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- PDB-4fjw: Crystal Structure of the apo form of the E131Q Mtb crotonase -

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Basic information

Entry
Database: PDB / ID: 4fjw
TitleCrystal Structure of the apo form of the E131Q Mtb crotonase
ComponentsProbable enoyl-CoA hydratase echA8
KeywordsLYASE / Structural Genomics / TB Structural Genomics Consortium / TBSGC / crotonase / enoyl CoA hydratase
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
Probable enoyl-CoA hydratase echA8 / Probable enoyl-CoA hydratase EchA8
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å
AuthorsBruning, J.B. / Delgado, E. / Ghosh, S. / Sacchettini, J.C. / TB Structural Genomics Consortium (TBSGC)
CitationJournal: To be Published
Title: Crystal Structure and Mechanism of the Prokaryotic Crotonase
Authors: Bruning, J.B. / Delgado, E. / Ghosh, S. / Sacchettini, J.C.
History
DepositionJun 12, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 22, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
D: Probable enoyl-CoA hydratase echA8
E: Probable enoyl-CoA hydratase echA8
F: Probable enoyl-CoA hydratase echA8


Theoretical massNumber of molelcules
Total (without water)81,8973
Polymers81,8973
Non-polymers00
Water8,107450
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12660 Å2
ΔGint-97 kcal/mol
Surface area27460 Å2
MethodPISA
2
D: Probable enoyl-CoA hydratase echA8
E: Probable enoyl-CoA hydratase echA8
F: Probable enoyl-CoA hydratase echA8

D: Probable enoyl-CoA hydratase echA8
E: Probable enoyl-CoA hydratase echA8
F: Probable enoyl-CoA hydratase echA8


Theoretical massNumber of molelcules
Total (without water)163,7956
Polymers163,7956
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area31480 Å2
ΔGint-216 kcal/mol
Surface area48760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)134.701, 134.044, 101.544
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11D-442-

HOH

21D-452-

HOH

31E-318-

HOH

41E-375-

HOH

51F-363-

HOH

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Components

#1: Protein Probable enoyl-CoA hydratase echA8


Mass: 27299.096 Da / Num. of mol.: 3 / Mutation: E131Q
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
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 450 / 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: 2.8 Å3/Da / Density % sol: 56.05 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 8
Details: 20% PEG3350, 0.2 M LiCl, pH 8, VAPOR DIFFUSION, temperature 298K

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Dec 11, 2011 / Details: mirrors
RadiationMonochromator: osmic mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.2→28.85 Å / Num. all: 46083 / Num. obs: 46083 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.38 % / Biso Wilson estimate: 37.64 Å2 / Rmerge(I) obs: 0.102 / Rsym value: 0.102 / Χ2: 0.97 / Net I/σ(I): 6.1 / Scaling rejects: 1179
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allΧ2% possible all
2.2-2.283.250.46321500945871.0698.7
2.28-2.373.290.4831.81503445491.0498.5
2.37-2.483.270.3992.21502745801.0498.4
2.48-2.613.30.3562.51507845571.0598.4
2.61-2.773.330.3112.81525745661.0398.2
2.77-2.993.340.2423.41546846011.0298.5
2.99-3.293.40.1651595946520.9899.3
3.29-3.763.490.1067.81650446780.9499.4
3.76-4.733.530.06512.81656746350.8498
4.73-28.853.60.04318.41712446780.7495.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
d*TREKdata scaling
d*TREK9.9Ldata reduction
PHASERphasing
PHENIX1.7.3_928refinement
PDB_EXTRACT3.11data extraction
CrystalCleardata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3PZK

