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- PDB-3q0g: Crystal Structure of the Mycobacterium tuberculosis Crotonase Bou... -

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Basic information

Entry
Database: PDB / ID: 3q0g
TitleCrystal Structure of the Mycobacterium tuberculosis Crotonase Bound to a Reaction Intermediate Derived from Crotonyl CoA
Componentsenoyl-CoA hydratase echA8
KeywordsLYASE / Structural Genomics / TB Structural Genomics Consortium / TBSGC / Crotonase / Enoyl CoA Hydratase / PSI-2 / Protein Structure Initiative
Function / homology
Function and homology information


enoyl-CoA hydratase / enoyl-CoA hydratase activity / fatty acid beta-oxidation / peptidoglycan-based cell wall / fatty acid metabolic process / plasma membrane
Similarity search - Function
Lyase 2-enoyl-coa Hydratase, Chain A, domain 2 / Lyase 2-enoyl-coa Hydratase; Chain A, domain 2 / Enoyl-CoA hydratase, C-terminal / Enoyl-CoA hydratase/isomerase, conserved site / Enoyl-CoA hydratase/isomerase signature. / Enoyl-CoA hydratase/isomerase / Enoyl-CoA hydratase/isomerase / 2-enoyl-CoA Hydratase; Chain A, domain 1 / 2-enoyl-CoA Hydratase; Chain A, domain 1 / ClpP/crotonase-like domain superfamily ...Lyase 2-enoyl-coa Hydratase, Chain A, domain 2 / Lyase 2-enoyl-coa Hydratase; Chain A, domain 2 / Enoyl-CoA hydratase, C-terminal / Enoyl-CoA hydratase/isomerase, conserved site / Enoyl-CoA hydratase/isomerase signature. / Enoyl-CoA hydratase/isomerase / Enoyl-CoA hydratase/isomerase / 2-enoyl-CoA Hydratase; Chain A, domain 1 / 2-enoyl-CoA Hydratase; Chain A, domain 1 / ClpP/crotonase-like domain superfamily / Alpha-Beta Complex / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Butyryl Coenzyme A / COENZYME A / Probable enoyl-CoA hydratase echA8 / Probable enoyl-CoA hydratase EchA8
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.38 Å
AuthorsBruning, J.B. / Delgado, E. / Ghosh, S. / Sacchettini, J.C. / TB Structural Genomics Consortium (TBSGC)
CitationJournal: To be Published
Title: Crystal Structure of the Prokaryotic Crotonase
Authors: Bruning, J.B. / Delgado, E. / Ghosh, S. / Sacchettini, J.C.
History
DepositionDec 15, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 25, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 11, 2015Group: Non-polymer description / Other
Revision 1.2Jan 27, 2016Group: Non-polymer description
Revision 1.3Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_related / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_related.db_name / _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: enoyl-CoA hydratase echA8
B: enoyl-CoA hydratase echA8
C: enoyl-CoA hydratase echA8
D: enoyl-CoA hydratase echA8
E: enoyl-CoA hydratase echA8
F: enoyl-CoA hydratase echA8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)165,73113
Polymers163,8006
Non-polymers1,9307
Water15,295849
1
A: enoyl-CoA hydratase echA8
B: enoyl-CoA hydratase echA8
C: enoyl-CoA hydratase echA8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,8767
Polymers81,9003
Non-polymers9764
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14330 Å2
ΔGint-103 kcal/mol
Surface area27260 Å2
MethodPISA
2
D: enoyl-CoA hydratase echA8
E: enoyl-CoA hydratase echA8
F: enoyl-CoA hydratase echA8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,8546
Polymers81,9003
Non-polymers9543
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13170 Å2
ΔGint-101 kcal/mol
Surface area27370 Å2
MethodPISA
3
A: enoyl-CoA hydratase echA8
B: enoyl-CoA hydratase echA8
C: enoyl-CoA hydratase echA8
hetero molecules

