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- PDB-4qs5: CRYSTAL STRUCTURE of 5-CARBOXYVANILLATE DECARBOXYLASE LIGW2 FROM ... -

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Basic information

Entry
Database: PDB / ID: 4qs5
TitleCRYSTAL STRUCTURE of 5-CARBOXYVANILLATE DECARBOXYLASE LIGW2 FROM NOVOSPHINGOBIUM AROMATICIVORANS DSM 12444 (TARGET EFI-505250) WITH BOUND MANGANESE AND 3-methoxy-4-hydroxy-5-nitrobenzoic acid, THE D314N MUTANT
ComponentsLigw2 Decarboxylase
KeywordsHYDROLASE/HYDROLASE INHIBITOR / AMIDOHYDROLASE / METAL BINDING SITE / DECARBOXYLASE / HYDROLASE-HYDROLASE INHIBITOR complex
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 / ACETATE ION / : / Amidohydrolase 2
Similarity search - Component
Biological speciesNovosphingobium aromaticivorans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsPatskovsky, Y. / Vladimirova, A. / Toro, R. / Bhosle, R. / Hillerich, B. / Seidel, R.D. / Raushel, M. / Almo, S.C.
CitationJournal: To be Published
Title: Crystal Structure of 5-CARBOXYVANILLATE Decarboxylase from Novosphingobium Aromaticivorans
Authors: Patskovsky, Y. / Vladimirova, A. / Toro, R. / Bhosle, R. / Gerlt, J.A. / Raushel, F.M. / Almo, S.C.
History
DepositionJul 2, 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 / pdbx_struct_conn_angle / 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 / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _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.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.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_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
C: Ligw2 Decarboxylase
D: Ligw2 Decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)171,81924
Polymers169,8214
Non-polymers1,99820
Water20,8071155
1
A: Ligw2 Decarboxylase
B: Ligw2 Decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,85312
Polymers84,9112
Non-polymers94210
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7000 Å2
ΔGint-75 kcal/mol
Surface area23660 Å2
MethodPISA
2
C: Ligw2 Decarboxylase
D: Ligw2 Decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,96612
Polymers84,9112
Non-polymers1,05610
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7110 Å2
ΔGint-57 kcal/mol
Surface area23540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.159, 60.590, 123.473
Angle α, β, γ (deg.)90.00, 112.84, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.717498, 0.616362, 0.324492), (0.615608, 0.343133, 0.709427), (0.32592, 0.708772, -0.625634)2.65759, 0.77461, -3.78444
3given(0.998788, 0.001379, -0.049197), (-0.000954, 0.999962, 0.008649), (0.049207, -0.008591, 0.998752)-26.53905, 0.42113, 55.6335
4given(-0.705207, 0.615156, 0.352513), (0.639995, 0.338355, 0.689871), (0.305104, 0.712108, -0.632308)39.5417, 24.75366, -47.24985

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Ligw2 Decarboxylase


Mass: 42455.293 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Novosphingobium aromaticivorans (bacteria)
Strain: DSM 12444 / F199 / Gene: Saro_0799 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q2GA79

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Non-polymers , 6 types, 1175 molecules

#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#3: Chemical
ChemComp-1DF / 4-hydroxy-3-methoxy-5-nitrobenzoic acid


Mass: 213.144 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H7NO6
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1155 / 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: 1.97 Å3/Da / Density % sol: 37.64 %
Crystal growpH: 5.6
Details: 0.085M SODIUM CITRATE, PH 5.6, 0.17M SODIUM ACETATE, 25% PEG 4000,15% GLYCEROL, 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
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: 1.8→50 Å / Num. obs: 123052 / % possible obs: 99.9 % / Observed criterion σ(I): -5 / Redundancy: 3.7 % / Rmerge(I) obs: 0.141 / Rsym value: 0.141 / Net I/σ(I): 8.9
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.85 / Mean I/σ(I) obs: 1.8 / Rsym value: 0.85 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.8.0071refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4INF

4inf


Resolution: 1.8→50 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.95 / SU B: 3.599 / SU ML: 0.105 / Cross valid method: THROUGHOUT / ESU R: 0.12 / ESU R Free: 0.124 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20999 3711 3 %RANDOM
Rwork0.15577 ---
obs0.15742 119106 99.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.92 Å2
Baniso -1Baniso -2Baniso -3
1--0.42 Å2-0 Å20.86 Å2
2---0.36 Å2-0 Å2
3---0.03 Å2
Refinement stepCycle: LAST / Resolution: 1.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11114 0 122 1155 12391
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01911591
X-RAY DIFFRACTIONr_bond_other_d0.0010.0210951
X-RAY DIFFRACTIONr_angle_refined_deg1.4311.96915646
X-RAY DIFFRACTIONr_angle_other_deg0.8132.99825188
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.87551418
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.79423.573557
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.727152011
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2361595
X-RAY DIFFRACTIONr_chiral_restr0.0840.21660
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02113121
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022678
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_it4.8073.2075611
X-RAY DIFFRACTIONr_mcbond_other4.7633.2055608
X-RAY DIFFRACTIONr_mcangle_it4.9894.9927015
X-RAY DIFFRACTIONr_mcangle_other4.9934.9927016
X-RAY DIFFRACTIONr_scbond_it13.6574.415980
X-RAY DIFFRACTIONr_scbond_other13.6564.415981
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other12.9686.3068621
X-RAY DIFFRACTIONr_long_range_B_refined12.13512.9114528
X-RAY DIFFRACTIONr_long_range_B_other12.13412.91114529
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.287 296 -
Rwork0.268 8736 -
obs--99.7 %

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