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- PDB-3qiv: Crystal structure of a putative short-chain dehydrogenase or 3-ox... -

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Basic information

Entry
Database: PDB / ID: 3qiv
TitleCrystal structure of a putative short-chain dehydrogenase or 3-oxoacyl-[acyl-carrier-protein] reductase from Mycobacterium paratuberculosis ATCC BAA-968 / K-10
Componentsshort-chain dehydrogenase or 3-oxoacyl-[acyl-carrier-protein] reductase
KeywordsOXIDOREDUCTASE / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID / NADB_Rossman superfamily
Function / homologyEnoyl-(Acyl carrier protein) reductase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding Rossmann-like Domain / oxidoreductase activity / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / Short-chain dehydrogenase
Function and homology information
Biological speciesMycobacterium avium subsp. paratuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.25 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
DepositionJan 27, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 16, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 22, 2015Group: Database references
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software
Revision 1.4Sep 13, 2023Group: Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: short-chain dehydrogenase or 3-oxoacyl-[acyl-carrier-protein] reductase
B: short-chain dehydrogenase or 3-oxoacyl-[acyl-carrier-protein] reductase


Theoretical massNumber of molelcules
Total (without water)53,3432
Polymers53,3432
Non-polymers00
Water2,144119
1
A: short-chain dehydrogenase or 3-oxoacyl-[acyl-carrier-protein] reductase
B: short-chain dehydrogenase or 3-oxoacyl-[acyl-carrier-protein] reductase

A: short-chain dehydrogenase or 3-oxoacyl-[acyl-carrier-protein] reductase
B: short-chain dehydrogenase or 3-oxoacyl-[acyl-carrier-protein] reductase


Theoretical massNumber of molelcules
Total (without water)106,6854
Polymers106,6854
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area6640 Å2
ΔGint-33 kcal/mol
Surface area31700 Å2
MethodPISA
2
A: short-chain dehydrogenase or 3-oxoacyl-[acyl-carrier-protein] reductase

A: short-chain dehydrogenase or 3-oxoacyl-[acyl-carrier-protein] reductase


Theoretical massNumber of molelcules
Total (without water)53,3432
Polymers53,3432
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area2300 Å2
ΔGint-11 kcal/mol
Surface area17250 Å2
MethodPISA
3
B: short-chain dehydrogenase or 3-oxoacyl-[acyl-carrier-protein] reductase

B: short-chain dehydrogenase or 3-oxoacyl-[acyl-carrier-protein] reductase


Theoretical massNumber of molelcules
Total (without water)53,3432
Polymers53,3432
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area1980 Å2
ΔGint-9 kcal/mol
Surface area16810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.440, 90.070, 92.255
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21221

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Components

#1: Protein short-chain dehydrogenase or 3-oxoacyl-[acyl-carrier-protein] reductase


Mass: 26671.291 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium avium subsp. paratuberculosis (bacteria)
Strain: ATCC BAA-968 / K-10 / Gene: MAP_0603 / Production host: Escherichia coli (E. coli) / References: UniProt: Q743I2
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 119 / 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: 46.86 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 16.94 mg/ml MypaA.00414.c.A1, 300 mM magnessium formate, 0.1 M Bis-Tris, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.97
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 13, 2010
RadiationMonochromator: Single crystal, cylindrically bent, Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.25→50 Å / Num. obs: 24019 / % possible obs: 99.1 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.055 / Χ2: 1 / Net I/σ(I): 14
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.25-2.294.20.35211831.043199.7
2.29-2.334.70.24411720.949199.5
2.33-2.384.80.18711970.905199.8
2.38-2.424.80.18411720.916199.9
2.42-2.484.80.1412040.97199.8
2.48-2.534.80.13911801.009199.7
2.53-2.64.80.12211950.978199.7
2.6-2.674.80.10911830.978199.6
2.67-2.754.80.10212051.035199.4
2.75-2.834.80.08312011.035199.7
2.83-2.944.80.07111861.011199.6
2.94-3.054.80.05911931.075199.4
3.05-3.194.80.05211951.045199.4
3.19-3.364.80.04811930.992198.8
3.36-3.574.80.04512110.995199.3
3.57-3.854.70.04712120.96198.7
3.85-4.234.60.05512101.085198.6
4.23-4.854.40.04912021.076197.6
4.85-6.14.50.04612370.991197.9
6.1-504.50.0212880.963195.7

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 54.98 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å40.47 Å
Translation2.5 Å40.47 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3GVC

3gvc


Resolution: 2.25→40.47 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.9 / WRfactor Rfree: 0.2452 / WRfactor Rwork: 0.2144 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.827 / SU B: 12.298 / SU ML: 0.138 / SU R Cruickshank DPI: 0.2567 / SU Rfree: 0.2121 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.257 / ESU R Free: 0.212 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2564 1221 5.1 %RANDOM
Rwork0.2153 ---
obs0.2173 23922 98.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 41.35 Å2 / Biso mean: 36.868 Å2 / Biso min: 2.81 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å20 Å2
2--0.06 Å20 Å2
3----0.03 Å2
Refinement stepCycle: LAST / Resolution: 2.25→40.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2826 0 0 119 2945
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0222857
X-RAY DIFFRACTIONr_bond_other_d0.0010.021825
X-RAY DIFFRACTIONr_angle_refined_deg0.8771.9553864
X-RAY DIFFRACTIONr_angle_other_deg0.80634470
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1295388
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.97225.135111
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.60515446
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0581514
X-RAY DIFFRACTIONr_chiral_restr0.050.2454
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.023279
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02559
X-RAY DIFFRACTIONr_mcbond_it0.3421.51925
X-RAY DIFFRACTIONr_mcbond_other0.051.5825
X-RAY DIFFRACTIONr_mcangle_it0.6523014
X-RAY DIFFRACTIONr_scbond_it0.9413932
X-RAY DIFFRACTIONr_scangle_it1.5884.5850
LS refinement shellResolution: 2.247→2.306 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.432 74 -
Rwork0.392 1623 -
all-1697 -
obs--96.81 %
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)
14.3004-0.3549-1.25675.42520.47046.0243-0.00490.1267-0.29280.1431-0.16170.46640.1736-0.79590.16660.1167-0.01590.01790.1642-0.04870.16895.59238.82314.27
21.828-0.562-2.20730.22280.44635.28220.14680.210.2171-0.0649-0.0505-0.0194-0.2872-0.4241-0.09630.20880.02020.02270.09530.00310.202215.02345.5287.051
35.6504-0.1041-0.47534.58110.77783.1347-0.04570.1261-0.3357-0.1684-0.04970.15320.4312-0.06250.09540.2458-0.02350.02030.0313-0.01230.141718.22332.12614.97
44.435-0.2884-0.22822.2870.47142.93440.0283-0.6508-0.24620.12440.1102-0.03010.00790.0771-0.13850.1096-0.02580.0050.1930.05920.155818.2230.1723.198
516.311-0.1939-6.1680.02090.0632.34020.1475-0.86270.2414-0.0013-0.05040.0235-0.04070.3671-0.09710.17730.0050.01440.3034-0.00910.157833.5981.436.217
63.87260.4859-0.32984.11150.01824.37110.15940.02930.29710.05110.0686-0.1008-0.38750.1212-0.2280.164-0.0180.04320.09730.01430.175815.34812.43513.208
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 26
2X-RAY DIFFRACTION2A27 - 128
3X-RAY DIFFRACTION3A129 - 241
4X-RAY DIFFRACTION4B0 - 89
5X-RAY DIFFRACTION5B90 - 125
6X-RAY DIFFRACTION6B126 - 242

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