3pzk


Resolution: 2.2→28.063 Å / Occupancy max: 1 / Occupancy min: 0.04 / FOM work R set: 0.7685 / SU ML: 0.39 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Phase error: 29.37 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.2619 2325 5.05 %random
Rwork0.2091 ---
all0.2117 46051 --
obs0.2117 46051 98.21 %-
Solvent computationShrinkage radii: 1.11 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.274 Å2 / ksol: 0.327 e/Å3
Displacement parametersBiso max: 103.64 Å2 / Biso mean: 44.4546 Å2 / Biso min: 17.48 Å2
Baniso -1Baniso -2Baniso -3
1-14.6804 Å2-0 Å2-0 Å2
2---4.4704 Å2-0 Å2
3----10.2099 Å2
Refinement stepCycle: LAST / Resolution: 2.2→28.063 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5620 0 0 450 6070
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075729
X-RAY DIFFRACTIONf_angle_d1.0287761
X-RAY DIFFRACTIONf_chiral_restr0.068917
X-RAY DIFFRACTIONf_plane_restr0.0051022
X-RAY DIFFRACTIONf_dihedral_angle_d14.2692079
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 17

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2-2.24490.41021330.35432563269698
2.2449-2.29370.35731240.30432552267699
2.2937-2.3470.37251510.31412532268398
2.347-2.40570.33191150.28962582269798
2.4057-2.47070.35021240.2692545266998
2.4707-2.54340.33531550.26242543269898
2.5434-2.62540.32561400.24572556269698
2.6254-2.71920.28281510.24242520267198
2.7192-2.82790.28221350.22442567270299
2.8279-2.95650.32961350.24482581271699
2.9565-3.11220.29261290.22792572270199
3.1122-3.30690.28041580.22052590274899
3.3069-3.56180.26241480.20932595274399
3.5618-3.91930.28151200.20092632275299
3.9193-4.48450.22281340.16722580271497
4.4845-5.64240.17991380.14532593273197
5.6424-28.06570.19021350.16992623275895
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)
10.0460.0505-0.26590.16910.30470.27620.04220.4135-0.3618-0.05480.0143-0.77670.04790.2472-0.00030.30820.06030.02360.4329-0.05280.370120.4519-52.9446-0.742
20.2606-0.0904-0.15850.5043-0.70050.28770.08690.12510.0484-0.0472-0.0847-0.1530.18370.2747-00.29580.01580.03550.24390.00160.260115.0868-52.44518.9085
30.01930.2282-0.09240.85380.10680.9750.01270.0420.1235-0.1535-0.05030.0785-0.029-0.0202-0.00010.18040.0220.00750.1961-0.00330.16725.6056-41.0235.1385
40.2167-0.02090.2450.0104-0.02690.3293-0.1006-0.40040.4196-0.24740.2911-0.6317-0.76160.2522-0.00990.4194-0.11870.18820.55180.06110.534724.5854-18.6262.3031
50.79720.0839-0.30770.4988-0.31710.3708-0.09060.1726-0.5436-0.4013-0.22231.01160.5252-0.7866-1.49330.2764-0.0778-0.1720.6035-0.11290.5396-32.2017-49.978613.2502
60.0920.0859-0.83550.8153-0.01290.4728-0.16630.2109-0.0050.22580.06160.25920.1862-0.333-0.01150.3024-0.0209-0.03490.4588-0.03780.3752-28.1884-42.157320.5278
70.0904-0.0457-0.09480.06540.17450.067-0.28240.24120.0661-0.07780.399-0.09110.1735-0.33410.00020.3428-0.0133-0.04420.3775-0.00560.3595-19.8945-47.800218.1599
80.2465-0.0782-0.01610.5959-0.4390.24580.03610.1620.1048-0.2935-0.0117-0.0366-0.0427-0.193500.33730.0367-0.06550.38170.01320.3044-18.5419-34.75658.0803
