/σ(I) obs: 2.46 / Num. unique all: 4440 / Rsym value: 0.633 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-3000data collection
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1F3T

1f3t


Resolution: 1.7→19.72 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.953 / SU B: 3.937 / SU ML: 0.069 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 1.4 / σ(I): 2 / ESU R: 0.102 / ESU R Free: 0.101 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21311 4528 5 %RANDOM
Rwork0.18077 ---
obs0.1824 85679 99.82 %-
all-85679 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.866 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å20 Å20 Å2
2--0.01 Å20 Å2
3---0.04 Å2
Refinement stepCycle: LAST / Resolution: 1.7→19.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5711 0 43 614 6368
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0225911
X-RAY DIFFRACTIONr_angle_refined_deg1.4191.9758040
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9365733
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.54824.639263
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.58715970
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.8171531
X-RAY DIFFRACTIONr_chiral_restr0.1290.2935
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024454
X-RAY DIFFRACTIONr_nbd_refined0.2090.22903
X-RAY DIFFRACTIONr_nbtor_refined0.3050.24132
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2080.2551
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1790.227
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0940.212
X-RAY DIFFRACTIONr_mcbond_it0.8491.53779
X-RAY DIFFRACTIONr_mcangle_it1.3325977
X-RAY DIFFRACTIONr_scbond_it2.18632375
X-RAY DIFFRACTIONr_scangle_it3.3864.52063
LS refinement shellResolution: 1.7→1.743 Å / Rfactor Rfree error: 0.001 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.423 327 -
Rwork0.353 6206 -
obs-4440 99.36 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.8964-2.8414-0.32787.27595.88946.9436-0.0534-0.241-0.04631.1768-0.3370.24691.1263-0.7120.39040.2019-0.16140.0645-0.0108-0.037-0.090759.01257.34333.088
20.76930.1902-0.10320.8633-0.14021.5144-0.01070.11480.0102-0.10940.06850.01660.02920.0157-0.05780.06520.0023-0.0233-0.0316-0.0091-0.031569.84569.0214.721
30.94970.0217-0.07331.0626-0.30572.82570.00670.14860.1642-0.15680.0940.1642-0.2892-0.1911-0.10070.10520.0252-0.0362-0.01390.0423-0.010661.02779.9140.916
40.6873-0.33890.64581.24440.32312.3662-0.0648-0.13530.11690.27790.04040.0435-0.0668-0.22070.02440.1460.02460.0134-0.0152-0.0256-0.031366.48675.07238.984
51.05870.210.97270.49210.15781.43520.06470.0186-0.05010.18860.0121-0.06410.04270.0072-0.07680.09650.0083-0.0098-0.0263-0.006-0.017669.80765.00427.192
60.7165-0.42930.05661.4586-0.38882.1129-0.07670.0293-0.04450.1464-0.0234-0.38610.17430.23680.10.02970.0313-0.0669-0.0743-0.01820.0757100.82771.55330.107
71.9843-0.4649-0.09762.05210.16031.9503-0.2196-0.2627-0.09910.34330.1152-0.07640.1191-0.0950.10440.22570.0728-0.0613-0.09530.011-0.073483.35967.25750.157
81.23320.2702-0.61081.4845-0.71982.1417-0.1538-0.31640.09360.51890.0564-0.1774-0.20070.01990.09740.33890.0953-0.1827-0.0027-0.05270.035292.61781.652.717
90.6645-0.0390.77861.26320.1742.2865-0.0570.07610.0604-0.07370.039-0.1486-0.19190.09240.0180.0691-0.02090.0084-0.0479-0.01180.01287.97682.25915.793
102.13180.60761.04430.9290.15471.98350.02880.0593-0.14260.0059-0.0019-0.19780.08420.0795-0.02690.07680.0116-0.0119-0.0483-0.02840.024490.03170.33722.216
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA3 - 3423 - 54
2X-RAY DIFFRACTION2AA35 - 17855 - 198
3X-RAY DIFFRACTION3AA179 - 276199 - 296
4X-RAY DIFFRACTION4AA277 - 362297 - 382
5X-RAY DIFFRACTION5AA363 - 390383 - 410
6X-RAY DIFFRACTION6BB18 - 8538 - 105
7X-RAY DIFFRACTION7BB86 - 177106 - 197
8X-RAY DIFFRACTION8BB178 - 268198 - 288
9X-RAY DIFFRACTION9BB269 - 362289 - 382
10X-RAY DIFFRACTION10BB363 - 390383 - 410

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