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- PDB-2w2a: Crystal Structure of p-coumaric Acid Decarboxylase from Lactobaci... -

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Basic information

Entry
Database: PDB / ID: 2w2a
TitleCrystal Structure of p-coumaric Acid Decarboxylase from Lactobacillus plantarum: structural insights into the active site and decarboxylation catalytic mechanism
ComponentsP-COUMARIC ACID DECARBOXYLASE
KeywordsLYASE / ACTIVE SITE / COUMARIC ACIDS / DECARBOXYLATION / CATALYTIC MECHANISM
Function / homology
Function and homology information


Lyases; Carbon-carbon lyases; Carboxy-lyases / carboxy-lyase activity
Similarity search - Function
Phenolic acid decarboxylase / Phenolic acid decarboxylase (PAD) / Calycin beta-barrel core domain / Calycin / Lipocalin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Phenolic acid decarboxylase / :
Similarity search - Component
Biological speciesLACTOBACILLUS PLANTARUM (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.38 Å
AuthorsRodriguez, H. / Angulo, I. / de las Rivas, B. / Campillo, N. / Paez, J.A. / Munoz, R. / Mancheno, J.M.
CitationJournal: Proteins / Year: 2010
Title: P-Coumaric Acid Decarboxylase from Lactobacillus Plantarum: Structural Insights Into the Active Site and Decarboxylation Catalytic Mechanism.
Authors: Rodriguez, H. / Angulo, I. / De Las Rivas, B. / Campillo, N. / Paez, J.A. / Munoz, R. / Mancheno, J.M.
History
DepositionOct 27, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 17, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 9, 2011Group: Database references / Derived calculations
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: P-COUMARIC ACID DECARBOXYLASE
B: P-COUMARIC ACID DECARBOXYLASE


Theoretical massNumber of molelcules
Total (without water)45,6872
Polymers45,6872
Non-polymers00
Water10,196566
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2340 Å2
ΔGint-10.9 kcal/mol
Surface area15150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.181, 43.181, 232.498
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: 5 / Auth seq-ID: 2 - 176 / Label seq-ID: 18 - 192

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein P-COUMARIC ACID DECARBOXYLASE


Mass: 22843.301 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) LACTOBACILLUS PLANTARUM (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): JM109(DE3) / References: UniProt: Q88RY7, UniProt: F9ULL2*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 566 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.6 Å3/Da / Density % sol: 52 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9762
DetectorType: ADSC CCD / Detector: CCD / Date: Jul 21, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.38→46.5 Å / Num. obs: 86850 / % possible obs: 100 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 13
Reflection shellResolution: 1.38→1.45 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 2.8 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2GC9

2gc9


Resolution: 1.38→40.49 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.944 / SU B: 1.75 / SU ML: 0.037 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.06 / ESU R Free: 0.06 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.209 4348 5 %RANDOM
Rwork0.191 ---
obs0.192 82379 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.31 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.38→40.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2918 0 0 566 3484
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0223008
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0221.9224090
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0485348
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.35924.756164
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.8115490
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.4571510
X-RAY DIFFRACTIONr_chiral_restr0.0730.2418
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022362
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1810.21412
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3080.22024
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0770.2505
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1040.233
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1580.259
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4221.51798
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.67622834
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.87731430
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.3444.51256
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A700medium positional0.030.5
2B700medium positional0.030.5
1A759loose positional0.245
2B759loose positional0.245
1A700medium thermal0.062
2B700medium thermal0.062
1A759loose thermal0.1610
2B759loose thermal0.1610
LS refinement shellResolution: 1.38→1.42 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.262 327
Rwork0.259 6028
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)
10.23390.1262-0.13040.7460.32350.693-0.0184-0.00210.0045-0.1187-0.00730.01020.0042-0.00920.02570.00410.01530.01-0.04470.005-0.01457.469820.985-0.2307
20.72440.1352-0.32090.26970.13550.7013-0.005-0.1203-0.00990.0009-0.0216-0.0060.0115-0.00770.0266-0.04570.0141-0.00350.0045-0.0098-0.0151-0.596929.061125.856
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 95
2X-RAY DIFFRACTION1A96 - 124
3X-RAY DIFFRACTION1A125 - 140
4X-RAY DIFFRACTION1A141 - 176
5X-RAY DIFFRACTION2B2 - 95
6X-RAY DIFFRACTION2B96 - 124
7X-RAY DIFFRACTION2B125 - 140
8X-RAY DIFFRACTION2B141 - 176

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