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Database: PDB / ID: 2w2f
TitleCRYSTAL STRUCTURE OF SINGLE POINT MUTANT ARG48GLN OF P-COUMARIC ACID DECARBOXYLASE FROM LACTOBACILLUS PLANTARUM STRUCTURAL INSIGHTS INTO THE ACTIVE SITE AND DECARBOXYLATION CATALYTIC MECHANISM
ComponentsP-COUMARIC ACID DECARBOXYLASE
KeywordsLYASE
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: 1.73 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 29, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 9, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Aug 3, 2011Group: Database references / Derived calculations
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / struct_site
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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _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 / _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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_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
C: P-COUMARIC ACID DECARBOXYLASE
D: P-COUMARIC ACID DECARBOXYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,5326
Polymers91,2574
Non-polymers2752
Water8,935496
1
A: P-COUMARIC ACID DECARBOXYLASE
B: P-COUMARIC ACID DECARBOXYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,7663
Polymers45,6282
Non-polymers1371
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2610 Å2
ΔGint-19.1 kcal/mol
Surface area14240 Å2
MethodPISA
2
C: P-COUMARIC ACID DECARBOXYLASE
D: P-COUMARIC ACID DECARBOXYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,7663
Polymers45,6282
Non-polymers1371
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2620 Å2
ΔGint-17.6 kcal/mol
Surface area14440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.248, 94.924, 106.722
Angle α, β, γ (deg.)90.00, 100.51, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

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
3CC
4DD

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Components

#1: Protein
P-COUMARIC ACID DECARBOXYLASE


Mass: 22814.234 Da / Num. of mol.: 4 / Mutation: YES
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: Chemical ChemComp-BA / BARIUM ION


Mass: 137.327 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ba
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 496 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, ARG 48 TO GLN ENGINEERED RESIDUE IN CHAIN B, ARG 48 TO GLN ...ENGINEERED RESIDUE IN CHAIN A, ARG 48 TO GLN ENGINEERED RESIDUE IN CHAIN B, ARG 48 TO GLN ENGINEERED RESIDUE IN CHAIN C, ARG 48 TO GLN ENGINEERED RESIDUE IN CHAIN D, ARG 48 TO GLN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.11 Å3/Da / Density % sol: 41 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM16 / Wavelength: 0.9791
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 29, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.73→52.4 Å / Num. obs: 55853 / % possible obs: 69.8 % / Redundancy: 2.7 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 13.2
Reflection shellResolution: 1.73→1.82 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 1.9 / % possible all: 69.8

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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 2W2A

2w2a


Resolution: 1.73→35.76 Å / Cor.coef. Fo:Fc: 0.894 / Cor.coef. Fo:Fc free: 0.858 / SU B: 5.921 / SU ML: 0.107 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.214 / ESU R Free: 0.187 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.273 2830 5.1 %RANDOM
Rwork0.226 ---
obs0.228 53004 69.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 7.86 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å2-0.04 Å2
2--0.01 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.73→35.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5828 0 2 496 6326
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0226008
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2271.9218172
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7415696
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.6925328
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.21515976
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.9621516
X-RAY DIFFRACTIONr_chiral_restr0.0890.2836
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024720
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2120.23092
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3070.24001
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1670.2559
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2920.298
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1960.219
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4421.53484
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.79625668
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.38732600
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.0514.52504
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 positional0.170.5
2B700medium positional0.160.5
3C700medium positional0.180.5
4D700medium positional0.20.5
1A757loose positional0.385
2B757loose positional0.475
3C757loose positional0.45
4D757loose positional0.455
1A700medium thermal0.482
2B700medium thermal0.62
3C700medium thermal0.612
4D700medium thermal0.582
1A757loose thermal1.2310
2B757loose thermal1.3710
3C757loose thermal1.4710
4D757loose thermal1.3710
LS refinement shellResolution: 1.73→1.77 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.462 41
Rwork0.319 991
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)
10.2435-0.1303-0.17840.24050.12610.62670.02420.02670.0095-0.0309-0.04780.0226-0.0076-0.00820.0236-0.03950.0066-0.002-0.00270.00160.017.551-16.24327.867
20.2408-0.152-0.1470.18680.12120.6825-0.0222-0.03070.0064-0.01520.0355-0.0284-0.1356-0.0218-0.0134-0.0190.0153-0.0057-0.0008-0.00040.0118-0.22-0.16549.603
30.33590.04360.18950.52240.09720.4181-0.00640.0061-0.0424-0.0131-0.01350.03560.0733-0.02070.0199-0.0175-0.00450.0159-0.0094-0.02120.0146-19.805-13.98576.577
40.31780.01130.12150.353-0.17830.46790.017-0.02970.02460.0219-0.00110.0127-0.00260.0377-0.0159-0.0444-0.00370.015-0.0135-0.00620.0112-12.0072.30598.208
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
9X-RAY DIFFRACTION3C2 - 95
10X-RAY DIFFRACTION3C96 - 124
11X-RAY DIFFRACTION3C125 - 140
12X-RAY DIFFRACTION3C141 - 176
13X-RAY DIFFRACTION4D2 - 95
14X-RAY DIFFRACTION4D96 - 124
15X-RAY DIFFRACTION4D125 - 140
16X-RAY DIFFRACTION4D141 - 176

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