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- PDB-3pe8: Crystal structure of Enoyl-CoA hydratase from Mycobacterium smegmatis -

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Basic information

Entry
Database: PDB / ID: 3pe8
TitleCrystal structure of Enoyl-CoA hydratase from Mycobacterium smegmatis
ComponentsEnoyl-CoA hydratase
KeywordsLYASE / Emerald BioStructures / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID
Function / homologyEnoyl-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 / metal ion binding / Alpha Beta / Enoyl-CoA hydratase
Function and homology information
Biological speciesMycobacterium smegmatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.6 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: Tuberculosis (Edinb) / Year: 2015
Title: Increasing the structural coverage of tuberculosis drug targets.
Authors: Baugh, L. / Phan, I. / Begley, D.W. / Clifton, M.C. / Armour, B. / Dranow, D.M. / Taylor, B.M. / Muruthi, M.M. / Abendroth, J. / Fairman, J.W. / Fox, D. / Dieterich, S.H. / Staker, B.L. / ...Authors: Baugh, L. / Phan, I. / Begley, D.W. / Clifton, M.C. / Armour, B. / Dranow, D.M. / Taylor, B.M. / Muruthi, M.M. / Abendroth, J. / Fairman, J.W. / Fox, D. / Dieterich, S.H. / Staker, B.L. / Gardberg, A.S. / Choi, R. / Hewitt, S.N. / Napuli, A.J. / Myers, J. / Barrett, L.K. / Zhang, Y. / Ferrell, M. / Mundt, E. / Thompkins, K. / Tran, N. / Lyons-Abbott, S. / Abramov, A. / Sekar, A. / Serbzhinskiy, D. / Lorimer, D. / Buchko, G.W. / Stacy, R. / Stewart, L.J. / Edwards, T.E. / Van Voorhis, W.C. / Myler, P.J.
History
DepositionOct 25, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 8, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 22, 2015Group: Database references
Revision 1.3Sep 6, 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_initial_refinement_model / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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

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Assembly

Deposited unit
A: Enoyl-CoA hydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,4343
Polymers27,3071
Non-polymers1272
Water5,350297
1
A: Enoyl-CoA hydratase
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)164,60618
Polymers163,8416
Non-polymers76512
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation4_556y,x,-z+11
crystal symmetry operation5_556x-y,-y,-z+11
crystal symmetry operation6_556-x,-x+y,-z+11
Buried area17640 Å2
ΔGint-343 kcal/mol
Surface area46630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.410, 87.410, 185.190
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-331-

HOH

21A-402-

HOH

31A-440-

HOH

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Components

#1: Protein Enoyl-CoA hydratase


Mass: 27306.865 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium smegmatis (bacteria) / Strain: ATCC 700084/MC2 155 / Gene: MSMEG_2641 / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0QVP0, enoyl-CoA hydratase
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 297 / 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: 2.43 Å3/Da / Density % sol: 49.42 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 5
Details: Internal tracking number 217319A12. PACT screen condition A12: 0.01 M ZnCl2, 0.1 M Na Oac pH 5, 20% PEG6000 MysmA.01566.a.A1 PW29040 at 25.27 mg/mL, vapor diffusion, sitting drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 0.9765 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 28, 2010
RadiationMonochromator: Asymmetric cut single crystal Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9765 Å / Relative weight: 1
ReflectionResolution: 1.6→39.5 Å / Num. all: 36265 / Num. obs: 35962 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 9.7 % / Biso Wilson estimate: 23.761 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 24.37
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique allNum. unique obs% possible all
1.6-1.646.460.4923.4157922650244592.3
1.64-1.690.4244.418994257199.6
1.69-1.740.3746.3233412508100
1.74-1.790.2988.6266962450100
1.79-1.850.23410.7260622384100
1.85-1.910.24412.323499224298
1.91-1.980.1791721300215697.5
1.98-2.070.12820.722494212699.8
2.07-2.160.10125.1209472070100
2.16-2.260.09127.818932192298.5
2.26-2.390.0753219182184498.8
2.39-2.530.06235.7188971775100
2.53-2.70.05738.617070166399.9
2.7-2.920.04943.2165031570100
2.92-3.20.04247.6149661451100
3.2-3.580.04151.512543129399.8
3.58-4.130.03953.510578115799.3
4.13-5.060.03157.29564100199.9
5.06-7.160.03156.3779578099.9
7.160.02556.5413645497

