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- PDB-3t7c: Crystal structure of carveol dehydrogenase from Mycobacterium avi... -

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Basic information

Entry
Database: PDB / ID: 3t7c
TitleCrystal structure of carveol dehydrogenase from Mycobacterium avium bound to NAD
ComponentsCarveol dehydrogenase
KeywordsOXIDOREDUCTASE / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID / MAV_1393 / (+)-trans-carveol dehydrogenase / nicotinamide adenine dinucleotide / NAD / (+)-(S)-carvone / 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: 1.95 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 29, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 17, 2011Provider: repository / Type: Initial release
Revision 1.1Apr 22, 2015Group: Database references
Revision 1.2Feb 8, 2017Group: Database references
Revision 1.3Sep 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: Carveol dehydrogenase
B: Carveol dehydrogenase
C: Carveol dehydrogenase
D: Carveol dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,5098
Polymers128,8564
Non-polymers2,6544
Water10,539585
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17200 Å2
ΔGint-111 kcal/mol
Surface area36260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.550, 108.410, 148.300
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Carveol dehydrogenase /


Mass: 32213.947 Da / Num. of mol.: 4 / Mutation: K230Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium avium (bacteria) / Strain: 104 / Gene: MAV_1393 / Plasmid: pAVA0421 / Production host: Escherichia coli (E. coli)
References: UniProt: A0QCJ8, UniProt: A0A0H2ZWY3*PLUS, (+)-trans-carveol dehydrogenase
#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 585 / 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: 2.17 Å3/Da / Density % sol: 43.3 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: MyavA.01326.e.A1 PS00804 at 43.4 mg/mL against JCSG+ H3 25% PEG 3350, 0.1 M BisTris pH 5.5, crystal tracking ID 218190h3, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 16, 2011 / Details: DCM
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. all: 82420 / Num. obs: 79986 / % possible obs: 97 % / Observed criterion σ(I): -3 / Redundancy: 4.1 % / Biso Wilson estimate: 26.586 Å2 / Rmerge(I) obs: 0.095 / Net I/σ(I): 13.78
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
1.95-23.70.483.84222556017595098.9
2-2.060.4044.6621948581098.9
2.06-2.120.3375.6121256563798.5
2.12-2.180.3156.5720890546298.2
2.18-2.250.2827.1220176526497.9
2.25-2.330.2388.1520202511698.4
2.33-2.420.1929.7820036497598.4
2.42-2.520.18510.4219563477698.1
2.52-2.630.16211.5618886455298
2.63-2.760.13613.8818226432297.4
2.76-2.910.12415.317889415597.2
2.91-3.080.09717.9916834390596.8
3.08-3.30.07721.0315890365996.3
3.3-3.560.0624.6214639340095.7
3.56-3.90.05127.8813603312395
3.9-4.360.04330.6712447282394.9
4.36-5.030.0432.4311139248593.9
5.03-6.170.0429.869659210092.8
6.17-8.720.03132.27536163091.3
8.720.02636.46374784280.7

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3.2 Å19.94 Å
Translation3.2 Å19.94 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 3OEC

3oec


Resolution: 1.95→50 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.946 / WRfactor Rfree: 0.1806 / WRfactor Rwork: 0.148 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.8873 / SU B: 6.311 / SU ML: 0.089 / SU R Cruickshank DPI: 0.1544 / SU Rfree: 0.1358 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.136 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.1954 3999 5 %RANDOM
Rwork0.1602 ---
obs0.162 79771 96.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 63.98 Å2 / Biso mean: 21.3268 Å2 / Biso min: 10.07 Å2
Baniso -1Baniso -2Baniso -3
1--0.6 Å20 Å20 Å2
2---0.27 Å20 Å2
3---0.87 Å2
Refinement stepCycle: LAST / Resolution: 1.95→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8232 0 176 585 8993
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0198670
X-RAY DIFFRACTIONr_angle_refined_deg1.5451.99511831
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.87351132
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.19623.125352
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.003151410
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1271587
X-RAY DIFFRACTIONr_chiral_restr0.0980.21393
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0216507
LS refinement shellResolution: 1.95→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.26 250 -
Rwork0.198 5376 -
all-5626 -
obs--98.65 %
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)
10.3457-0.0773-0.06030.268-0.02660.3989-0.0629-0.05140.00510.03920.0377-0.02380.030600.02520.02580.0024-0.01140.02250.00260.014119.6237-13.4512-5.6397
20.4649-0.04360.05190.1736-0.11670.3226-0.00180.12580.0353-0.0025-0.02020.0045-0.01220.00350.02210.0422-0.0023-0.00910.04150.01940.0286-5.2224.6982-36.5466
30.4384-0.10110.0440.31760.07140.3393-0.0587-0.07480.10330.04930.02680.0248-0.03-0.0150.03190.02970.0118-0.0140.0173-0.02130.0414-3.7687.5866-3.815
40.5304-0.01020.06390.0756-0.03430.5352-0.00670.1220.069-0.02360.0132-0.044-0.06280.0875-0.00650.0268-0.02470.01380.05560.01130.042826.1055-0.0827-34.981
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 278
2X-RAY DIFFRACTION1A279
3X-RAY DIFFRACTION1A280 - 585
4X-RAY DIFFRACTION2B2 - 278
5X-RAY DIFFRACTION2B279
6X-RAY DIFFRACTION2B280 - 578
7X-RAY DIFFRACTION3C1 - 278
8X-RAY DIFFRACTION3C279
9X-RAY DIFFRACTION3C280 - 582
10X-RAY DIFFRACTION4D2 - 278
11X-RAY DIFFRACTION4D279
12X-RAY DIFFRACTION4D280 - 584

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