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- PDB-3lvy: Crystal Structure of Carboxymuconolactone Decarboxylase Family Pr... -

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Basic information

Entry
Database: PDB / ID: 3lvy
TitleCrystal Structure of Carboxymuconolactone Decarboxylase Family Protein SMU.961 from Streptococcus mutans
ComponentsCarboxymuconolactone decarboxylase family
KeywordsLYASE / alpha-structure / Structural Genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


peroxiredoxin activity
Similarity search - Function
Alkylhydroperoxidase AhpD core / AhpD-like / Carboxymuconolactone decarboxylase-like / AhpD-like / Carboxymuconolactone decarboxylase family / AhpD-like / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
BETA-MERCAPTOETHANOL / Carboxymuconolactone decarboxylase-like domain-containing protein
Similarity search - Component
Biological speciesStreptococcus mutans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å
AuthorsKim, Y. / Xu, X. / Cui, H. / Chin, S. / Edwards, A. / Savchenko, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal Structure of Carboxymuconolactone Decarboxylase Family Protein SMU.961 from Streptococcus mutans
Authors: Kim, Y. / Xu, X. / Cui, H. / Chin, S. / Edwards, A. / Savchenko, A. / Joachimiak, A.
History
DepositionFeb 22, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 9, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 26, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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 / _struct_conn.pdbx_leaving_atom_flag / _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: Carboxymuconolactone decarboxylase family
B: Carboxymuconolactone decarboxylase family
C: Carboxymuconolactone decarboxylase family
D: Carboxymuconolactone decarboxylase family
E: Carboxymuconolactone decarboxylase family
F: Carboxymuconolactone decarboxylase family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,31011
Polymers136,9876
Non-polymers3235
Water7,512417
1
A: Carboxymuconolactone decarboxylase family
B: Carboxymuconolactone decarboxylase family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,8896
Polymers45,6622
Non-polymers2274
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4570 Å2
ΔGint-50 kcal/mol
Surface area15560 Å2
MethodPISA
2
C: Carboxymuconolactone decarboxylase family
D: Carboxymuconolactone decarboxylase family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,7583
Polymers45,6622
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3930 Å2
ΔGint-43 kcal/mol
Surface area15440 Å2
MethodPISA
3
E: Carboxymuconolactone decarboxylase family
F: Carboxymuconolactone decarboxylase family


Theoretical massNumber of molelcules
Total (without water)45,6622
Polymers45,6622
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3670 Å2
ΔGint-29 kcal/mol
Surface area15550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.996, 73.741, 183.708
Angle α, β, γ (deg.)90.00, 98.68, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Carboxymuconolactone decarboxylase family


Mass: 22831.092 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus mutans (bacteria) / Strain: UA159 / Gene: SMU_961 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 magic / References: UniProt: Q8DUG8
#2: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 417 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.39 Å3/Da / Density % sol: 48.64 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M Hepes pH 7.5, 0.2 M Ammonium Sulphate, 25 % PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97921 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Dec 3, 2009 / Details: mirrors
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97921 Å / Relative weight: 1
ReflectionResolution: 2.1→34.16 Å / Num. all: 75930 / Num. obs: 75930 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 36.97 Å2 / Rsym value: 0.08 / Net I/σ(I): 12.6
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 2.9 % / Mean I/σ(I) obs: 2 / Num. unique all: 3736 / Rsym value: 0.583 / % possible all: 98.5

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000data collection
HKL-3000phasing
PHENIXmodel building
PHENIX(phenix.refine: 1.6_289)refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.1→34.16 Å / SU ML: 0.32 / Isotropic thermal model: mixed / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 29.32 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.236 3775 5.03 %random
Rwork0.184 ---
all0.187 75088 --
obs0.187 75088 99.09 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 63.11 Å2 / ksol: 0.308 e/Å3
Displacement parametersBiso mean: 64.7 Å2
Baniso -1Baniso -2Baniso -3
1-21.9867 Å20 Å2-10.6839 Å2
2---6.1716 Å20 Å2
3----15.8151 Å2
Refinement stepCycle: LAST / Resolution: 2.1→34.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8386 0 15 417 8818
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0118539
X-RAY DIFFRACTIONf_angle_d1.23811653
X-RAY DIFFRACTIONf_dihedral_angle_d18.0093130
X-RAY DIFFRACTIONf_chiral_restr0.081410
X-RAY DIFFRACTIONf_plane_restr0.0061534
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
2.1-2.17510.30063590.27827059741898
2.1751-2.26210.32383640.25617116748099
2.2621-2.36510.30373790.22637106748599
2.3651-2.48970.23513920.18970657457100
2.4897-2.64570.26463560.190372007556100
2.6457-2.84990.26543690.190471157484100
2.8499-3.13650.27843650.19871857550100
3.1365-3.58990.23063970.17937176757399
3.5899-4.52120.18873980.14247127752599
4.5212-34.16610.20633960.16157164756097
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)
10.69030.1644-0.07440.88790.25651.01250.07330.2174-0.1361-0.05460.03450.05270.2608-0.1227-0.09570.19590.0325-0.01980.1863-0.03190.300655.1193-20.3081165.4946
21.431-0.2464-0.18770.67250.62461.2109-0.03290.10650.22120.08760.0138-0.1248-0.30950.00330.01630.19920.02560.01350.08380.03940.305854.73320.3146174.2982
31.65690.01210.38531.3493-0.28151.06670.00120.70110.2122-0.5547-0.0219-0.0691-0.61420.25040.03260.53460.02980.03930.58110.14170.265755.7108-1.9201139.7846
40.6734-0.10750.64041.3210.41411.50070.0810.4946-0.0664-0.554-0.18380.4297-0.0607-0.62430.06590.50470.1405-0.12590.75050.03490.379835.119-10.6081139.0927
50.9654-0.3298-0.45720.04980.26150.55380.2414-0.0741-0.01850.3077-0.0708-0.01690.4543-0.2536-0.06480.7981-0.109-0.1540.94010.02490.130736.7476-29.1476111.69
60.23150.02650.36830.5401-0.25790.5130.21180.16960.01450.1231-0.07090.1409-0.0696-0.0428-0.09050.57790.0112-0.07411.09330.02120.139649.3177-17.611198.0326
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain AA1 - 192
2X-RAY DIFFRACTION2chain BB1 - 192
3X-RAY DIFFRACTION3chain CC1 - 183
4X-RAY DIFFRACTION4chain DD2 - 191
5X-RAY DIFFRACTION5chain EE4 - 177
6X-RAY DIFFRACTION6chain FF2 - 184

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