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å39.5 Å
Translation2.5 Å39.5 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.004data extraction
ADSCQuantumdata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3H81

3h81


Resolution: 1.6→39.5 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.966 / SU B: 2.178 / SU ML: 0.035 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.062 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16 1812 5 %RANDOM
Rwork0.148 ---
obs0.149 35962 99.17 %-
all-36265 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.247 Å2
Baniso -1Baniso -2Baniso -3
1--0.17 Å2-0.08 Å20 Å2
2---0.17 Å20 Å2
3---0.25 Å2
Refinement stepCycle: LAST / Resolution: 1.6→39.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1618 0 5 297 1920
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0221677
X-RAY DIFFRACTIONr_bond_other_d0.0010.021089
X-RAY DIFFRACTIONr_angle_refined_deg1.5141.9622293
X-RAY DIFFRACTIONr_angle_other_deg0.96632655
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3585227
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.66623.52171
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.58115260
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6071516
X-RAY DIFFRACTIONr_chiral_restr0.0940.2276
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211916
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02336
X-RAY DIFFRACTIONr_mcbond_it0.7961.51101
X-RAY DIFFRACTIONr_mcbond_other0.251.5449
X-RAY DIFFRACTIONr_mcangle_it1.44721756
X-RAY DIFFRACTIONr_scbond_it2.383576
X-RAY DIFFRACTIONr_scangle_it3.8574.5532
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.241 129 -
Rwork0.214 2314 -
all-2443 -
obs-2445 92.26 %
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)
11.7078-0.6279-0.01711.6681-0.0130.63330.0003-0.12710.19250.05810.0358-0.2975-0.0690.1412-0.03610.0159-0.0173-0.01260.0547-0.03290.083225.84915.67874.599
20.958-0.04340.0681.04770.12960.64430.003-0.07960.03690.04670.0009-0.10970.01020.0494-0.0040.0129-0.003-0.00280.0313-0.01230.023919.3567.99773.852
31.5324-1.06750.75155.0431-4.28565.41360.05740.0574-0.076-0.3939-0.2471-0.25540.35780.3390.18960.04170.0120.02020.03430.00280.038518.998-3.98567.48
40.44960.271-0.14941.79930.50451.4825-0.0182-0.038-0.07520.02120.0073-0.0935-0.01450.03370.01090.01610.0037-0.00420.02530.00180.020812.791-5.29676.477
50.7938-0.1002-0.43231.03650.21520.55970.01450.02490.0937-0.02650.01310.0192-0.0171-0.0157-0.02760.0230.0014-0.0130.02080.0010.02169.78712.80268.798
60.7673-1.36260.64746.51860.26192.29410.0239-0.1306-0.09390.26870.10410.0853-0.0476-0.0323-0.1280.13410.0211-0.01390.08690.01670.015511.438-1.53989.308
718.1423-14.3852-8.86632.488217.783626.983-0.7289-0.81640.29991.70571.3109-1.76550.88961.3457-0.5820.25260.1229-0.23710.2125-0.03090.287123.588-11.75589.49
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 51
2X-RAY DIFFRACTION2A52 - 116
3X-RAY DIFFRACTION3A117 - 127
4X-RAY DIFFRACTION4A128 - 156
5X-RAY DIFFRACTION5A157 - 209
6X-RAY DIFFRACTION6A210 - 224
7X-RAY DIFFRACTION7A225 - 232

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