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- PDB-3rrv: Crystal structure of an enoyl-CoA hydratase/isomerase from Mycoba... -

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Basic information

Entry
Database: PDB / ID: 3rrv
TitleCrystal structure of an enoyl-CoA hydratase/isomerase from Mycobacterium paratuberculosis
Componentsenoyl-CoA hydratase/isomerase
KeywordsISOMERASE / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID / enoyl CoA hydratase / fatty acid biosynthesis
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 avium subsp. paratuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.45 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
DepositionApr 30, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 11, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 22, 2015Group: Database references
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_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_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.ptnr1_auth_asym_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_asym_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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_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

Downloads & links

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Assembly

Deposited unit
A: enoyl-CoA hydratase/isomerase
B: enoyl-CoA hydratase/isomerase
C: enoyl-CoA hydratase/isomerase
D: enoyl-CoA hydratase/isomerase
E: enoyl-CoA hydratase/isomerase
F: enoyl-CoA hydratase/isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)177,77017
Polymers177,3166
Non-polymers45411
Water8,089449
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22890 Å2
ΔGint-212 kcal/mol
Surface area44300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.080, 134.050, 140.970
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: 6 / Auth seq-ID: 7 - 249 / Label seq-ID: 29 - 271

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD
5EE
6FF

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Components

#1: Protein
enoyl-CoA hydratase/isomerase


Mass: 29552.680 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium avium subsp. paratuberculosis (bacteria)
Strain: ATCC BAA-968 / K-10 / Gene: MAP_0683 / Production host: Escherichia coli (E. coli) / References: UniProt: Q743A2
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 449 / 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: 2.05 Å3/Da / Density % sol: 40.11 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8
Details: MypaA.00829.c.A1 PW29413 at 25.67 mg/mL against PACT screen condition D11, 0.2 M CaCl2, 0.1 M Tris pH 8.0, 20% PEG 6000 with 25% ethylene glycol as cryo-protectant, crystal tracking ID ...Details: MypaA.00829.c.A1 PW29413 at 25.67 mg/mL against PACT screen condition D11, 0.2 M CaCl2, 0.1 M Tris pH 8.0, 20% PEG 6000 with 25% ethylene glycol as cryo-protectant, crystal tracking ID 220560d11, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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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 315r / Detector: CCD / Date: Mar 24, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9765 Å / Relative weight: 1
ReflectionResolution: 2.45→50 Å / Num. all: 54480 / Num. obs: 54320 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 6 % / Biso Wilson estimate: 36.336 Å2 / Rmerge(I) obs: 0.116 / Net I/σ(I): 13.36
Reflection shell
Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique allNum. unique obs% possible all
2.45-2.516.20.5433.472470340044004100
2.51-2.580.4164.49238363876100
2.58-2.660.3964.7923301377499.9
2.66-2.740.3685.4722264364999.8
2.74-2.830.2916.3621899355699.9
2.83-2.930.2477.5421009340799.8
2.93-3.040.2158.3720540334599.9
3.04-3.160.17210.32195493184100
3.16-3.30.13512.88188703084100
3.3-3.460.12214.5917462294299.6
3.46-3.650.09617.5417025282799.8
3.65-3.870.08519.9915229262898.9
3.87-4.140.07322.1614080247598.9
4.14-4.470.05726.0613930233599.9
4.47-4.90.05726.3512750216199.9
4.9-5.480.06323.3511735198099.7
5.48-6.330.06522.8210067174299.6
6.33-7.750.05126.848868151199.6
7.75-10.960.03834.166762116298.8
10.960.03534.62365767896.4

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 55.55 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3 Å48.57 Å
Translation3 Å48.57 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3q1t

3q1t


Resolution: 2.45→50 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.908 / WRfactor Rfree: 0.214 / WRfactor Rwork: 0.1627 / Occupancy max: 1 / Occupancy min: 0.4 / FOM work R set: 0.8445 / SU B: 18.782 / SU ML: 0.196 / SU R Cruickshank DPI: 0.6826 / SU Rfree: 0.2826 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.283 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2381 2747 5.1 %RANDOM
Rwork0.179 ---
obs0.182 54142 99.39 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 65.95 Å2 / Biso mean: 26.9718 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-0.62 Å20 Å20 Å2
2--0.08 Å20 Å2
3----0.69 Å2
Refinement stepCycle: LAST / Resolution: 2.45→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11101 0 14 449 11564
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.02211317
X-RAY DIFFRACTIONr_angle_refined_deg1.4381.97615458
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2551511
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.98923.62442
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.548151755
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.4951590
X-RAY DIFFRACTIONr_chiral_restr0.0930.21894
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0218498
X-RAY DIFFRACTIONr_mcbond_it0.5521.57519
X-RAY DIFFRACTIONr_mcangle_it1.053211989
X-RAY DIFFRACTIONr_scbond_it1.86533798
X-RAY DIFFRACTIONr_scangle_it3.0884.53469
Refine LS restraints NCS

Ens-ID: 1 / Number: 1750 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1ALOOSE POSITIONAL0.265
2BLOOSE POSITIONAL0.285
3CLOOSE POSITIONAL0.235
4DLOOSE POSITIONAL0.275
5ELOOSE POSITIONAL0.285
6FLOOSE POSITIONAL0.285
1ALOOSE THERMAL3.4910
2BLOOSE THERMAL3.2210
3CLOOSE THERMAL1.9710
4DLOOSE THERMAL3.810
5ELOOSE THERMAL2.5210
6FLOOSE THERMAL1.5710
LS refinement shellResolution: 2.45→2.513 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.312 180 -
Rwork0.21 3804 -
all-3984 -
obs--99.65 %
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)
10.47270.2387-0.0370.8090.06540.37310.06380.04230.00720.0314-0.01620.006-0.0416-0.0532-0.04770.06960.02690.0170.03490.00490.02555.897118.935430.0297
20.8622-0.0589-0.29510.3376-0.13840.44130.0322-0.00980.0321-0.06030.0158-0.00280.1176-0.018-0.0480.0893-0.0111-0.01970.012-0.00850.029211.5257-15.85729.1842
30.4877-0.1873-0.0781.7097-0.24140.2433-0.035-0.00080.01620.01090.0335-0.2075-0.01820.02180.00150.01240.01320.01020.0534-0.00220.057538.23017.013827.3117
40.691-0.5987-0.12641.1805-0.27320.75230.0924-0.06910.060.0181-0.0798-0.0347-0.10170.2159-0.01260.0356-0.05430.01070.1082-0.00910.005835.839116.060258.337
51.18810.0415-0.21080.2876-0.19740.93020.06290.1299-0.03870.0928-0.0048-0.02970.15490.0045-0.05810.10060.021-0.03360.0770.00670.015724.8581-17.069258.9518
60.21470.41230.08551.7153-0.13460.5968-0.005-0.01150.01860.06640.15130.1217-0.068-0.0844-0.14640.0110.02070.01930.09170.03550.04642.07119.091260.7293
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 254
2X-RAY DIFFRACTION2B1 - 254
3X-RAY DIFFRACTION3C2 - 250
4X-RAY DIFFRACTION4D2 - 250
5X-RAY DIFFRACTION5E1 - 252
6X-RAY DIFFRACTION6F1 - 250

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