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- PDB-3sx2: Crystal structure of a putative 3-ketoacyl-(acyl-carrier-protein)... -

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Basic information

Entry
Database: PDB / ID: 3sx2
TitleCrystal structure of a putative 3-ketoacyl-(acyl-carrier-protein) reductase from Mycobacterium paratuberculosis in complex with NAD
ComponentsPutative 3-ketoacyl-(acyl-carrier-protein) reductase
KeywordsOXIDOREDUCTASE / SSGCID / 3-KETOACYL-(ACYL-CARRIER-PROTEIN) REDUCTASE / MYCOBACERIUM PARATUBERCULOSIS / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / putative 3-KETOACYL-(ACYL-CARRIER-PROTEIN) REDUCTASE
Function / homology
Function and homology information


oxidoreductase activity / nucleotide binding
Similarity search - Function
Mycofactocin-dependent oxidoreductase / Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / Enoyl-(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
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Uncharacterized protein
Similarity search - Component
Biological speciesMycobacterium avium subsp. paratuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / molecular replacement / Resolution: 1.5 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
Citation
Journal: Sci Rep / Year: 2017
Title: Mycofactocin-associated mycobacterial dehydrogenases with non-exchangeable NAD cofactors.
Authors: Haft, D.H. / Pierce, P.G. / Mayclin, S.J. / Sullivan, A. / Gardberg, A.S. / Abendroth, J. / Begley, D.W. / Phan, I.Q. / Staker, B.L. / Myler, P.J. / Marathias, V.M. / Lorimer, D.D. / Edwards, T.E.
#1: Journal: 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
DepositionJul 14, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 3, 2011Provider: repository / Type: Initial release
Revision 1.1Apr 22, 2015Group: Database references
Revision 1.2Feb 1, 2017Group: Database references
Revision 1.3Feb 8, 2017Group: Database references
Revision 1.4Sep 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: Putative 3-ketoacyl-(acyl-carrier-protein) reductase
B: Putative 3-ketoacyl-(acyl-carrier-protein) reductase
C: Putative 3-ketoacyl-(acyl-carrier-protein) reductase
D: Putative 3-ketoacyl-(acyl-carrier-protein) reductase
E: Putative 3-ketoacyl-(acyl-carrier-protein) reductase
F: Putative 3-ketoacyl-(acyl-carrier-protein) reductase
G: Putative 3-ketoacyl-(acyl-carrier-protein) reductase
H: Putative 3-ketoacyl-(acyl-carrier-protein) reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)234,63821
Polymers228,7408
Non-polymers5,89813
Water28,1571563
1
A: Putative 3-ketoacyl-(acyl-carrier-protein) reductase
B: Putative 3-ketoacyl-(acyl-carrier-protein) reductase
C: Putative 3-ketoacyl-(acyl-carrier-protein) reductase
D: Putative 3-ketoacyl-(acyl-carrier-protein) reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,26010
Polymers114,3704
Non-polymers2,8906
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15970 Å2
ΔGint-131 kcal/mol
Surface area32390 Å2
MethodPISA
2
E: Putative 3-ketoacyl-(acyl-carrier-protein) reductase
F: Putative 3-ketoacyl-(acyl-carrier-protein) reductase
G: Putative 3-ketoacyl-(acyl-carrier-protein) reductase
H: Putative 3-ketoacyl-(acyl-carrier-protein) reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,37811
Polymers114,3704
Non-polymers3,0087
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15980 Å2
ΔGint-139 kcal/mol
Surface area32540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.460, 70.760, 125.680
Angle α, β, γ (deg.)97.01, 93.92, 86.91
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Putative 3-ketoacyl-(acyl-carrier-protein) reductase


Mass: 28592.520 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium avium subsp. paratuberculosis (bacteria)
Strain: ATCC BAA-968/K-10 / Gene: MAP_2861 / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q73W00
#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1563 / 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: 2.49 Å3/Da / Density % sol: 51 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: EBS JCSG+ SCREEN D5 OPTIMIZED TO: 100MM HEPES PH 6.5, 70% MPD; MYPAA.01326.D.A1 PW29473 AT 23MG/ ML, VAPOR DIFFUSION, SITTING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 0.976484 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 21, 2010
RadiationMonochromator: Single crystal, cylindrically bent, Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976484 Å / Relative weight: 1
ReflectionResolution: 1.5→20 Å / Num. all: 351856 / Num. obs: 333445 / % possible obs: 94.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Biso Wilson estimate: 21.16 Å2 / Rmerge(I) obs: 0.039 / Net I/σ(I): 21.04
Reflection shellResolution: 1.5→1.54 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.304 / Mean I/σ(I) obs: 4.1 / Num. unique all: 26062 / Rsym value: 0.304 / % possible all: 90.3

