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- PDB-3tzq: Crystal structure of a short-chain type dehydrogenase/reductase f... -

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Basic information

Entry
Database: PDB / ID: 3tzq
TitleCrystal structure of a short-chain type dehydrogenase/reductase from Mycobacterium marinum
ComponentsShort-chain type dehydrogenase/reductase
KeywordsOXIDOREDUCTASE / SSGCID / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homologyEnoyl-(Acyl carrier protein) reductase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / DI(HYDROXYETHYL)ETHER / Short-chain type dehydrogenase/reductase
Function and homology information
Biological speciesMycobacterium marinum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / molecular replacement / Resolution: 2.5 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
DepositionSep 27, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 5, 2011Provider: repository / Type: Initial release
Revision 1.1Apr 22, 2015Group: Database references
Revision 1.2Sep 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 / 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
B: Short-chain type dehydrogenase/reductase
A: Short-chain type dehydrogenase/reductase
D: Short-chain type dehydrogenase/reductase
C: Short-chain type dehydrogenase/reductase
F: Short-chain type dehydrogenase/reductase
E: Short-chain type dehydrogenase/reductase
H: Short-chain type dehydrogenase/reductase
G: Short-chain type dehydrogenase/reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)228,16826
Polymers226,6358
Non-polymers1,53418
Water12,538696
1
B: Short-chain type dehydrogenase/reductase
A: Short-chain type dehydrogenase/reductase
D: Short-chain type dehydrogenase/reductase
C: Short-chain type dehydrogenase/reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,94812
Polymers113,3174
Non-polymers6318
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18820 Å2
ΔGint-104 kcal/mol
Surface area31610 Å2
MethodPISA
2
F: Short-chain type dehydrogenase/reductase
E: Short-chain type dehydrogenase/reductase
H: Short-chain type dehydrogenase/reductase
G: Short-chain type dehydrogenase/reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,22014
Polymers113,3174
Non-polymers90310
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19920 Å2
ΔGint-99 kcal/mol
Surface area31490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.670, 122.070, 125.290
Angle α, β, γ (deg.)90.00, 101.03, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Short-chain type dehydrogenase/reductase


Mass: 28329.318 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium marinum (bacteria) / Strain: ATCC BAA-535 / M / Gene: MMAR_0271 / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B2HKN3, Oxidoreductases
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 696 / 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: 2.31 Å3/Da / Density % sol: 46.69 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Internal tracking number 218453, JCSG screen D06: 0.1 M Tris, pH 8.5, 200 mM magnesium chloride, 20% w/v PEG8000, MYMAA.00472.C.A1 PS00808 26.49 mg/mL, VAPOR DIFFUSION, SITTING DROP, temperature 290.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.9774 / Wavelength: 0.9774 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 10, 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
ReflectionResolution: 2.5→19.92 Å / Num. all: 71016 / Num. obs: 69690 / % possible obs: 97.9 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 2.632 % / Biso Wilson estimate: 24.7 Å2 / Rmerge(I) obs: 0.119 / Net I/σ(I): 8.96
Reflection shellResolution: 2.5→2.56 Å / Redundancy: 2.238 % / Rmerge(I) obs: 0.389 / Mean I/σ(I) obs: 2.4 / Num. unique all: 10922 / % possible all: 92.9

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
REFMAC5.6.0117refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: molecular replacement
Starting model: PDB ENTRY 3GVC

3gvc


Resolution: 2.5→19.92 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.876 / SU B: 17.746 / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 2 / ESU R: 1.18 / ESU R Free: 0.306 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.244 3526 5.1 %RANDOM
Rwork0.18 ---
all0.183 71016 --
obs0.183 69690 97.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.74 Å2
Baniso -1Baniso -2Baniso -3
1-0.58 Å20 Å2-0.03 Å2
2---0.47 Å20 Å2
3----0.12 Å2
Refinement stepCycle: LAST / Resolution: 2.5→19.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15121 0 100 696 15917
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01915467
X-RAY DIFFRACTIONr_bond_other_d0.0010.029849
X-RAY DIFFRACTIONr_angle_refined_deg1.3631.95621082
X-RAY DIFFRACTIONr_angle_other_deg0.942324069
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9952073
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.47723580
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.835152293
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0515119
X-RAY DIFFRACTIONr_chiral_restr0.0710.22599
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02117511
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023060
LS refinement shellResolution: 2.5→2.56 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.342 225 -
Rwork0.265 4564 -
obs-4564 92.7 %
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)
10.86480.2849-0.12050.7335-0.33961.0073-0.00740.02890.04950.02220.05620.0767-0.1223-0.0416-0.04890.01910.0056-0.0020.00590.00290.018229.7431.7954-1.5235
20.63450.26250.15070.9973-0.18691.13180.0364-0.05550.02020.215-0.0811-0.122-0.19960.17230.04470.0944-0.0529-0.02360.07860.00670.020938.905727.198625.3274
30.44670.4075-0.09840.679-0.26351.15160.0537-0.0487-0.0140.17570.01240.13320.0325-0.1341-0.06620.0783-0.00070.05940.0820.00420.08115.26329.425628.4606
41.08330.3232-0.22111.0489-0.29110.7847-0.06850.0956-0.0172-0.15920.11050.16790.2302-0.1045-0.0420.0749-0.033-0.02510.05010.00030.040117.40184.53250.0676
50.54860.0791-0.02680.49310.16960.9852-0.0142-0.0104-0.137-0.02440.0493-0.09010.10830.0522-0.03510.04550.0124-0.00980.0133-0.00620.058160.2285-3.612765.9802
60.74590.1289-0.10141.00380.13650.67610.01130.0771-0.1117-0.1173-0.10070.15840.0441-0.09360.08950.03210.0016-0.03360.0531-0.03810.078331.93451.562863.8068
70.77580.0783-0.21861.09620.28570.65070.0158-0.0780.03740.0894-0.03490.132-0.0118-0.05610.01910.013-0.01330.01130.0766-0.00350.018535.292119.003487.9464
80.3362-0.0790.14310.7547-0.02461.0565-0.0016-0.03570.04190.0125-0.0021-0.0984-0.08270.08480.00370.0113-0.01960.00110.0454-0.01260.026361.972723.660878.2762
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 263
2X-RAY DIFFRACTION2B3 - 263
3X-RAY DIFFRACTION3C3 - 263
4X-RAY DIFFRACTION4D3 - 261
5X-RAY DIFFRACTION5E3 - 262
6X-RAY DIFFRACTION6F3 - 263
7X-RAY DIFFRACTION7G3 - 262
8X-RAY DIFFRACTION8H3 - 263

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