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- PDB-3khp: Crystal structure of a possible dehydrogenase from Mycobacterium ... -

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Basic information

Entry
Database: PDB / ID: 3khp
TitleCrystal structure of a possible dehydrogenase from Mycobacterium tuberculosis at 2.3A resolution
ComponentsMaoC family protein
KeywordsOXIDOREDUCTASE / mycobacterium tuberculosis / dehydrogenase / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID
Function / homology
Function and homology information


enoyl-CoA hydratase 2 / 3-hydroxyacyl-CoA dehydratase activity / 17-beta-hydroxysteroid dehydrogenase (NAD+) activity / Lyases; Carbon-oxygen lyases; Hydro-lyases / (3S)-3-hydroxyacyl-CoA dehydrogenase (NAD+) activity / enoyl-CoA hydratase activity / (3R)-hydroxyacyl-[acyl-carrier-protein] dehydratase activity / Oxidoreductases / fatty acid beta-oxidation / peptidoglycan-based cell wall ...enoyl-CoA hydratase 2 / 3-hydroxyacyl-CoA dehydratase activity / 17-beta-hydroxysteroid dehydrogenase (NAD+) activity / Lyases; Carbon-oxygen lyases; Hydro-lyases / (3S)-3-hydroxyacyl-CoA dehydrogenase (NAD+) activity / enoyl-CoA hydratase activity / (3R)-hydroxyacyl-[acyl-carrier-protein] dehydratase activity / Oxidoreductases / fatty acid beta-oxidation / peptidoglycan-based cell wall / fatty acid biosynthetic process / plasma membrane / cytosol
Similarity search - Function
: / MFE-2 hydratase 2 N-terminal domain / MaoC-like dehydratase domain / MaoC like domain / Hotdog Thioesterase / Thiol Ester Dehydrase; Chain A / HotDog domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
L(+)-TARTARIC ACID / 3-hydroxyacyl-thioester dehydratase Y / (R)-specific enoyl-CoA hydratase
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID) / Seattle 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 30, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 1, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 22, 2015Group: Database references
Revision 1.3Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.4Sep 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 / 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 / _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: MaoC family protein
B: MaoC family protein
C: MaoC family protein
D: MaoC family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,86112
Polymers130,4634
Non-polymers3988
Water10,016556
1
A: MaoC family protein
C: MaoC family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,3385
Polymers65,2312
Non-polymers1063
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3300 Å2
ΔGint-36 kcal/mol
Surface area23280 Å2
MethodPISA
2
B: MaoC family protein
D: MaoC family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,5237
Polymers65,2312
Non-polymers2925
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3800 Å2
ΔGint-47 kcal/mol
Surface area23470 Å2
MethodPISA
3
B: MaoC family protein
D: MaoC family protein
hetero molecules

A: MaoC family protein
C: MaoC family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,86112
Polymers130,4634
Non-polymers3988
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x+1/2,-y+1,z+1/21
Buried area9080 Å2
ΔGint-99 kcal/mol
Surface area44760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.290, 135.170, 162.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1115A8 - 68
2115B8 - 68
3115C8 - 68
4115D8 - 68
1215A78 - 105
2215B78 - 105
3215C78 - 105
4215D78 - 105
1315A118 - 124
2315B118 - 124
3315C118 - 124
4315D118 - 124
1415A130 - 140
2415B130 - 140
3415C130 - 140
4415D130 - 140
1515A153 - 195
2515B153 - 195
3515C153 - 195
4515D153 - 195
1614A207 - 290
2614B207 - 290
3614C207 - 290
4614D207 - 290

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Components

#1: Protein
MaoC family protein / possible dehydrogenase / Putative uncharacterized protein / MYTUD.00504.A


Mass: 32615.719 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Strain: H37RV / Gene: MT3496, Rv3389c / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q11198, UniProt: I6YBZ8*PLUS, Oxidoreductases
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-TLA / L(+)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O6
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 556 / 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: 2.61 Å3/Da / Density % sol: 53 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6
Details: Wizard screen condition g12, 1M Na/K tartrate, 100mM MES pH 6.0, MYTUD.00504.A AT 56MG/ml, VAPOR DIFFUSION, SITTING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Oct 16, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→40 Å / Num. all: 63818 / Num. obs: 62471 / % possible obs: 97.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.1 % / Biso Wilson estimate: 35.15 Å2 / Rmerge(I) obs: 0.095 / Net I/σ(I): 18.74
Reflection shellResolution: 2.3→2.36 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.514 / Mean I/σ(I) obs: 3.7 / Num. unique all: 4627 / % possible all: 80.4

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Processing

Software
NameVersionClassification
StructureStudiodata collection
PHASERphasing
REFMAC5.5.0104refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1s9c modified with ccp4 program chainsaw

1s9c


Resolution: 2.3→40 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.889 / SU B: 6.079 / SU ML: 0.151 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.29 / ESU R Free: 0.238 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE
RfactorNum. reflection% reflectionSelection details
Rfree0.263 3166 5.1 %RANDOM
Rwork0.206 ---
all0.209 63818 --
obs0.209 62387 97.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.71 Å2
Baniso -1Baniso -2Baniso -3
1-0.45 Å2-0 Å2-0 Å2
2--1.52 Å20 Å2
3----1.97 Å2
Refinement stepCycle: LAST / Resolution: 2.3→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8064 0 17 556 8637
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0228326
X-RAY DIFFRACTIONr_bond_other_d0.0010.025526
X-RAY DIFFRACTIONr_angle_refined_deg1.5651.96811376
X-RAY DIFFRACTIONr_angle_other_deg0.906313446
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.41551106
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.76722.783327
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.197151196
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9441570
X-RAY DIFFRACTIONr_chiral_restr0.0890.21321
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0219464
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021690
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8191.55481
X-RAY DIFFRACTIONr_mcbond_other0.2641.52254
X-RAY DIFFRACTIONr_mcangle_it1.49628765
X-RAY DIFFRACTIONr_scbond_it2.05632845
X-RAY DIFFRACTIONr_scangle_it3.2444.52602
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDNumberTypeRms dev position (Å)Weight position
A1840medium positional0.340.5
B1840medium positional0.330.5
C1840medium positional0.340.5
D1840medium positional0.320.5
A919loose positional0.545
B919loose positional0.655
C919loose positional0.495
D919loose positional0.495
A1840medium thermal1.072
B1840medium thermal1.662
C1840medium thermal0.992
D1840medium thermal1.832
A919loose thermal1.1310
B919loose thermal1.4410
C919loose thermal0.9510
D919loose thermal1.5910
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.345 196 -
Rwork0.26 3525 -
obs--80.37 %

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