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- PDB-2w2b: Crystal Structure of single point mutant Tyr20Phe p-coumaric Acid... -

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Basic information

Entry
Database: PDB / ID: 2w2b
TitleCrystal Structure of single point mutant Tyr20Phe 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
ACETATE ION / ISOPROPYL ALCOHOL / Phenolic acid decarboxylase / :
Similarity search - Component
Biological speciesLACTOBACILLUS PLANTARUM (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 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. / D Elas 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 1.1Nov 9, 2011Group: Database references / Derived calculations / Version format compliance
Revision 1.2Dec 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 / 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 / _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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)45,8936
Polymers45,6552
Non-polymers2384
Water8,971498
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3360 Å2
ΔGint-0.4 kcal/mol
Surface area14840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.384, 43.384, 232.858
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: LYS / End label comp-ID: LYS / Refine code: 5 / Auth seq-ID: 2 - 178 / Label seq-ID: 18 - 194

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

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Components

#1: Protein P-COUMARIC ACID DECARBOXYLASE


Mass: 22827.301 Da / Num. of mol.: 2 / 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-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL / Isopropyl alcohol


Mass: 60.095 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 498 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, TYR 20 TO PHE ENGINEERED RESIDUE IN CHAIN B, TYR 20 TO PHE
Sequence detailsSINGLE POINT MUTANT (TYR20PHE) OF LACTOBACILLUS PLANTARUM P-COUMARIC ACID DECARBOXYLASE

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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: ID29 / Wavelength: 0.9789
DetectorType: ADSC CCD / Detector: CCD / Date: Mar 5, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 1.4→58.22 Å / Num. obs: 76941 / % possible obs: 91.5 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 15.6
Reflection shellResolution: 1.4→1.48 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 1.6 / % possible all: 91.5

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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: 1.4→58.22 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.938 / SU B: 1.99 / SU ML: 0.042 / Cross valid method: THROUGHOUT / ESU R: 0.071 / ESU R Free: 0.071 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.221 3875 5 %RANDOM
Rwork0.199 ---
obs0.2 72949 91.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.35 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.4→58.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2950 0 16 498 3464
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0223052
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0721.9254142
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9995352
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.51124.819166
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.85915500
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.3271510
X-RAY DIFFRACTIONr_chiral_restr0.0760.2422
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022392
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1830.21448
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3110.22032
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0810.2449
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1160.230
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1740.247
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5191.51823
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.81222870
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.01331445
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.6014.51272
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
1A708medium positional0.030.5
2B708medium positional0.030.5
1A767loose positional0.155
2B767loose positional0.155
1A708medium thermal0.082
2B708medium thermal0.082
1A767loose thermal0.2110
2B767loose thermal0.2110
LS refinement shellResolution: 1.4→1.44 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.309 153
Rwork0.297 2846

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