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- PDB-3ucx: The structure of a Short chain dehydrogenase from Mycobacterium s... -

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Basic information

Entry
Database: PDB / ID: 3ucx
TitleThe structure of a Short chain dehydrogenase from Mycobacterium smegmatis
ComponentsShort chain dehydrogenase
KeywordsOXIDOREDUCTASE / SSGCID / Seattle Structural Genomics Center for Infectious Disease / dehydrogenase
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 / Short chain dehydrogenase
Function and homology information
Biological speciesMycobacterium smegmatis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.85 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 27, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 9, 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
A: Short chain dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,3854
Polymers27,9911
Non-polymers3943
Water3,873215
1
A: Short chain dehydrogenase
hetero molecules

A: Short chain dehydrogenase
hetero molecules

A: Short chain dehydrogenase
hetero molecules

A: Short chain dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,53916
Polymers111,9634
Non-polymers1,57612
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_655-x+1,-y,z1
crystal symmetry operation8_556x-y,-y,-z+11
crystal symmetry operation11_656-x+y+1,y,-z+11
Buried area13270 Å2
ΔGint-118 kcal/mol
Surface area36610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.430, 105.430, 94.970
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number180
Space group name H-MP6222
Components on special symmetry positions
IDModelComponents
11A-355-

HOH

21A-356-

HOH

31A-405-

HOH

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Components

#1: Protein Short chain dehydrogenase


Mass: 27990.828 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium smegmatis (bacteria) / Strain: ATCC 700084 / mc(2)155 / Gene: MSMEG_5931 / Production host: Escherichia coli (E. coli) / References: UniProt: A0R4R9, Oxidoreductases
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400 / Polyethylene glycol


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#4: Chemical ChemComp-PG0 / 2-(2-METHOXYETHOXY)ETHANOL / PEG 6000 / 2-(2-Methoxyethoxy)ethanol


Mass: 120.147 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H12O3 / Comment: inhibitor, precipitant*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 215 / 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: 2.72 Å3/Da / Density % sol: 54.81 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 51.1 mg/mL MysmA.00762.a.A1 PS00612, 40% PEG300, 0.1 M cacodylate, pH 6.5, 200 mM calcium acetate, cryo-protectant: 25% ethylene glycol , 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 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Oct 12, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.85→46.091 Å / Num. all: 27142 / Num. obs: 26756 / % possible obs: 98.5 % / Rmerge(I) obs: 0.072 / Rsym value: 0.062 / Net I/σ(I): 32.84
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsRsym valueDiffraction-ID% possible all
1.85-1.90.4773.640.456190.5
1.9-1.95195.5
1.95-2.01196.9
2.01-2.07198.4
2.07-2.14199.6
2.14-2.21199.9
2.21-2.29199.9
2.29-2.39199.9
2.39-2.49199.9
2.49-2.62199.9
2.62-2.76199.9
2.76-2.931100
2.93-3.13199.1
3.13-3.38199.8
3.38-3.71100
3.7-4.14199.9
4.14-4.781100
4.78-5.851100
5.85-8.271100
8.27-46.091197.2

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å46.09 Å
Translation2.5 Å46.09 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.3.0phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3PGX

3pgx


Resolution: 1.85→46.091 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.943 / WRfactor Rfree: 0.1675 / WRfactor Rwork: 0.1533 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.8899 / SU B: 3.916 / SU ML: 0.062 / SU R Cruickshank DPI: 0.1154 / SU Rfree: 0.1028 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.115 / ESU R Free: 0.103 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1879 1343 5 %RANDOM
Rwork0.172 ---
obs0.1729 26755 98.57 %-
all-26778 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 56.81 Å2 / Biso mean: 22.69 Å2 / Biso min: 9.35 Å2
Baniso -1Baniso -2Baniso -3
1--0.21 Å2-0.1 Å20 Å2
2---0.21 Å20 Å2
3---0.31 Å2
Refinement stepCycle: LAST / Resolution: 1.85→46.091 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1873 0 25 215 2113
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0191935
X-RAY DIFFRACTIONr_bond_other_d0.0010.021247
X-RAY DIFFRACTIONr_angle_refined_deg1.3011.9732624
X-RAY DIFFRACTIONr_angle_other_deg0.91733069
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4955263
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.54224.72272
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.03215308
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.3921510
X-RAY DIFFRACTIONr_chiral_restr0.0740.2316
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022188
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02366
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.276 76 -
Rwork0.23 1566 -
all-1642 -
obs--89.73 %
Refinement TLS params.Method: refined / Origin x: 67.1762 Å / Origin y: -4.4337 Å / Origin z: 31.219 Å
111213212223313233
T0.0555 Å2-0.0093 Å20.0345 Å2-0.0226 Å2-0.0132 Å2--0.036 Å2
L0.4124 °20.1058 °20.0408 °2-0.5343 °2-0.1253 °2--0.3284 °2
S-0.0456 Å °0.0598 Å °-0.0771 Å °-0.09 Å °0.0277 Å °-0.0655 Å °0.0434 Å °0.0625 Å °0.018 Å °

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