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- PDB-4qs6: CRYSTAL STRUCTURE of 5-CARBOXYVANILLATE DECARBOXYLASE LIGW2 FROM ... -

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Basic information

Entry
Database: PDB / ID: 4qs6
TitleCRYSTAL STRUCTURE of 5-CARBOXYVANILLATE DECARBOXYLASE LIGW2 FROM NOVOSPHINGOBIUM AROMATICIVORANS DSM 12444 (TARGET EFI-505250) WITH BOUND 4-HYDROXY-3-METHOXY-5-NITROBENZOIC ACID, NO METAL, THE D314N MUTANT
ComponentsLigw2 Decarboxylase
KeywordsHYDROLASE / AMIDOHYDROLASE / METAL BINDING SITE / DECARBOXYLASE
Function / homology
Function and homology information


secondary metabolic process / : / : / carboxy-lyase activity / hydrolase activity / metal ion binding / cytosol
Similarity search - Function
2-amino-3-carboxymuconate-6-semialdehyde decarboxylase / Amidohydrolase / Amidohydrolase-related / Metal-dependent hydrolases / Metal-dependent hydrolase / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
4-hydroxy-3-methoxy-5-nitrobenzoic acid / Amidohydrolase 2
Similarity search - Component
Biological speciesNovosphingobium aromaticivorans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.76 Å
AuthorsPatskovsky, Y. / Vladimirova, A. / Toro, R. / Bhosle, R. / Gerlt, J.A. / Raushel, F.M. / Almo, S.C.
CitationJournal: To be Published
Title: Crystal Structure of Ligw2 Decarboxylase from Novosphingobium Aromaticivorans
Authors: Patskovsky, Y. / Vladimirova, A. / Toro, R. / Bhosle, R. / Raushel, F.M. / Almo, S.C.
History
DepositionJul 3, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 6, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ligw2 Decarboxylase
B: Ligw2 Decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,6849
Polymers84,9112
Non-polymers7737
Water13,601755
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6830 Å2
ΔGint-64 kcal/mol
Surface area23300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.422, 85.396, 141.616
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.318579, -0.939565, -0.125402), (-0.939149, -0.330795, 0.092589), (-0.128475, 0.088274, -0.987776)21.51023, 31.0566, -6.16419

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Components

#1: Protein Ligw2 Decarboxylase


Mass: 42455.293 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Novosphingobium aromaticivorans (bacteria)
Strain: DSM 12444 / F199 / Gene: Saro_0799 / Plasmid: PET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q2GA79
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-1DF / 4-hydroxy-3-methoxy-5-nitrobenzoic acid


Mass: 213.144 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H7NO6
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 755 / Source method: isolated from a natural source / Formula: H2O

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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: 2.15 Å3/Da / Density % sol: 42.83 %
Crystal growpH: 5.6
Details: 0.085M SODIUM CITRATE, PH 5.6, 0.17M SODIUM ACETATE, 25% PEG 4000,15% GLYCEROL, 50MM 3-methoxy-4-hydroxy-5-nitrobenzoic acid, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 4, 2014 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 1.76→50 Å / Num. all: 73295 / Num. obs: 73152 / % possible obs: 100 % / Observed criterion σ(I): -5 / Redundancy: 6 % / Rmerge(I) obs: 0.173 / Rsym value: 0.173 / Net I/σ(I): 10.8
Reflection shellResolution: 1.76→1.79 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.95 / Mean I/σ(I) obs: 2 / Rsym value: 0.95 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.8.0069refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4QS5

4qs5


Resolution: 1.76→50 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.944 / SU B: 3.058 / SU ML: 0.091 / Cross valid method: THROUGHOUT / ESU R: 0.109 / ESU R Free: 0.11 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20531 2262 3.1 %RANDOM
Rwork0.16216 ---
obs0.16347 70717 99.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 28.719 Å2
Baniso -1Baniso -2Baniso -3
1-1.74 Å2-0 Å20 Å2
2---2.03 Å2-0 Å2
3---0.29 Å2
Refinement stepCycle: LAST / Resolution: 1.76→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5564 0 50 755 6369
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0195813
X-RAY DIFFRACTIONr_bond_other_d0.0020.025511
X-RAY DIFFRACTIONr_angle_refined_deg1.4221.9727870
X-RAY DIFFRACTIONr_angle_other_deg0.816312677
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9775718
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.51123.546282
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.751151014
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9711549
X-RAY DIFFRACTIONr_chiral_restr0.0850.2837
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0216601
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021356
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.2283.9892815
X-RAY DIFFRACTIONr_mcbond_other4.2283.9882814
X-RAY DIFFRACTIONr_mcangle_it4.8426.2493522
X-RAY DIFFRACTIONr_mcangle_other4.8426.253523
X-RAY DIFFRACTIONr_scbond_it13.8825.1032998
X-RAY DIFFRACTIONr_scbond_other13.8845.0992994
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other12.637.4584334
X-RAY DIFFRACTIONr_long_range_B_refined12.56516.2667498
X-RAY DIFFRACTIONr_long_range_B_other12.55716.2587494
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.761→1.806 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.285 159 -
Rwork0.243 4958 -
obs--95.86 %

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