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- PDB-4hdt: Crystal structure of a Carnitinyl-CoA dehydratase from Mycobacter... -

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Basic information

Entry
Database: PDB / ID: 4hdt
TitleCrystal structure of a Carnitinyl-CoA dehydratase from Mycobacterium thermoresistibile
Components3-hydroxyisobutyryl-CoA hydrolase
KeywordsISOMERASE / SSGCID / Carnitinyl-CoA dehydratase / Enoyl-CoA hydratase/isomerase / Mycobacterium thermoresistibile / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


3-hydroxyisobutyryl-CoA hydrolase / 3-hydroxyisobutyryl-CoA hydrolase activity / L-valine catabolic process / metal ion binding / cytosol
Similarity search - Function
Enoyl-CoA hydratase/isomerase, HIBYL-CoA-H type / Enoyl-CoA hydratase/isomerase domain / 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
ACETATE ION / 3-hydroxyisobutyryl-CoA hydrolase
Similarity search - Component
Biological speciesMycobacterium thermoresistibile (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Zn-SAD / SAD / 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 2, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 10, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 11, 2015Group: Database references
Revision 1.2Apr 15, 2015Group: Database references
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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.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

Downloads & links

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Assembly

Deposited unit
A: 3-hydroxyisobutyryl-CoA hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,9478
Polymers37,5251
Non-polymers4227
Water5,098283
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.200, 62.400, 56.880
Angle α, β, γ (deg.)90.000, 109.590, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein 3-hydroxyisobutyryl-CoA hydrolase


Mass: 37525.266 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium thermoresistibile (bacteria)
Strain: ATCC 19527 / NCTC 10409 / Gene: KEK_02971, NODE_1249_length_5618_cov_9.770559_39 / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: G7CC99
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 283 / 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: 2.17 Å3/Da / Density % sol: 43 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 5
Details: EMBioPACT screen A12: 10mM ZnCl2, 100mM NaOAc pH 5.0, 20% PEG 6000; MythA.01530.a.A1.PW28690 at 29mg/ml; 25% EG as cryo, VAPOR DIFFUSION, SITTING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.9774 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 23, 2011
RadiationMonochromator: Si(220) Asymmetric cut single crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9774 Å / Relative weight: 1
ReflectionNumber: 157472 / Rmerge(I) obs: 0.042 / D res high: 1.6 Å / Num. obs: 80460 / % possible obs: 97.5
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)Num. obs% possible obs (%)IDRmerge(I) obs
1.61.64485379.410.355
1.641.69573595.510.314
1.691.74570999.610.27
1.741.79564299.710.222
1.791.85542399.910.177
1.851.91522799.410.158
1.911.98500899.210.124
1.982.07487299.510.096
2.072.16462798.410.071
2.162.26441898.110.06
2.262.39424699.710.047
2.392.53402999.910.04
2.532.7377599.310.037
2.72.92349899.310.03
2.923.232249910.026
3.23.58289098.810.022
3.584.13254998.410.022
4.135.06216298.810.017
5.067.16168898.810.016
ReflectionResolution: 1.6→50 Å / Num. all: 42068 / Num. obs: 41586 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Biso Wilson estimate: 22.954 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 16.77
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.6-1.640.4182.5374702773189.6
1.64-1.690.3663.62105863009198.9
1.69-1.740.34.8113952898199.8
1.74-1.790.2535.72112742865199.8
1.79-1.850.2016.981088327541100
1.85-1.910.1788.05104452658199.6
1.91-1.980.1410.1697782558199.8
1.98-2.070.1112.0597582483199.8
2.07-2.160.08216.291382373199.3
2.16-2.260.0718.4985802273199.2
2.26-2.390.05620.9285832164199.8
2.39-2.530.0523.58814920571100
2.53-2.70.04526.1575921936199.6
2.7-2.920.03929.0770771793199.6
2.92-3.20.03332.6365281664199.7
3.2-3.580.02837.8857701499199.9
3.58-4.130.02740.7149031325199.2
4.13-5.060.02344.5143261124199.3
34608891
17804911

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Phasing

PhasingMethod: SAD
Phasing MADD res high: 1.6 Å / D res low: 45.41 Å / FOM : 0.323 / FOM acentric: 0.33 / FOM centric: 0.168 / Reflection: 41571 / Reflection acentric: 38854 / Reflection centric: 1533

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.3.0phasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
BOSdata collection
XDSdata reduction
RefinementMethod to determine structure: Zn-SAD / Resolution: 1.6→45.45 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.953 / WRfactor Rfree: 0.1752 / WRfactor Rwork: 0.1495 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.8907 / SU B: 3.014 / SU ML: 0.052 / SU R Cruickshank DPI: 0.0824 / SU Rfree: 0.0825 / Isotropic thermal model: isotropic, TLS / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.082 / ESU R Free: 0.083 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1892 2097 5 %RANDOM
Rwork0.1597 ---
all0.1611 42068 --
obs0.1611 41568 98.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 53.08 Å2 / Biso mean: 17.9527 Å2 / Biso min: 7.58 Å2
Baniso -1Baniso -2Baniso -3
1--0.32 Å20 Å2-0.38 Å2
2--0.38 Å20 Å2
3---0.06 Å2
Refinement stepCycle: LAST / Resolution: 1.6→45.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2488 0 10 283 2781
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0192580
X-RAY DIFFRACTIONr_bond_other_d0.0010.022431
X-RAY DIFFRACTIONr_angle_refined_deg1.5261.9613526
X-RAY DIFFRACTIONr_angle_other_deg0.83835569
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8315348
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.84823.238105
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.39315379
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.0541520
X-RAY DIFFRACTIONr_chiral_restr0.0920.2407
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212994
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02566
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.334 150 -
Rwork0.256 2620 -
all-2770 -
obs--89.7 %
Refinement TLS params.Method: refined / Origin x: 2.007 Å / Origin y: 29.574 Å / Origin z: 43.971 Å
111213212223313233
T0.0092 Å20.0021 Å20.0225 Å2-0.0059 Å20.0132 Å2--0.1202 Å2
L1.0871 °20.0724 °20.0664 °2-0.7243 °2-0.2196 °2--0.5842 °2
S0.0228 Å °0.067 Å °0.0325 Å °0.0411 Å °-0.0221 Å °-0.0492 Å °0.0102 Å °0.0151 Å °-0.0007 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 348
2X-RAY DIFFRACTION1A400 - 406
3X-RAY DIFFRACTION1A501 - 783

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