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- PDB-1vke: Crystal structure of carboxymuconolactone decarboxylase family pr... -

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Basic information

Entry
Database: PDB / ID: 1vke
TitleCrystal structure of carboxymuconolactone decarboxylase family protein possibly involved in antioxidative response (TM1620) from Thermotoga maritima at 1.56 A resolution
Componentscarboxymuconolactone decarboxylase family protein
KeywordsLYASE / TM1620 / CARBOXYMUCONOLACTONE DECARBOXYLASE FAMILY PROTEIN POSSIBLY INVOLVED IN ANTIOXIDATIVE RESPONSE / STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI / Joint Center for Structural Genomics
Function / homology
Function and homology information


peroxiredoxin activity / oxidoreductase activity
Similarity search - Function
Alkylhydroperoxidase AhpD core / AhpD-like / AhpD-like / Carboxymuconolactone decarboxylase-like / Carboxymuconolactone decarboxylase family / AhpD-like / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Unknown ligand / Carboxymuconolactone decarboxylase-like domain-containing protein
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.56 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of carboxymuconolactone decarboxylase family protein possibly involved in antioxidative response (TM1620) from Thermotoga maritima at 1.56 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionMay 13, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 8, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.3Jan 25, 2023Group: Database references / Derived calculations / Category: database_2 / 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
Revision 1.4Sep 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: carboxymuconolactone decarboxylase family protein
B: carboxymuconolactone decarboxylase family protein
C: carboxymuconolactone decarboxylase family protein
D: carboxymuconolactone decarboxylase family protein
E: carboxymuconolactone decarboxylase family protein
F: carboxymuconolactone decarboxylase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,74819
Polymers91,6306
Non-polymers11813
Water7,837435
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20490 Å2
ΔGint-160 kcal/mol
Surface area23380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.922, 67.975, 90.077
Angle α, β, γ (deg.)90.00, 97.52, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
carboxymuconolactone decarboxylase family protein


Mass: 15271.636 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Details: possibly involved in antioxidative response / Source: (gene. exp.) Thermotoga maritima (bacteria) / Strain: MSB8 / Gene: TM1620 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9X1V5, Lyases; Carbon-carbon lyases
#2: Chemical
ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 12 / Source method: obtained synthetically
#3: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 435 / 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: 2.69 Å3/Da / Density % sol: 53.93 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop, nanodrop
Details: 5.5 MES 25 MPD 0.2 Li2SO4, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1
DetectorType: ADSC / Detector: CCD / Date: Oct 24, 2003
RadiationMonochromator: Single crystal, cylindrically bent, Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.56→50 Å / Num. obs: 106734 / % possible obs: 92.29 % / Redundancy: 3.8 % / Biso Wilson estimate: 30.49 Å2 / Rsym value: 0.04 / Net I/σ(I): 32.69
Reflection shellResolution: 1.56→1.62 Å / Redundancy: 1.78 % / Mean I/σ(I) obs: 1.32 / Num. unique all: 6403 / Rsym value: 0.48 / % possible all: 55.27

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMAC5.2.0003refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1P8C

