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- PDB-3d7i: Crystal structure of carboxymuconolactone decarboxylase family pr... -

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Basic information

Entry
Database: PDB / ID: 3d7i
TitleCrystal structure of carboxymuconolactone decarboxylase family protein possibly involved in oxygen detoxification (1591455) from METHANOCOCCUS JANNASCHII at 1.75 A resolution
Componentscarboxymuconolactone decarboxylase family protein
KeywordsLYASE / 1591455 / carboxymuconolactone decarboxylase family protein possibly involved in oxygen detoxification / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homologyAhpD-like / Carboxymuconolactone decarboxylase-like / AhpD-like / Carboxymuconolactone decarboxylase family / AhpD-like / oxidoreductase activity / Up-down Bundle / Mainly Alpha / Uncharacterized protein MJ0742
Function and homology information
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.75 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of carboxymuconolactone decarboxylase family protein possibly involved in oxygen detoxification (1591455) from METHANOCOCCUS JANNASCHII at 1.75 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionMay 21, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 15, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_struct_assembly_auth_evidence / software / Item: _software.classification / _software.name
Revision 1.3Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Feb 1, 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 1.5Nov 6, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,9947
Polymers35,5123
Non-polymers4824
Water1,874104
1
A: carboxymuconolactone decarboxylase family protein
B: carboxymuconolactone decarboxylase family protein
C: carboxymuconolactone decarboxylase family protein
hetero molecules

A: carboxymuconolactone decarboxylase family protein
B: carboxymuconolactone decarboxylase family protein
C: carboxymuconolactone decarboxylase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,98914
Polymers71,0246
Non-polymers9658
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area20480 Å2
ΔGint-298 kcal/mol
Surface area19500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.571, 92.672, 111.237
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
DetailsAUTHORS STATE THAT SIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING SUPPORTS THE ASSIGNMENT OF A HEXAMER AS A SIGNIFICANT OLIGOMERIZATION STATE.

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Components

#1: Protein carboxymuconolactone decarboxylase family protein


Mass: 11837.287 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (archaea)
Gene: 1591455, MJ0742 / Plasmid: MH4a / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q58152
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 104 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE. THE CONSTRUCT WAS ENGINEERED WITH THE FOLLOWING MUTATIONS: K15A, E16A, K17A. SITES OF MUTATIONS WERE SELECTED FROM HIGH ENTROPY SITES PREDICTED BY THE UCLA SURFACE ENTROPY REDUCTION SERVER.

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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: 2.67 Å3/Da / Density % sol: 53.92 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 3.7
Details: 0.2M ammonium sulfate, 17.8% polyethylene glycol 300, 10.0% Glycerol, 0.1M phosphate-citrate pH 3.7, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.91162,0.97929,0.97907
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 1, 2008 / Details: Flat collimating mirror, toroid focusing mirror
RadiationMonochromator: Double crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.911621
20.979291
30.979071
ReflectionResolution: 1.75→28.952 Å / Num. obs: 38442 / % possible obs: 99.5 % / Redundancy: 4.9 % / Rmerge(I) obs: 0.078 / Rsym value: 0.078 / Net I/σ(I): 4.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.75-1.850.5351.41403027890.53598.9
1.8-1.8450.441.71376227380.4499.3
1.84-1.950.3372.31329226350.33799.2
1.9-1.9650.2642.91295825810.26499.2
1.96-2.0250.2013.71264425140.20199.3
2.02-2.0950.1624.61218724310.16299.6
2.09-2.1750.145.11180323540.1499.6
2.17-2.2650.124.61134322640.1299.7
2.26-2.3650.1036.61090921790.10399.7
2.36-2.4750.097.41036420880.0999.7
2.47-2.6150.0867.4986419810.08699.9
2.61-2.774.90.088.2926218760.0899.9
2.77-2.964.90.0738.5887718050.07399.8
2.96-3.24.90.0698.6811116500.069100
3.2-3.54.80.0669.2754315560.066100
3.5-3.914.80.069.8665613840.06100
3.91-4.524.70.0589.4591212460.05899.9
4.52-5.534.70.069.6491010540.06100
5.53-7.834.50.069838258450.06999.9
7.83-28.954.20.0648.519714720.06496.2

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
SCALAdata scaling
PDB_EXTRACT3.004data extraction
MOSFLMdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.75→28.952 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.954 / SU B: 3.541 / SU ML: 0.055 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.09 / ESU R Free: 0.089
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1.HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2.ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3.A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN ...Details: 1.HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2.ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3.A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4. SULFATE, GLYCEROL, AND PEG WERE MODELED BASED ON CRYSTALLIZATION CONDITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.197 1930 5 %RANDOM
Rwork0.17 ---
obs0.172 38417 99.44 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.084 Å2
Baniso -1Baniso -2Baniso -3
1-0.13 Å20 Å20 Å2
2--0.3 Å20 Å2
3----0.43 Å2
Refinement stepCycle: LAST / Resolution: 1.75→28.952 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2128 0 28 104 2260
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0222305
X-RAY DIFFRACTIONr_bond_other_d0.0010.021491
X-RAY DIFFRACTIONr_angle_refined_deg1.4342.0123155
X-RAY DIFFRACTIONr_angle_other_deg0.99133744
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8075332
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.52725.53865
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.88815432
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.592156
X-RAY DIFFRACTIONr_chiral_restr0.0820.2407
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022522
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02404
X-RAY DIFFRACTIONr_nbd_refined0.2210.2556
X-RAY DIFFRACTIONr_nbd_other0.1690.21516
X-RAY DIFFRACTIONr_nbtor_refined0.1790.21181
X-RAY DIFFRACTIONr_nbtor_other0.0870.21119
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1410.2100
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3250.230
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2470.262
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2140.210
X-RAY DIFFRACTIONr_mcbond_it1.96131578
X-RAY DIFFRACTIONr_mcbond_other0.4443613
X-RAY DIFFRACTIONr_mcangle_it2.82452464
X-RAY DIFFRACTIONr_scbond_it4.5768835
X-RAY DIFFRACTIONr_scangle_it5.80711668
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.283 145 -
Rwork0.212 2632 -
all-2777 -
obs--98.69 %
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)
11.3082-0.1347-1.22840.5479-0.2012.0585-0.0502-0.2787-0.05090.15170.0389-0.10660.02670.26920.0114-0.07180.022-0.0095-0.05640.0139-0.10534.576944.434235.3467
20.68961.0466-0.48291.9157-0.8420.92380.0668-0.15080.04740.2538-0.0951-0.2646-0.09530.23590.0284-0.0205-0.0351-0.0055-0.0085-0.04090.00751.662870.604341.0202
30.59590.3398-0.30172.5771-0.80920.41210.04210.05430.0803-0.11190.03530.25940.0406-0.177-0.0774-0.05940.00480.0317-0.0412-0.0082-0.0313-14.100262.998236.9439
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA8 - 1049 - 105
2X-RAY DIFFRACTION2BB7 - 1048 - 105
3X-RAY DIFFRACTION3CC9 - 10410 - 105

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