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- PDB-4l6d: Crystal structure of 5-carboxyvanillate decarboxylase from Sphing... -

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Basic information

Entry
Database: PDB / ID: 4l6d
TitleCrystal structure of 5-carboxyvanillate decarboxylase from Sphingomonas paucimobilis complexed with vanillic acid
Components5-carboxyvanillate decarboxylase
KeywordsHYDROLASE / amidohydrolase fold / vanillic acid
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
: / DI(HYDROXYETHYL)ETHER / 4-HYDROXY-3-METHOXYBENZOATE / 5-carboxyvanillate decarboxylase
Similarity search - Component
Biological speciesSphingomonas paucimobilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.449 Å
AuthorsFedorov, A.A. / Fedorov, E.V. / Vladimirova, A. / Raushel, F.M. / Almo, S.C.
CitationJournal: To be Published
Title: Crystal structure of 5-carboxyvanillate decarboxylase from Sphingomonas paucimobilis complexed with vanillic acid
Authors: Fedorov, A.A. / Fedorov, E.V. / Vladimirova, A. / Raushel, F.M. / Almo, S.C.
History
DepositionJun 12, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 13, 2013Provider: 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_auth_seq_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

Downloads & links

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Assembly

Deposited unit
A: 5-carboxyvanillate decarboxylase
B: 5-carboxyvanillate decarboxylase
C: 5-carboxyvanillate decarboxylase
D: 5-carboxyvanillate decarboxylase
E: 5-carboxyvanillate decarboxylase
F: 5-carboxyvanillate decarboxylase
G: 5-carboxyvanillate decarboxylase
H: 5-carboxyvanillate decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)302,51247
Polymers296,5708
Non-polymers5,94239
Water62,2243454
1
A: 5-carboxyvanillate decarboxylase
H: 5-carboxyvanillate decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,62012
Polymers74,1422
Non-polymers1,47710
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8500 Å2
ΔGint-64 kcal/mol
Surface area21940 Å2
MethodPISA
2
B: 5-carboxyvanillate decarboxylase
G: 5-carboxyvanillate decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,73212
Polymers74,1422
Non-polymers1,58910
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7580 Å2
ΔGint-58 kcal/mol
Surface area21620 Å2
MethodPISA
3
C: 5-carboxyvanillate decarboxylase
F: 5-carboxyvanillate decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,49011
Polymers74,1422
Non-polymers1,3479
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8050 Å2
ΔGint-59 kcal/mol
Surface area21880 Å2
MethodPISA
4
D: 5-carboxyvanillate decarboxylase
E: 5-carboxyvanillate decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,67112
Polymers74,1422
Non-polymers1,52810
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7750 Å2
ΔGint-56 kcal/mol
Surface area21710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.592, 96.917, 97.029
Angle α, β, γ (deg.)109.71, 90.53, 111.89
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 8 molecules ABCDEFGH

#1: Protein
5-carboxyvanillate decarboxylase


Mass: 37071.203 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sphingomonas paucimobilis (bacteria) / Gene: ligW / Production host: Escherichia coli (E. coli) / References: UniProt: Q8RJ47

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Non-polymers , 6 types, 3493 molecules

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


Mass: 54.938 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Mn
#3: Chemical
ChemComp-VNL / 4-HYDROXY-3-METHOXYBENZOATE / vanillate


Mass: 167.139 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: C8H7O4
#4: Chemical
ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3454 / 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: 2.21 Å3/Da / Density % sol: 44.23 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 20% PEG 10000, 0.1M Hepes, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 16, 2012
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 1.449→37.219 Å / Num. all: 423754 / Num. obs: 423754 / % possible obs: 94.08 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

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Processing

Software
NameVersionClassification
CBASSdata collection
BALBESphasing
PHENIX(phenix.refine: 1.8_1069)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ICM

