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- PDB-2gc9: Crystal structure of p-coumaric acid decarboxylase (NP_786857.1) ... -

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Basic information

Entry
Database: PDB / ID: 2gc9
TitleCrystal structure of p-coumaric acid decarboxylase (NP_786857.1) from Lactobacillus plantarum at 1.70 A resolution
Componentsp-coumaric acid decarboxylase
KeywordsLYASE / NP_786857.1 / P-COUMARIC ACID DECARBOXYLASE / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI
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
CITRIC ACID / Phenolic acid decarboxylase / :
Similarity search - Component
Biological speciesLactobacillus plantarum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.7 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of p-coumaric acid decarboxylase (NP_786857.1) from Lactobacillus plantarum at 1.70 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionMar 13, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 21, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.3Jan 25, 2023Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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 / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Remark 999SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ...SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,28037
Polymers42,8422
Non-polymers2,43835
Water5,314295
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6530 Å2
ΔGint-48 kcal/mol
Surface area15870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.170, 64.170, 83.120
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number145
Space group name H-MP32

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Components

#1: Protein p-coumaric acid decarboxylase


Mass: 21420.773 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus plantarum (bacteria) / Strain: WCFS1 / Gene: pc05870a / Production host: Escherichia coli (E. coli)
References: UniProt: Q88RY7, UniProt: F9ULL2*PLUS, Lyases; Carbon-carbon lyases; Carboxy-lyases
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#4: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 30 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 295 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.16 Å3/Da / Density % sol: 42.69 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop, nanodrop / pH: 4
Details: 2.4M (NH4)2SO4, 0.1M Citrate pH 4.0, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.918370, 0.979035
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 13, 2006 / Details: Flat mirror (vertical focusing)
RadiationMonochromator: Single crystal Si(111) bent monochromator (horizontal focusing)
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.9790351
ReflectionResolution: 1.7→27.79 Å / Num. obs: 41971 / % possible obs: 99.1 % / Redundancy: 3.81 % / Biso Wilson estimate: 14 Å2 / Rmerge(I) obs: 0.087 / Net I/σ(I): 7.45
Reflection shell

Diffraction-ID: 1

Resolution (Å)% possible obs (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.7-1.76820.4871.7813015678794.6
1.76-1.8389.40.3712.5146137573
1.83-1.9192.40.2923144947520
1.91-2.0294.70.2194168058755
2.02-2.1496.50.1625.2149457776
2.14-2.3197.90.1236.7162288433
2.31-2.5498.60.0958.3158308226
2.54-2.9990.089.4158898263
2.9-27.7999.60.05213.3162868503

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0005refinement
XSCALEdata scaling
PDB_EXTRACT1.701data extraction
XDSdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.7→27.79 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.929 / SU B: 4.305 / SU ML: 0.073 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.106 / ESU R Free: 0.105
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. RESIDUES 161-178 IN CHAIN B, ARE DISORDERED AND NOT INCLUDED IN THE MODEL. 4. RESIDUE PROLINE 132 IN CHAIN B HAS TORSIONS LYING OUTSIDE THE ALLOWED RAMACHANDRAN REGION, BUT SUPPORTED BY THE DENSITY. 5. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.212 2125 5.1 %RANDOM
Rwork0.175 ---
all0.177 ---
obs0.17682 42001 99.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 12.824 Å2
Baniso -1Baniso -2Baniso -3
1-0.38 Å20.19 Å20 Å2
2--0.38 Å20 Å2
3----0.58 Å2
Refinement stepCycle: LAST / Resolution: 1.7→27.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2797 0 153 295 3245
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0223019
X-RAY DIFFRACTIONr_bond_other_d0.0010.022606
X-RAY DIFFRACTIONr_angle_refined_deg1.1281.9534045
X-RAY DIFFRACTIONr_angle_other_deg0.71936082
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6165339
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.86224.834151
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.73715481
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.858158
X-RAY DIFFRACTIONr_chiral_restr0.070.2406
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023237
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02601
X-RAY DIFFRACTIONr_nbd_refined0.1790.2618
X-RAY DIFFRACTIONr_nbd_other0.1670.22723
X-RAY DIFFRACTIONr_nbtor_refined0.1790.21411
X-RAY DIFFRACTIONr_nbtor_other0.080.21573
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1230.2266
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2130.224
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1710.286
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1490.224
X-RAY DIFFRACTIONr_mcbond_it1.09531813
X-RAY DIFFRACTIONr_mcbond_other0.2613689
X-RAY DIFFRACTIONr_mcangle_it1.49152752
X-RAY DIFFRACTIONr_scbond_it2.93281510
X-RAY DIFFRACTIONr_scangle_it3.843111292
LS refinement shellResolution: 1.7→1.745 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.262 170 -
Rwork0.218 2912 -
obs-3082 99.1 %
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)
10.81950.1582-0.79560.5349-0.11150.9757-0.0589-0.0216-0.0312-0.0367-0.0044-0.0441-0.01540.07190.06330.00180.0078-0.0019-0.00920.0052-0.002722.25816.65517.922
20.6198-0.2401-0.09350.838-0.30990.5171-0.0209-0.05750.0091-0.0084-0.002-0.01680.0352-0.03110.0229-0.0090.0128-0.00140.01450.0003-0.01775.7267.04336.321
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA1 - 1782 - 179
22BB0 - 1601 - 161

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