A: enoyl-CoA hydratase echA8
B: enoyl-CoA hydratase echA8
C: enoyl-CoA hydratase echA8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)165,75314
Polymers163,8006
Non-polymers1,9528
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area34770 Å2
ΔGint-229 kcal/mol
Surface area48400 Å2
MethodPISA
4
D: enoyl-CoA hydratase echA8
E: enoyl-CoA hydratase echA8
F: enoyl-CoA hydratase echA8
hetero molecules

D: enoyl-CoA hydratase echA8
E: enoyl-CoA hydratase echA8
F: enoyl-CoA hydratase echA8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)165,70912
Polymers163,8006
Non-polymers1,9086
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area32670 Å2
ΔGint-227 kcal/mol
Surface area48410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.640, 133.170, 133.690
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11B-592-

HOH

21C-586-

HOH

31E-596-

HOH

41E-625-

HOH

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Components

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Protein , 1 types, 6 molecules ABCDEF

#1: Protein
enoyl-CoA hydratase echA8


Mass: 27300.080 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: h37rv / Gene: echA8, MT1100, MTV017.23c, Rv1070c / Plasmid: pVP16 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P64016, UniProt: P9WNN9*PLUS, enoyl-CoA hydratase

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Non-polymers , 5 types, 856 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-COA / COENZYME A / Coenzyme A


Mass: 767.534 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#5: Chemical ChemComp-BCO / Butyryl Coenzyme A / S-{(3S,5S,9R)-1-[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)tetrahydrofuran-2-yl]-3,5,9-trihydroxy-8,8-dimethyl-3,5-dioxido-10,14-dioxo-2,4,6-trioxa-11,15-diaza-3lambda~5~,5lambda~5~-diphosphaheptadecan-17-yl} butanethioate (non-preferred name)


Mass: 837.624 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H42N7O17P3S
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 849 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer detailsTHE COMPOUND PUT DOWN FOR CRYSTALLIZATION IS CROTONYL COA. THE LIGAND (BCO) OBSERVED IN THE ENTRY ...THE COMPOUND PUT DOWN FOR CRYSTALLIZATION IS CROTONYL COA. THE LIGAND (BCO) OBSERVED IN THE ENTRY IS THE REACTION INTERMEDIATE AND THE LIGAND (COA) OBSERVED IN THE ENTRY COULD BE THE HYDROLYSED CROTONYL COA

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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: 2.76 Å3/Da / Density % sol: 55.46 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 20% PEG3350, 0.2 M LiCl, and 20% glycerol, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.9795 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 23, 2009 / Details: mirrors
RadiationMonochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.38→20 Å / Num. all: 70756 / Num. obs: 70756 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Rmerge(I) obs: 0.1 / Rsym value: 0.1 / Net I/σ(I): 7.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsRsym valueDiffraction-ID% possible all
2.38-2.443.70.4893.410.489197.6
2.44-2.493.80.4463.890.446197.9
2.49-2.533.80.4084.330.408198.1
2.53-2.583.70.3724.890.372198.4
2.58-2.643.80.355.20.35198.8
2.64-2.73.80.3115.730.311198.8
2.7-2.773.70.2956.330.295198.7
2.77-2.843.70.267.50.26198.9
2.84-2.933.70.2328.280.232199
2.93-3.023.70.19810.210.198198.5
3.02-3.133.70.1712.130.17198.9
3.13-3.253.70.14214.710.142198.8
3.25-3.43.70.11818.160.118199
3.4-3.583.70.10222.580.102198.7
3.58-3.83.90.09126.050.091198.6
3.8-4.0940.08230.420.082198.6
4.09-4.54.20.07235.310.072197.9
4.5-5.144.40.06237.530.062197.6
5.14-6.444.40.05835.440.058197.6
6.44-204.30.04144.150.041195.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHASERphasing
REFMAC5.5.0102refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1MJ3