90.0528-0.0197-0.22330.9117-0.64891.4294-0.59140.44880.0295-0.139-0.4309-0.41930.6810.335-0.35510.3918-0.1648-0.13010.4447-0.17260.2436-21.1598-55.27152.4306
100.3433-0.5551-0.36350.13830.25750.0272-0.08260.1690.0527-0.03550.05030.11550.03650.1196-00.24440.0075-0.00480.240.00630.2522-2.2173-52.289618.9669
110.0809-0.0051-0.050.1312-0.05020.0176-0.4009-0.0206-0.490.1821-0.25070.5787-0.0455-0.0227-00.5621-0.0759-0.00130.4173-0.06650.4844-4.4989-70.42289.1368
120.672-0.2239-0.79940.18910.06431.32830.06280.0680.7325-0.11070.13590.0952-0.45910.02160.18470.61570.06620.04880.27650.11080.5197-3.5619-4.46145.8333
130.0461-0.04580.07670.0209-0.04120.05330.20.12130.28670.2092-0.143-0.0062-0.44880.0300.49510.02310.02050.29140.06830.4997-1.2423-6.542514.6639
141.04280.196-0.34930.11050.17290.250.44060.08180.8826-0.3854-0.0769-0.0029-0.4108-0.14780.04750.49240.09880.0310.24980.0690.4027-1.6931-10.18016.9423
150.1548-0.0330.1333-0.03070.4375-0.057-0.0326-0.0973-0.1183-0.20470.13830.0227-0.5487-0.0364-0.00530.4036-0.02190.03490.2880.02560.36565.7221-14.404515.8928
160.2198-0.1058-0.06340.02040.010.03410.0230.1741-0.087-0.1339-0.0186-0.0259-0.1074-0.004100.37110.01170.02440.25190.03050.24333.9311-24.11974.2462
170.1770.1979-0.00090.3775-0.07550.0224-0.18370.75270.0369-0.81080.13110.0599-0.1885-0.347-0.0240.4370.0425-0.07670.5408-0.03180.2754-4.2092-26.7979-2.6864
180.2715-0.0241-0.2780.07180.07130.5667-0.32530.40120.0752-0.4704-0.16940.2273-0.1004-0.7189-0.02350.35420.0658-0.02460.53160.16110.5061-16.4809-13.66231.0872
190.15720.5494-0.01250.44060.1949-0.07240.1888-0.0603-0.0623-0.2575-0.08220.19690.0048-0.100900.23660.03210.03030.30280.00760.3024-15.3757-27.196722.6013
200.020.04230.09320.02340.02550.0285-0.0495-0.64240.40760.3625-0.05240.2381-0.1251-0.16550.00020.37230.1184-0.05590.4963-0.01750.5739-33.3249-18.819817.9416
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'D' and (resseq 1:29)D1 - 29
2X-RAY DIFFRACTION2chain 'D' and (resseq 30:101)D30 - 101
3X-RAY DIFFRACTION3chain 'D' and (resseq 102:235)D102 - 235
4X-RAY DIFFRACTION4chain 'D' and (resseq 236:256)D236 - 256
5X-RAY DIFFRACTION5chain 'E' and (resseq 2:29)E2 - 29
6X-RAY DIFFRACTION6chain 'E' and (resseq 30:84)E30 - 84
7X-RAY DIFFRACTION7chain 'E' and (resseq 85:101)E85 - 101
8X-RAY DIFFRACTION8chain 'E' and (resseq 102:181)E102 - 181
9X-RAY DIFFRACTION9chain 'E' and (resseq 182:198)E182 - 198
10X-RAY DIFFRACTION10chain 'E' and (resseq 199:235)E199 - 235
11X-RAY DIFFRACTION11chain 'E' and (resseq 236:254)E236 - 254
12X-RAY DIFFRACTION12chain 'F' and (resseq 1:29)F1 - 29
13X-RAY DIFFRACTION13chain 'F' and (resseq 30:44)F30 - 44
14X-RAY DIFFRACTION14chain 'F' and (resseq 45:70)F45 - 70
15X-RAY DIFFRACTION15chain 'F' and (resseq 71:101)F71 - 101
16X-RAY DIFFRACTION16chain 'F' and (resseq 102:161)F102 - 161
17X-RAY DIFFRACTION17chain 'F' and (resseq 162:181)F162 - 181
18X-RAY DIFFRACTION18chain 'F' and (resseq 182:198)F182 - 198
19X-RAY DIFFRACTION19chain 'F' and (resseq 199:235)F199 - 235
20X-RAY DIFFRACTION20chain 'F' and (resseq 236:255)F236 - 255

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