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- PDB-2p8g: Crystal structure of phenolic acid decarboxylase (2635953) from B... -

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Basic information

Entry
Database: PDB / ID: 2p8g
TitleCrystal structure of phenolic acid decarboxylase (2635953) from Bacillus subtilis at 1.36 A resolution
ComponentsPhenolic acid decarboxylase
KeywordsLYASE / 2635953 / Phenolic acid decarboxylase (PAD) / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


phenacrylate decarboxylase / carboxy-lyase activity / catabolic process / response to toxic substance
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 PadC
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.36 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of phenolic acid decarboxylase (2635953) from Bacillus subtilis at 1.36 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionMar 22, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 17, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Oct 20, 2021Group: 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 1.5Jan 25, 2023Group: Database references / Category: struct_ref_seq_dif / Item: _struct_ref_seq_dif.details
Revision 1.6Sep 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.7Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.8Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 300 BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN. ... BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN. SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). EBI PISA ANALYSIS SUPPORTS THE ASSIGNMENT OF A DIMER AS THE SIGNIFICANT OLIGOMERIZATION STATE.
Remark 999 SEQUENCE 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. THE RESIDUE LYS 146 HAS BEEN MUTATED TO TYR.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phenolic acid decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,0169
Polymers19,5201
Non-polymers4978
Water4,576254
1
A: Phenolic acid decarboxylase
hetero molecules

A: Phenolic acid decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,03318
Polymers39,0402
Non-polymers99316
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation24_565-z+3/4,-y+7/4,-x+3/41
Unit cell
Length a, b, c (Å)117.475, 117.475, 117.475
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number213
Space group name H-MP4132

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Components

#1: Protein Phenolic acid decarboxylase / PAD


Mass: 19519.801 Da / Num. of mol.: 1 / Mutation: K146Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: 168 / Gene: padC, pad, BSU34400 / Plasmid: speedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100
References: UniProt: O07006, Lyases; Carbon-carbon lyases; Carboxy-lyases
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 254 / 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: 3.46 Å3/Da / Density % sol: 64.44 %
Description: THE STRUCTURE WAS SOLVED BY MOLECULAR REPLACEMENT USING PDB ENTRY 2GC9 AS A TEMPLATE AGAINST A 1.6A DATASET FROM ANOTHER CRYSTAL. THE STRUCTURE WAS SUBSEQUENTLY REFINED AGAINST THIS ...Description: THE STRUCTURE WAS SOLVED BY MOLECULAR REPLACEMENT USING PDB ENTRY 2GC9 AS A TEMPLATE AGAINST A 1.6A DATASET FROM ANOTHER CRYSTAL. THE STRUCTURE WAS SUBSEQUENTLY REFINED AGAINST THIS DATASET AT 1.36A RESOLUTION.
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.2
Details: NANODROP, 0.2M NaCl, 10.0% PEG 8000, 1.0M LiCl, 20.0% PEG 6000, 0.1M Na,K Phosphate pH 6.2, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 21, 2006
RadiationMonochromator: Single crystal, cylindrically bent, asymmetrically cut Si(220) crystal
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.36→58.722 Å / Num. obs: 59580 / % possible obs: 99.6 % / Redundancy: 18.2 % / Rmerge(I) obs: 0.107 / Rsym value: 0.107 / Net I/σ(I): 5.6
Reflection shell

Rmerge(I) obs: 0.01 / Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.36-1.438.10.76753283231.03697.4
1.43-1.5213110565681180.755100
1.52-1.6320.11.515383676700.494100
1.63-1.7620.82.414874571660.305100
1.76-1.9221.3414089766080.179100
1.92-2.1521.96.213201460170.116100
2.15-2.4821.97.911734553480.088100
2.48-3.0421.679849645670.089100
3.04-4.320.311.27317536120.053100
4.3-83.0420.414.44382421510.037100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
REFMAC5.2.0019refinement
SCALAdata scaling
PDB_EXTRACT2data extraction
ADSCQUANTUMdata collection
MOSFLMdata reduction
CCP4(SCALA)data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2CG9

2cg9


Resolution: 1.36→58.722 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.975 / SU B: 1.059 / SU ML: 0.021 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.034 / ESU R Free: 0.035 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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. EDO MOLECULES FROM THE CRYSTALLIZATION/CRYO SOLUTION ARE MODELED. 4. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.146 2999 5.1 %RANDOM
Rwork0.133 ---
all0.134 ---
obs0.134 59375 99.35 %-
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: 14.486 Å2
Refinement stepCycle: LAST / Resolution: 1.36→58.722 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1348 0 32 254 1634
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0221456
X-RAY DIFFRACTIONr_bond_other_d0.0020.021013
X-RAY DIFFRACTIONr_angle_refined_deg1.4891.9411967
X-RAY DIFFRACTIONr_angle_other_deg0.84732451
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8285173
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.90224.05179
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.43715247
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.996159
X-RAY DIFFRACTIONr_chiral_restr0.0930.2200
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021609
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02308
X-RAY DIFFRACTIONr_nbd_refined0.2030.2289
X-RAY DIFFRACTIONr_nbd_other0.210.21129
X-RAY DIFFRACTIONr_nbtor_refined0.1970.2746
X-RAY DIFFRACTIONr_nbtor_other0.0930.2779
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1420.2207
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.230.215
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2780.249
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1460.231
X-RAY DIFFRACTIONr_mcbond_it1.6663868
X-RAY DIFFRACTIONr_mcbond_other0.3533333
X-RAY DIFFRACTIONr_mcangle_it2.13551352
X-RAY DIFFRACTIONr_scbond_it3.7138707
X-RAY DIFFRACTIONr_scangle_it5.66211609
LS refinement shellResolution: 1.36→1.395 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.259 218 -
Rwork0.257 3892 -
obs-4110 94.57 %
Refinement TLS params.Method: refined / Origin x: 12.664 Å / Origin y: 96.845 Å / Origin z: 92.106 Å
111213212223313233
T-0.0285 Å20.0064 Å20.0025 Å2--0.034 Å20.0026 Å2---0.0387 Å2
L0.6993 °2-0.1819 °20.0446 °2-0.2286 °2-0.2071 °2--0.2338 °2
S-0.0002 Å °-0.0256 Å °0.0049 Å °0.0388 Å °0.0081 Å °-0.0041 Å °-0.0133 Å °0.0066 Å °-0.0079 Å °
Refinement TLS groupSelection: ALL

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