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- PDB-3pxx: Crystal structure of carveol dehydrogenase from Mycobacterium avi... -

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Basic information

Entry
Database: PDB / ID: 3pxx
TitleCrystal structure of carveol dehydrogenase from Mycobacterium avium bound to nicotinamide adenine dinucleotide
ComponentsCarveol dehydrogenase
KeywordsOXIDOREDUCTASE / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID / carveol dehydrogenase / NAD / Mycobacterium / tuberculosis / non-pathogenic strain / ortholog
Function / homology
Function and homology information


(+)-trans-carveol dehydrogenase / (+)-trans-carveol dehydrogenase activity / nucleotide binding
Similarity search - Function
Mycofactocin-dependent oxidoreductase / 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 / Carveol dehydrogenase / Carveol dehydrogenase
Similarity search - Component
Biological speciesMycobacterium avium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 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
DepositionDec 10, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 29, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 22, 2015Group: Database references
Revision 1.3Feb 8, 2017Group: Database references
Revision 1.4Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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: Carveol dehydrogenase
B: Carveol dehydrogenase
C: Carveol dehydrogenase
D: Carveol dehydrogenase
E: Carveol dehydrogenase
F: Carveol dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)184,33412
Polymers180,3536
Non-polymers3,9816
Water15,691871
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21520 Å2
ΔGint-145 kcal/mol
Surface area52200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)156.470, 147.510, 83.240
Angle α, β, γ (deg.)90.000, 102.490, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Carveol dehydrogenase /


Mass: 30058.887 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium avium (bacteria) / Strain: 104 / Gene: MAV_2598 / Production host: Escherichia coli (E. coli)
References: UniProt: A0QFV1, UniProt: A0A0H2ZV91*PLUS, (+)-trans-carveol dehydrogenase
#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 871 / 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: 2.6 Å3/Da / Density % sol: 52.69 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: MyavA01326iA1 PS00693 at 36.4 mg/mL against JCSG+ screen condition A5, 0.2 M MgFormate, 20% PEG 3350 with 25% ethylene glycol as cryo-protectant, Crystal tracking ID 216974a5, VAPOR ...Details: MyavA01326iA1 PS00693 at 36.4 mg/mL against JCSG+ screen condition A5, 0.2 M MgFormate, 20% PEG 3350 with 25% ethylene glycol as cryo-protectant, Crystal tracking ID 216974a5, 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: 0.97946 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 15, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 121812 / % possible obs: 98.1 % / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Biso Wilson estimate: 32.649 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 12.42
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique allNum. unique obs% possible all
2-2.052.80.3692.5228748066806688.2
2.05-2.113.20.3263.3276918611861196.3
2.11-2.170.2824.23170786608660100
2.17-2.240.2554.8317738453845399.6
2.24-2.310.2086302938072807299.6
2.31-2.390.1757297147914791499.5
2.39-2.480.1498.3283837564756499.5
2.48-2.580.1299.5273447304730499.4
2.58-2.70.10911262197022702299.2
2.7-2.830.09313246676675667599
2.83-2.980.07815.1233256350635099.1
2.98-3.160.06617.4218035974597498.6
3.16-3.380.05819.5202615602560298.5
3.38-3.650.04922.7188205238523898.6
3.65-40.04324.7170744816481698.3
4-4.470.03927.2156114385438598.5
4.47-5.160.03728.2136183841384198.6
5.16-6.320.03627.4117423303330399.2
6.32-8.940.033095622558255899.6
8.940.02431.651771404140497.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 53 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3 Å47.84 Å
Translation3 Å47.84 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→50 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.939 / WRfactor Rfree: 0.2071 / WRfactor Rwork: 0.1657 / Occupancy max: 1 / Occupancy min: 0.4 / FOM work R set: 0.8691 / SU B: 8.911 / SU ML: 0.109 / SU R Cruickshank DPI: 0.1623 / SU Rfree: 0.1493 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.149 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES:RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2144 6117 5 %RANDOM
Rwork0.1708 ---
obs0.173 121719 98.13 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 75.7 Å2 / Biso mean: 28.4339 Å2 / Biso min: 6.03 Å2
Baniso -1Baniso -2Baniso -3
1--0.52 Å20 Å2-0.67 Å2
2--0.91 Å20 Å2
3----0.68 Å2
Refinement stepCycle: LAST / Resolution: 2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12194 0 264 871 13329
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.02212747
X-RAY DIFFRACTIONr_angle_refined_deg1.5011.99117413
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.96151658
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.724.349522
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.666151889
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.8731578
X-RAY DIFFRACTIONr_chiral_restr0.0970.22037
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0219677
X-RAY DIFFRACTIONr_mcbond_it0.691.58244
X-RAY DIFFRACTIONr_mcangle_it1.181213147
X-RAY DIFFRACTIONr_scbond_it2.01634503
X-RAY DIFFRACTIONr_scangle_it3.1594.54259
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.298 430 -
Rwork0.253 7615 -
all-8045 -
obs--88.13 %
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)
10.6855-0.015-0.08160.36390.04940.5546-0.0451-0.06150.02680.00370.0545-0.00910.0051-0.0692-0.00940.0360.0295-0.01020.08810.00780.024942.94447.953346.0742
20.67620.2107-0.05280.36860.09970.8652-0.00070.0326-0.0593-0.0494-0.0059-0.02560.0720.06170.00660.05680.0333-0.01090.04280.0090.043459.1035-2.915419.2285
30.733-0.12710.01760.4765-0.15250.93160.10040.0055-0.0442-0.04030.02530.03050.1744-0.095-0.12570.0872-0.0199-0.04740.03540.00480.032435.2662-5.2795-3.3784
40.68510.1624-0.22451.4738-0.13840.63860.09120.02870.1143-0.10360.11430.1015-0.11-0.0577-0.20550.0640.02760.03830.03840.02650.071328.322925.9569-10.7573
50.98020.29810.26991.390.05020.93270.0123-0.010.1079-0.12650.03350.0213-0.0918-0.2034-0.04590.07930.06740.04050.09020.0450.061112.246136.935316.2159
61.5278-0.30421.06250.3382-0.49971.3279-0.2611-0.26180.33110.05390.0704-0.1834-0.2067-0.10290.19080.06990.0451-0.04120.0808-0.11710.213135.995339.563338.5602
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-10 - 9999
2X-RAY DIFFRACTION2B-10 - 9999
3X-RAY DIFFRACTION3C-10 - 9999
4X-RAY DIFFRACTION4D-10 - 9999
5X-RAY DIFFRACTION5E-10 - 9999
6X-RAY DIFFRACTION6F-10 - 9999

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