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- PDB-4icm: Crystal structure of 5-carboxyvanillate decarboxylase LigW from S... -

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Basic information

Entry
Database: PDB / ID: 4icm
TitleCrystal structure of 5-carboxyvanillate decarboxylase LigW from Sphingomonas paucimobilis
Components5-carboxyvanillate decarboxylase
KeywordsLYASE / Amidohydrolase fold / LigW
Function / homology
Function and homology information


carboxy-lyase activity / hydrolase activity / metal ion binding
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 / 5-carboxyvanillate decarboxylase
Similarity search - Component
Biological speciesSphingobium sp. SYK-6 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.825 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 LigW from Sphingomonas paucimobilis
Authors: Fedorov, A.A. / Fedorov, E.V. / Vladimirova, A. / Raushel, F.M. / Almo, S.C.
History
DepositionDec 10, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 11, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

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)297,29919
Polymers296,5708
Non-polymers73011
Water40,3722241
1
A: 5-carboxyvanillate decarboxylase
H: 5-carboxyvanillate decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,3445
Polymers74,1422
Non-polymers2023
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6090 Å2
ΔGint-48 kcal/mol
Surface area22220 Å2
MethodPISA
2
B: 5-carboxyvanillate decarboxylase
G: 5-carboxyvanillate decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,2524
Polymers74,1422
Non-polymers1102
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5870 Å2
ΔGint-49 kcal/mol
Surface area22310 Å2
MethodPISA
3
C: 5-carboxyvanillate decarboxylase
F: 5-carboxyvanillate decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,4506
Polymers74,1422
Non-polymers3084
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6180 Å2
ΔGint-47 kcal/mol
Surface area22100 Å2
MethodPISA
4
D: 5-carboxyvanillate decarboxylase
E: 5-carboxyvanillate decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,2524
Polymers74,1422
Non-polymers1102
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5810 Å2
ΔGint-49 kcal/mol
Surface area22150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.817, 96.897, 97.004
Angle α, β, γ (deg.)109.58, 90.48, 111.66
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
5-carboxyvanillate decarboxylase


Mass: 37071.203 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sphingobium sp. SYK-6 (bacteria) / Gene: ligW, SLG_07850 / Production host: Escherichia coli (E. coli) / References: UniProt: G2IN12
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2241 / 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: 2.22 Å3/Da / Density % sol: 44.52 %
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: Jun 19, 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: 1.825→38.509 Å / Num. all: 219197 / Num. obs: 219197 / % possible obs: 96.67 % / 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 / Resolution: 1.825→38.509 Å / SU ML: 0.21 / σ(F): 0 / Phase error: 21.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2052 10966 5 %RANDOM
Rwork0.163 ---
obs0.1651 219197 96.67 %-
all-219197 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.825→38.509 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20872 0 27 2241 23140
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00721446
X-RAY DIFFRACTIONf_angle_d1.1129173
X-RAY DIFFRACTIONf_dihedral_angle_d12.7617862
X-RAY DIFFRACTIONf_chiral_restr0.0783222
X-RAY DIFFRACTIONf_plane_restr0.0063844
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8245-1.84530.33183390.26145947X-RAY DIFFRACTION84
1.8453-1.8670.28243580.23436982X-RAY DIFFRACTION96
1.867-1.88970.28093450.22946805X-RAY DIFFRACTION95
1.8897-1.91370.29383470.23036888X-RAY DIFFRACTION96
1.9137-1.93880.27563540.21926931X-RAY DIFFRACTION96
1.9388-1.96540.26783430.20116877X-RAY DIFFRACTION96
1.9654-1.99350.2593520.20386839X-RAY DIFFRACTION96
1.9935-2.02320.25743760.1976974X-RAY DIFFRACTION96
2.0232-2.05480.25713590.19466881X-RAY DIFFRACTION96
2.0548-2.08850.25163510.18826913X-RAY DIFFRACTION96
2.0885-2.12450.24743830.17586945X-RAY DIFFRACTION96
2.1245-2.16320.24133700.17476910X-RAY DIFFRACTION97
2.1632-2.20480.22483610.17226967X-RAY DIFFRACTION97
2.2048-2.24980.23563630.18066943X-RAY DIFFRACTION97
2.2498-2.29870.20173790.15536947X-RAY DIFFRACTION97
2.2987-2.35210.21033540.15796926X-RAY DIFFRACTION97
2.3521-2.4110.22553730.15936988X-RAY DIFFRACTION97
2.411-2.47610.22693660.16286999X-RAY DIFFRACTION97
2.4761-2.5490.23243700.16987009X-RAY DIFFRACTION97
2.549-2.63120.22363690.16726977X-RAY DIFFRACTION98
2.6312-2.72520.22083790.16367012X-RAY DIFFRACTION98
2.7252-2.83430.21473690.16736977X-RAY DIFFRACTION98
2.8343-2.96330.21733890.16357055X-RAY DIFFRACTION98
2.9633-3.11940.21023690.17157082X-RAY DIFFRACTION98
3.1194-3.31480.19293930.16486978X-RAY DIFFRACTION98
3.3148-3.57060.1923410.16577127X-RAY DIFFRACTION98
3.5706-3.92960.18113790.15227075X-RAY DIFFRACTION99
3.9296-4.49740.1643680.12987103X-RAY DIFFRACTION99
4.4974-5.66340.14513900.12857094X-RAY DIFFRACTION99
5.6634-38.51720.15923770.13847080X-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)
10.32830.0244-0.10380.3466-0.19730.4013-0.09890.0733-0.1484-0.27460.09530.11090.3286-0.1122-0.02920.1668-0.1326-0.06130.0128-0.0390.1153-48.249655.951347.3248
20.3643-0.0205-0.0260.5717-0.11930.5182-0.0293-0.0912-0.08020.06380.03490.12350.0962-0.05420.00270.083-0.0030.02090.1040.04110.1071-50.540152.14892.5748
30.51220.0007-0.08930.37530.04860.4863-0.0362-0.18350.04320.09420.06880.1017-0.1589-0.23810.01450.11840.08330.03330.1985-0.00460.1035-65.548294.963995.5179
40.5436-0.1439-0.01470.43820.01830.48410.00370.03340.0556-0.0448-0.01590.0732-0.0817-0.06150.00530.04780.011-0.01870.06150.01360.0968-63.508998.673350.4148
50.4818-0.00310.05330.5272-0.21980.5197-0.02680.06090.17480.0303-0.0422-0.0864-0.19660.1317-0.01080.1176-0.0504-0.01810.06580.02580.1462-34.822112.796458.4106
60.4776-0.1152-0.03670.54840.05430.6029-0.0237-0.150.07310.16030.037-0.0478-0.15980.0613-0.00760.1531-0.0056-0.02040.1427-0.04530.0827-33.650199.9075101.9001
70.49590.03350.02480.5091-0.03390.5029-0.0345-0.0877-0.05620.02710.0095-0.07170.09540.15890.01820.05890.0379-0.00260.14010.02010.0685-18.532358.885189.1271
80.6384-0.0387-0.08510.6176-0.00490.4979-0.01240.0379-0.0286-0.1005-0.0095-0.0790.06330.06830.01510.05590.00150.00760.0589-0.00180.0486-19.639472.025745.6309
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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