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- PDB-3qre: Crystal structure of an enoyl-coA hydratase EchA12_1 from Mycobac... -

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Basic information

Entry
Database: PDB / ID: 3qre
TitleCrystal structure of an enoyl-coA hydratase EchA12_1 from Mycobacterium marinum
ComponentsEnoyl-CoA hydratase, EchA12_1
KeywordsLYASE / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID / mycobacterium / tuberculosis / enoyl-coA / coenzyme A / hydratase / fatty acid metabolism / opportunistic infections in humans / associated with swimming / fish-tank
Function / homology
Function and homology information


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 / Alpha Beta
Similarity search - Domain/homology
: / Enoyl-CoA hydratase, EchA12_1
Similarity search - Component
Biological speciesMycobacterium marinum M (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 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
DepositionFeb 17, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 2, 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_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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_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, EchA12_1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9063
Polymers31,8311
Non-polymers752
Water1,17165
1
A: Enoyl-CoA hydratase, EchA12_1
hetero molecules

A: Enoyl-CoA hydratase, EchA12_1
hetero molecules

A: Enoyl-CoA hydratase, EchA12_1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,7189
Polymers95,4943
Non-polymers2246
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area5990 Å2
ΔGint-78 kcal/mol
Surface area21320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.700, 87.700, 87.700
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number198
Space group name H-MP213
Components on special symmetry positions
IDModelComponents
11A-279-

K

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Components

#1: Protein Enoyl-CoA hydratase, EchA12_1 /


Mass: 31831.471 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium marinum M (bacteria) / Strain: ATCC BAA-535 / M / Gene: echA12_1, MMAR_4015 / Production host: Escherichia coli (E. coli) / References: UniProt: B2HQD1
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 65 / 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: 1.765866 Å3/Da / Density % sol: 30.345789 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 39.66 mg/mL MymaA.00305.a.A1 PS00827 against PACT screen condition F10: 0.02 M Na/K phosphate, 0.1 M Bis-Tris propane, pH 6.5, 20% PEG3350 with 25% ethylene glycol as cryo-protectant, ...Details: 39.66 mg/mL MymaA.00305.a.A1 PS00827 against PACT screen condition F10: 0.02 M Na/K phosphate, 0.1 M Bis-Tris propane, pH 6.5, 20% PEG3350 with 25% ethylene glycol as cryo-protectant, crystal tracking ID 218672f10, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Jan 31, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. all: 9052 / Num. obs: 9040 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 7.1 % / Biso Wilson estimate: 46.082 Å2 / Rmerge(I) obs: 0.063 / Net I/σ(I): 24.74
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
2.4-2.467.10.5194.334758667667100
2.46-2.530.3885.64469965799.4
2.53-2.60.3815.734354606100
2.6-2.680.2837.384363606100
2.68-2.770.2488.16427259599.8
2.77-2.870.2129.064063565100
2.87-2.980.15911.53391154299.8
2.98-3.10.13313.343952547100
3.1-3.240.116.843638506100
3.24-3.40.07223.243405472100
3.4-3.580.05831.743468479100
3.58-3.80.04639.373169440100
3.8-4.060.03547.75301141899.8
4.06-4.380.0354.37278539299.5
4.38-4.80.02758.42514354100
4.8-5.370.02758.912336328100
5.37-6.20.03248.142060295100
6.2-7.590.02855.071726252100
7.59-10.740.0275.031318199100
10.740.01777.5869312097.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 29.05 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å43.85 Å
Translation2.5 Å43.85 Å

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Processing

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

3gow
PDB Unreleased entry


Resolution: 2.4→50 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.929 / WRfactor Rfree: 0.1999 / WRfactor Rwork: 0.1567 / Occupancy max: 1 / Occupancy min: 0.33 / FOM work R set: 0.8642 / SU B: 13.371 / SU ML: 0.142 / SU R Cruickshank DPI: 0.3425 / SU Rfree: 0.2359 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.343 / ESU R Free: 0.236 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.229 471 5.2 %RANDOM
Rwork0.1796 ---
obs0.1821 9002 99.45 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 66.23 Å2 / Biso mean: 36.3734 Å2 / Biso min: 15.88 Å2
Refinement stepCycle: LAST / Resolution: 2.4→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1443 0 2 65 1510
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0221473
X-RAY DIFFRACTIONr_angle_refined_deg1.3231.9692008
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6795196
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.4321.76551
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.99915212
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9431512
X-RAY DIFFRACTIONr_chiral_restr0.0830.2236
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211111
X-RAY DIFFRACTIONr_mcbond_it0.6221.5981
X-RAY DIFFRACTIONr_mcangle_it1.15721550
X-RAY DIFFRACTIONr_scbond_it1.9963492
X-RAY DIFFRACTIONr_scangle_it3.2514.5458
LS refinement shellResolution: 2.401→2.463 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.283 39 -
Rwork0.206 624 -
all-663 -
obs--99.1 %
Refinement TLS params.Method: refined / Origin x: 5.3749 Å / Origin y: 20.0564 Å / Origin z: -6.6945 Å
111213212223313233
T0.0199 Å2-0.0018 Å2-0.0038 Å2-0.0619 Å20.0201 Å2--0.0165 Å2
L0.7843 °2-0.6163 °2-0.2331 °2-1.0928 °20.1381 °2--1.113 °2
S0.0991 Å °0.0784 Å °0.0376 Å °-0.0786 Å °-0.0671 Å °-0.0256 Å °-0.0193 Å °-0.1027 Å °-0.032 Å °

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