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Processing

Software
NameVersionClassification
BOSdata collection
PHASERphasing
REFMAC5.5.0110refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: molecular replacement
Starting model: PDB entry 3oec modified with CCP4 program CHAINSAW

3oec


Resolution: 1.5→20 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.968 / SU B: 1.882 / SU ML: 0.032 / Isotropic thermal model: isotropic, TLS / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.058 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE
RfactorNum. reflection% reflectionSelection details
Rfree0.159 16842 5.1 %RANDOM
Rwork0.14 ---
all0.141 351856 --
obs0.141 333440 94.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.48 Å2
Baniso -1Baniso -2Baniso -3
1--0.11 Å20.08 Å20.14 Å2
2--0.01 Å20.47 Å2
3---0.22 Å2
Refinement stepCycle: LAST / Resolution: 1.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14978 0 392 1563 16933
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.02216066
X-RAY DIFFRACTIONr_bond_other_d0.0030.0210045
X-RAY DIFFRACTIONr_angle_refined_deg1.7111.99122126
X-RAY DIFFRACTIONr_angle_other_deg1.609324765
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.89352210
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.72124.271569
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.28152333
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1731597
X-RAY DIFFRACTIONr_chiral_restr0.0930.22622
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02118245
X-RAY DIFFRACTIONr_gen_planes_other0.0040.023008
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_it0.8441.510565
X-RAY DIFFRACTIONr_mcbond_other0.261.54390
X-RAY DIFFRACTIONr_mcangle_it1.419216919
X-RAY DIFFRACTIONr_scbond_it2.2235501
X-RAY DIFFRACTIONr_scangle_it3.5314.55152
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.5→1.54 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.262 1165 -
Rwork0.235 22248 -
obs-23546 90.39 %
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)
10.4025-0.04630.05030.2166-0.09060.22930.00410.02950.082-0.0210.00030.01370.0060.0017-0.00440.01860.00720.00730.02110.00430.0356-22.72683.461-25.872
20.3383-0.06980.02570.3442-0.14760.54690.0333-0.018-0.0808-0.05560.010.05510.1015-0.0132-0.04330.0466-0.0091-0.01130.0074-0.00390.0389-26.75453.116-16.497
30.43150.0660.06290.3522-0.11330.27960.0156-0.1167-0.03630.0138-0.0083-0.01060.0053-0.0305-0.00730.02640.00880.00010.05350.00510.0055-6.67959.9579.678
40.5662-0.0693-0.05740.2475-0.09870.16070.0053-0.04240.13420.0109-0.0265-0.0547-0.01390.03390.02110.0074-0.00480.0020.0234-0.02230.074.30184.896-6.902
50.48060.04050.12310.5214-0.09860.33180.00940.1364-0.1495-0.1040.0414-0.00930.05380.0648-0.05080.0530.00360.00060.0498-0.04440.0484-39.70985.530.405
60.3580.08770.09310.3678-0.00060.1723-0.03790.00740.0301-0.03120.01850.064-0.01680.0070.01950.0129-0.0006-0.00610.03510.02130.0229-50.634113.5441.788
70.2573-0.0293-0.02360.26520.01250.2079-0.0142-0.00680.02080.02920.0112-0.037-0.02240.00670.00310.01550.00440.00280.04310.00320.0166-23.776115.43360.655
80.3164-0.0876-0.0310.51210.01070.3325-0.0036-0.0064-0.11850.0243-0.0044-0.06690.02450.02090.0080.0150.0190.00790.02760.02030.0756-18.86283.81156.994
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 276
2X-RAY DIFFRACTION2B7 - 276
3X-RAY DIFFRACTION3C7 - 276
4X-RAY DIFFRACTION4D7 - 276
5X-RAY DIFFRACTION5E7 - 276
6X-RAY DIFFRACTION6F3 - 276
7X-RAY DIFFRACTION7G7 - 276
8X-RAY DIFFRACTION8H7 - 275

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