1mj3


Resolution: 2.38→19.87 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.909 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 18.789 / SU ML: 0.204 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / ESU R: 0.504 / ESU R Free: 0.31 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28783 3444 5.1 %RANDOM
Rwork0.23312 ---
obs0.23588 64507 93.05 %-
all-67951 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 43.544 Å2
Baniso -1Baniso -2Baniso -3
1--0.06 Å20 Å20 Å2
2--0.15 Å20 Å2
3----0.09 Å2
Refinement stepCycle: LAST / Resolution: 2.38→19.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11126 0 121 849 12096
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.02311423
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2961.97715469
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.62651525
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.61623.863453
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.266151866
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.551591
X-RAY DIFFRACTIONr_chiral_restr0.0810.21827
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0218511
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4061.57531
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.749211914
X-RAY DIFFRACTIONr_scbond_it1.30933892
X-RAY DIFFRACTIONr_scangle_it2.1314.53547
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.38→2.443 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.335 102 -
Rwork0.241 2062 -
obs--41.19 %
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)
13.4913-0.484-0.26292.3899-0.13381.4204-0.0296-0.40040.27530.3567-0.0238-0.0241-0.27190.16110.05350.2084-0.1122-0.02420.1513-0.07710.139421.244917.6509-47.9608
20.78270.2909-0.08320.30910.10561.1372-0.0111-0.03390.04070.04260.0112-0.0935-0.11020.2673-0.00010.1143-0.0405-0.00630.1630.00690.175620.37748.408-61.8442
30.91170.47170.13310.61730.33311.04230.0797-0.0416-0.2690.1266-0.0247-0.1230.27260.1735-0.0550.17450.061-0.03730.07240.02610.225211.3965-20.7807-57.106
432.44385.216822.32552.0553.620915.38150.1196-0.8364-0.2550.77460.1492-0.13010.1362-0.6223-0.26870.49480.116-0.03340.51530.04970.102815.121-4.4101-30.7324
51.00620.37370.62931.1747-0.20061.218-0.09830.3883-0.0349-0.26790.1423-0.0259-0.07860.1315-0.04390.1428-0.01290.07550.2913-0.020.101115.27371.4485-92.0285
60.8113-0.02960.07030.871-0.05730.55380.01880.1338-0.1375-0.0645-0.0221-0.10160.10820.22130.00330.12050.03180.02060.1938-0.04590.148115.4482-9.2304-77.6593
72.43820.4787-0.61662.40521.01882.3910.14210.3840.3032-0.34310.0060.1089-0.4233-0.2985-0.14810.21040.1182-0.00020.14810.09360.133727.538818.4017-18.1699
80.623-0.24010.02750.5540.02851.0160.07070.0220.03-0.06660.01010.1089-0.1267-0.2146-0.08080.11680.03770.01650.16310.03290.162831.27918.4984-5.8367
91.167-0.45180.05560.4358-0.16111.32110.12380.0335-0.3026-0.09320.04190.16020.3226-0.1818-0.16570.1958-0.0879-0.12030.06330.01060.241939.1523-21.8396-8.8623
1012.1393.386612.75151.85873.513.40210.05970.4177-0.2117-0.18690.1671-0.07660.06180.4046-0.22680.24390.0466-0.00820.30640.0340.12238.5083-2.4549-31.3282
110.89360.34720.0451.7572-0.08551.47060.0182-0.2937-0.0270.18060.09180.0721-0.0688-0.2783-0.10990.11140.00130.03710.2930.04380.081733.9970.364322.1439
120.7382-0.49040.06590.77660.12810.7360.074-0.176-0.16150.01210.05460.12940.1629-0.1769-0.12850.1178-0.0582-0.0450.17260.0760.18636.9182-11.8329.6247
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 85
2X-RAY DIFFRACTION2A86 - 255
3X-RAY DIFFRACTION3B2 - 231
4X-RAY DIFFRACTION4B232 - 254
5X-RAY DIFFRACTION5C1 - 88
6X-RAY DIFFRACTION6C89 - 255
7X-RAY DIFFRACTION7D2 - 70
8X-RAY DIFFRACTION8D76 - 255
9X-RAY DIFFRACTION9E2 - 224
10X-RAY DIFFRACTION10E225 - 254
11X-RAY DIFFRACTION11F3 - 133
12X-RAY DIFFRACTION12F134 - 254

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