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- PDB-2qeu: Crystal structure of putative carboxymuconolactone decarboxylase ... -

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Basic information

Entry
Database: PDB / ID: 2qeu
TitleCrystal structure of putative carboxymuconolactone decarboxylase (YP_555818.1) from Burkholderia xenovorans LB400 at 1.65 A resolution
ComponentsPutative carboxymuconolactone decarboxylase
KeywordsLYASE / YP_555818.1 / Putative carboxymuconolactone decarboxylase / Carboxymuconolactone decarboxylase family / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


peroxiredoxin activity
Similarity search - Function
AhpD-like / Carboxymuconolactone decarboxylase-like / AhpD-like / Carboxymuconolactone decarboxylase family / AhpD-like / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
ACETATE ION / CITRIC ACID / Carboxymuconolactone decarboxylase
Similarity search - Component
Biological speciesBurkholderia xenovorans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.65 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of Putative carboxymuconolactone decarboxylase (YP_555818.1) from Burkholderia xenovorans LB400 at 1.65 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJun 26, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 17, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations ...Advisory / Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Jul 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 1.5Jan 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 1.6Oct 30, 2024Group: Data collection / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id
Remark 999 SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ... SEQUENCE 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.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative carboxymuconolactone decarboxylase
B: Putative carboxymuconolactone decarboxylase
C: Putative carboxymuconolactone decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,55417
Polymers47,1963
Non-polymers1,35814
Water7,386410
1
A: Putative carboxymuconolactone decarboxylase
B: Putative carboxymuconolactone decarboxylase
C: Putative carboxymuconolactone decarboxylase
hetero molecules

A: Putative carboxymuconolactone decarboxylase
B: Putative carboxymuconolactone decarboxylase
C: Putative carboxymuconolactone decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,10934
Polymers94,3926
Non-polymers2,71628
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x-y,-y,-z1
Buried area26620 Å2
ΔGint-151 kcal/mol
Surface area27140 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)71.173, 71.173, 325.501
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: GLY / End label comp-ID: GLY / Refine code: 6 / Auth seq-ID: 9 - 137 / Label seq-ID: 10 - 138

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC

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Components

#1: Protein Putative carboxymuconolactone decarboxylase


Mass: 15732.073 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia xenovorans (bacteria) / Strain: LB400 / Gene: YP_555818.1, Bxeno_C0540, Bxe_C0569 / Plasmid: speedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q13HH1
#2: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H8O7
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 410 / 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: 2.52 Å3/Da / Density % sol: 51.2 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.57
Details: NANODROP, 23.4% PEG 4000, 15.0% Glycerol, 0.17M Ammonium acetate, 0.1M Citric acid pH 5.57, 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: 0.91837, 0.97903, 0.97920
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jun 3, 2007 / Details: Flat collimating mirror, toroid focusing mirror
RadiationMonochromator: Double crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.979031
30.97921
ReflectionResolution: 1.65→29.761 Å / Num. obs: 60310 / % possible obs: 100 % / Redundancy: 10.6 % / Biso Wilson estimate: 17.94 Å2 / Rmerge(I) obs: 0.147 / Rsym value: 0.147 / Net I/σ(I): 13.8
Reflection shell

Rmerge(I) obs: 0.012 / Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.65-1.6910.824694543531.24100
1.69-1.7410.80.74572942351.064100
1.74-1.7910.80.94432441160.837100
1.79-1.8410.81.14352340270.7100
1.84-1.9110.81.34212539020.581100
1.91-1.9710.81.64098437910.468100
1.97-2.0510.82.23949736580.355100
2.05-2.1310.82.83793735280.268100
2.13-2.2210.83.43669334090.222100
2.22-2.3310.84.23491132410.179100
2.33-2.4610.74.53359131300.163100
2.46-2.6110.753147029430.144100
2.61-2.7910.65.42955127840.128100
2.79-3.0110.65.92766226190.116100
3.01-3.310.472539124310.094100
3.3-3.6910.48.12294322110.077100
3.69-4.2610.292024719840.067100
4.26-5.229.991699217180.064100
5.22-7.389.68.61323313800.072100
7.38-29.7618.58.472068500.06298.4

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
SCALAdata scaling
PDB_EXTRACT3data extraction
MAR345CCDdata collection
MOSFLMdata reduction
SHELXDphasing
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.65→29.761 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.963 / SU B: 3.175 / SU ML: 0.053 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.077 / ESU R Free: 0.078
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. ACETATE, CITRATE AND GLYCEROL FROM THE CRYSTALLIZATON ARE MODELED. 5. UNEXPLAINED ELECTRON DENSITIES NEAR RESIDUES 119 OF CHAINS A, B AND C WERE NOT MODELED.
RfactorNum. reflection% reflectionSelection details
Rfree0.18 3039 5.1 %RANDOM
Rwork0.152 ---
obs0.154 60156 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 9.037 Å2
Baniso -1Baniso -2Baniso -3
1-0.51 Å20.25 Å20 Å2
2--0.51 Å20 Å2
3----0.76 Å2
Refinement stepCycle: LAST / Resolution: 1.65→29.761 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3025 0 91 410 3526
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0223415
X-RAY DIFFRACTIONr_bond_other_d0.0010.022298
X-RAY DIFFRACTIONr_angle_refined_deg1.7642.0034632
X-RAY DIFFRACTIONr_angle_other_deg1.05435640
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4285441
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.89823.852135
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.70215598
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.4081522
X-RAY DIFFRACTIONr_chiral_restr0.10.2511
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023867
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02656
X-RAY DIFFRACTIONr_nbd_refined0.2350.2896
X-RAY DIFFRACTIONr_nbd_other0.190.22467
X-RAY DIFFRACTIONr_nbtor_refined0.1820.21720
X-RAY DIFFRACTIONr_nbtor_other0.0850.21577
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1940.2338
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0590.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3530.233
X-RAY DIFFRACTIONr_symmetry_vdw_other0.280.287
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1950.241
X-RAY DIFFRACTIONr_mcbond_it1.87332239
X-RAY DIFFRACTIONr_mcbond_other0.5113859
X-RAY DIFFRACTIONr_mcangle_it2.47753420
X-RAY DIFFRACTIONr_scbond_it4.94781367
X-RAY DIFFRACTIONr_scangle_it7.126111212
Refine LS restraints NCS

Ens-ID: 1 / Number: 1537 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1ALOOSE POSITIONAL0.375
2BLOOSE POSITIONAL0.45
3CLOOSE POSITIONAL0.295
1ALOOSE THERMAL2.8710
2BLOOSE THERMAL4.8510
3CLOOSE THERMAL3.2510
LS refinement shellResolution: 1.65→1.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.289 241 -
Rwork0.225 4104 -
obs-4345 100 %
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)
10.9480.06260.47170.45530.31981.60330.0216-0.1801-0.0270.1574-0.02360.0591-0.0153-0.24320.002-0.01280.0230.0305-0.02220.0254-0.044662.70967.437719.1155
20.21730.15760.06111.24860.26811.0213-0.03-0.0147-0.04430.0928-0.05560.28560.2795-0.40950.0856-0.0358-0.10910.02450.04480.0050.017650.4912-15.0419-0.7459
30.4067-0.06810.15150.98140.57721.4453-0.0138-0.0055-0.05820.12350.1043-0.06710.28220.2048-0.09060.00210.0504-0.0142-0.05290.0057-0.036481.9569-11.60372.2024
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA7 - 1388 - 139
2X-RAY DIFFRACTION2BB8 - 1409 - 141
3X-RAY DIFFRACTION3CC7 - 1388 - 139

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