1p8c


Resolution: 1.56→44.65 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.966 / SU B: 2.8 / SU ML: 0.047 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.068 / ESU R Free: 0.068 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 2. CHAIN A 4-17 HAS VERY POOR DENSITY, OCCUPANCY SET TO 0.5 3. THERE ARE UNEXPLAINED DENSITIES NEAR PUTATIVE ACTIVE SITES (AROUND 59-62 ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 2. CHAIN A 4-17 HAS VERY POOR DENSITY, OCCUPANCY SET TO 0.5 3. THERE ARE UNEXPLAINED DENSITIES NEAR PUTATIVE ACTIVE SITES (AROUND 59-62 DISULFIDE BOND), SOME RESEMBLE MPD. HOWEVER, NOT ALL OF THEM LOOKED SIMILAR. AS A RESULT, ONLY ONE WAS MODELLED AS MPD, THE REST OF THEM ARE MODELLED AS UNL, "UNKNOWN LIGAND" 4. UNL 2-7 O1 ATOM IS HEAVIER THAN OXYGEN, IT FITS THE DENSITY BETTER TO MODEL EACH AS A SULFATE AND A CLOSE ASSOCIATED WATER
RfactorNum. reflection% reflectionSelection details
Rfree0.17834 5361 5 %RANDOM
Rwork0.15816 ---
obs0.15918 101346 92.21 %-
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: 15.887 Å2
Baniso -1Baniso -2Baniso -3
1--0.77 Å20 Å2-0.85 Å2
2---0.82 Å20 Å2
3---1.36 Å2
Refinement stepCycle: LAST / Resolution: 1.56→44.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4870 0 68 435 5373
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0225038
X-RAY DIFFRACTIONr_bond_other_d0.0010.024871
X-RAY DIFFRACTIONr_angle_refined_deg1.441.9766795
X-RAY DIFFRACTIONr_angle_other_deg0.863311214
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6225627
X-RAY DIFFRACTIONr_dihedral_angle_2_deg24.84423.172227
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.94315932
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.0321552
X-RAY DIFFRACTIONr_chiral_restr0.0950.2815
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025515
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021029
X-RAY DIFFRACTIONr_nbd_refined0.3220.21272
X-RAY DIFFRACTIONr_nbd_other0.1710.24871
X-RAY DIFFRACTIONr_nbtor_other0.0820.22860
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1710.2334
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0780.24
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2690.239
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1320.215
X-RAY DIFFRACTIONr_mcbond_it1.95633248
X-RAY DIFFRACTIONr_mcbond_other0.4831318
X-RAY DIFFRACTIONr_mcangle_it2.73255079
X-RAY DIFFRACTIONr_scbond_it4.7781963
X-RAY DIFFRACTIONr_scangle_it7.281111716
LS refinement shellResolution: 1.56→1.6 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.304 240 5.35 %
Rwork0.275 4242 -
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)
110.15180.72-5.487118.8357-6.115836.72940.3850.44660.6302-1.14330.62460.82452.48810.5654-1.00960.27860.0829-0.1262-0.0707-0.09490.068310.117-20.7549.965
218.998420.34224.372127.06782.75291.7095-0.28-0.2445-0.5289-0.7143-0.0453-0.96180.33260.02950.32540.0440.01340.1060.023-0.00040.156232.762-16.39926.883
33.2729-4.81195.54587.8036-9.037611.40580.3467-0.0478-0.3826-0.6883-0.0350.13110.938-0.3263-0.31170.1342-0.0418-0.00560.05390.01650.1865-1.496-17.21417.961
411.35625.17148.47533.04124.16576.5571-0.25930.82750.2384-0.21590.28810.0179-0.10930.5765-0.02880.1036-0.02040.02110.16040.00440.001620.01214.7618.358
54.34223.6515-3.18265.3789-3.81843.48520.1392-0.30080.11030.49690.02780.0458-0.15130.1161-0.1670.17650.0186-0.010.09590.00720.023526.3112.46843.551
64.83174.24214.16524.36743.84854.9674-0.23490.01780.4805-0.0592-0.14270.2833-0.3708-0.22760.37760.11910.0115-0.00940.0657-0.00010.087510.57319.53912.903
76.87846.2576-2.98155.765-2.67072.0407-0.2491-0.0678-0.47760.00570.0116-0.46560.15490.19320.23760.10070.02230.01230.06880.02540.088529.926-7.13739.071
84.8477-4.75464.71976.0851-5.13385.625-0.3557-0.4147-0.16810.23370.49640.2981-0.059-0.7725-0.14070.0263-0.00020.03730.16410.07160.1623-6.093-12.43627.595
90.5643-0.0399-0.12360.81690.0521.7148-0.08420.149-0.2346-0.08040.05810.03950.0731-0.07010.02620.0889-0.02470.00790.0937-0.03660.07936.587-6.1367.53
102.5661-0.05660.31070.4507-0.12520.64670.09130.2368-0.11750.024-0.0431-0.1593-0.00630.0789-0.04820.074400.01490.0962-0.02020.052830.4256.02618.947
110.37450.0746-0.12361.38520.01710.7225-0.0538-0.11440.08670.12160.01940.0012-0.0932-0.01940.03440.13640.0029-0.00520.0789-0.02090.042820.5115.46233.327
122.85070.08920.49611.0578-0.01270.7364-0.0576-0.05410.06550.05560.09240.0982-0.1738-0.1872-0.03490.07630.03260.00330.09090.01440.0498-2.1668.74717.53
130.4419-0.04640.14352.5511-0.16430.0553-0.0025-0.0275-0.10220.01580.1051-0.02930.1457-0.06-0.10260.11010.00930.01410.03630.02060.086318.915-17.52630.853
141.3121-0.34460.52391.9739-1.08422.9862-0.121-0.1904-0.12690.33070.16850.3253-0.226-0.3594-0.04750.10120.05380.08050.11150.06350.07364.651-7.54439.693
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA4 - 1716 - 29
22EE2 - 1714 - 29
33AA19 - 3931 - 51
44BB21 - 3933 - 51
55CC21 - 3933 - 51
66DD19 - 3931 - 51
77EE19 - 3931 - 51
88FF20 - 3932 - 51
99AA40 - 12152 - 133
1010BB40 - 12152 - 133
1111CC40 - 12052 - 132
1212DD40 - 11952 - 131
1313EE40 - 12152 - 133
1414FF40 - 11652 - 128

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