4icm


Resolution: 1.449→37.219 Å / SU ML: 0.13 / σ(F): 1.97 / Phase error: 16.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1683 21271 5.02 %
Rwork0.1456 --
obs0.1468 423754 94.08 %
all-423754 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.449→37.219 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20872 0 342 3454 24668
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00621940
X-RAY DIFFRACTIONf_angle_d1.16329856
X-RAY DIFFRACTIONf_dihedral_angle_d12.6078123
X-RAY DIFFRACTIONf_chiral_restr0.0813241
X-RAY DIFFRACTIONf_plane_restr0.0083940
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.449-1.46530.27057230.237812560X-RAY DIFFRACTION88
1.4653-1.48250.24457010.227412900X-RAY DIFFRACTION91
1.4825-1.50060.25366910.217113007X-RAY DIFFRACTION91
1.5006-1.51960.246610.21713178X-RAY DIFFRACTION91
1.5196-1.53960.22367200.204113004X-RAY DIFFRACTION92
1.5396-1.56070.22326410.186313064X-RAY DIFFRACTION91
1.5607-1.5830.20687250.176913016X-RAY DIFFRACTION91
1.583-1.60660.20666600.168913075X-RAY DIFFRACTION92
1.6066-1.63170.19386820.166513000X-RAY DIFFRACTION92
1.6317-1.65840.19656460.161313161X-RAY DIFFRACTION92
1.6584-1.6870.19016900.155313217X-RAY DIFFRACTION92
1.687-1.71770.19677400.159913170X-RAY DIFFRACTION93
1.7177-1.75070.19687110.162513200X-RAY DIFFRACTION93
1.7507-1.78650.1936990.155413184X-RAY DIFFRACTION93
1.7865-1.82530.17677140.145513296X-RAY DIFFRACTION93
1.8253-1.86780.17076690.142513420X-RAY DIFFRACTION94
1.8678-1.91450.18317090.146113340X-RAY DIFFRACTION94
1.9145-1.96630.17657430.142813452X-RAY DIFFRACTION94
1.9663-2.02410.186920.139813539X-RAY DIFFRACTION95
2.0241-2.08940.16136460.132113663X-RAY DIFFRACTION96
2.0894-2.16410.14647020.126713690X-RAY DIFFRACTION96
2.1641-2.25070.15997190.136613782X-RAY DIFFRACTION96
2.2507-2.35320.16077350.136713791X-RAY DIFFRACTION97
2.3532-2.47720.16177860.141313883X-RAY DIFFRACTION97
2.4772-2.63240.16447580.142813827X-RAY DIFFRACTION97
2.6324-2.83560.16077310.143713929X-RAY DIFFRACTION98
2.8356-3.12080.16637530.143613974X-RAY DIFFRACTION98
3.1208-3.5720.15747330.139814004X-RAY DIFFRACTION98
3.572-4.49920.13137430.122814068X-RAY DIFFRACTION99
4.4992-37.23120.14517480.134514089X-RAY DIFFRACTION99
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)
10.37620.06970.03520.45080.00090.42390.00010.0197-0.039-0.0450.00790.02250.0497-0.0145-0.00330.0475-0.0116-0.00440.04960.00350.0468-47.196657.451346.7784
20.3852-0.0348-0.00940.3813-0.00310.377-0.004-0.0303-0.03120.02830.01150.03940.0441-0.0437-0.00350.0497-0.00930.00340.0570.00650.0433-49.192653.363991.9387
30.4729-0.0830.130.5348-0.02710.5217-0.0317-0.090.01840.05820.01970.0998-0.0422-0.11660.01190.05160.01480.01720.0966-0.00820.0837-63.872496.082294.7065
40.3739-0.07170.04690.45140.02170.355-0.01520.02070.034-0.02730.00130.0433-0.0365-0.04130.00940.0361-0.0003-0.00230.0540.00460.0589-62.072899.977250.0368
50.4281-0.07790.14960.3974-0.14110.8993-0.06220.02540.09310.0162-0.0178-0.0411-0.18710.10050.02790.0747-0.0376-0.0180.04940.01750.0867-33.0044114.110457.5531
60.4009-0.10710.1090.54520.03090.5194-0.0454-0.05450.05360.08710.0347-0.0598-0.04390.02260.00680.06330.0044-0.01710.0604-0.01420.0688-31.8974101.1654101.0951
70.4111-0.05860.02030.3836-0.02380.39070.0011-0.0215-0.00430.02180.0019-0.06260.02090.053-0.0010.04330.0028-0.00380.0555-0.00280.0567-16.965960.058888.6257
80.40840.06950.03830.5451-0.00750.3018-0.01610.0573-0.0262-0.06320.0211-0.08390.01120.05440.00510.0389-0.00920.01920.0771-0.00550.0635-18.27673.436445.0768
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B
3X-RAY DIFFRACTION3chain C
4X-RAY DIFFRACTION4chain D
5X-RAY DIFFRACTION5chain E
6X-RAY DIFFRACTION6chain F
7X-RAY DIFFRACTION7chain G
8X-RAY DIFFRACTION8chain H

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