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- PDB-3uve: Crystal structure of Carveol dehydrogenase ((+)-trans-carveol deh... -

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Basic information

Entry
Database: PDB / ID: 3uve
TitleCrystal structure of Carveol dehydrogenase ((+)-trans-carveol dehydrogenase) from Mycobacterium avium
ComponentsCarveol dehydrogenase ((+)-trans-carveol dehydrogenase)
KeywordsOXIDOREDUCTASE / SSGCID / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


(+)-trans-carveol dehydrogenase / (+)-trans-carveol dehydrogenase 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 / Carveol dehydrogenase ((+)-trans-carveol dehydrogenase) / Carveol dehydrogenase ((+)-trans-carveol dehydrogenase)
Similarity search - Component
Biological speciesMycobacterium avium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.55 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
DepositionNov 29, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 14, 2011Provider: repository / Type: Initial release
Revision 1.1Mar 11, 2015Group: Database references
Revision 1.2Apr 15, 2015Group: 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 ((+)-trans-carveol dehydrogenase)
B: Carveol dehydrogenase ((+)-trans-carveol dehydrogenase)
C: Carveol dehydrogenase ((+)-trans-carveol dehydrogenase)
D: Carveol dehydrogenase ((+)-trans-carveol dehydrogenase)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,96317
Polymers121,2224
Non-polymers3,74113
Water16,087893
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19030 Å2
ΔGint-98 kcal/mol
Surface area35820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.610, 59.440, 108.650
Angle α, β, γ (deg.)90.000, 90.100, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Carveol dehydrogenase ((+)-trans-carveol dehydrogenase)


Mass: 30305.566 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium avium (bacteria) / Strain: 104 / Gene: MAV_0896 / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: A0QB72, UniProt: A0A0H2ZTN5*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: Chemical
ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 893 / 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: 2.63 Å3/Da / Density % sol: 53.3 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 4.62
Details: EBS internal tracking number 224967H10. From a focus screen based on JCSG C6. Reservoir: 42.5% PEG 300, 0.1 M phosphate-citrate, MyavA.01326.d.A1 PS00817 at 48 mg/mL, pH 4.62, VAPOR ...Details: EBS internal tracking number 224967H10. From a focus screen based on JCSG C6. Reservoir: 42.5% PEG 300, 0.1 M phosphate-citrate, MyavA.01326.d.A1 PS00817 at 48 mg/mL, pH 4.62, VAPOR DIFFUSION, SITTING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 28, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.55→50 Å / Num. all: 180725 / Num. obs: 161312 / % possible obs: 89.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 2.72 % / Biso Wilson estimate: 20.012 Å2 / Rmerge(I) obs: 0.061 / Net I/σ(I): 12.79
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.55-1.592.40.4682.4295371242393.6
1.59-1.630.3873301851212593.5
1.63-1.680.3483.4298981181193.3
1.68-1.730.2934.1291441132092.8
1.73-1.790.2455288481101092.4
1.79-1.850.2016281301052591.7
1.85-1.920.1537.7275811013091.2
1.92-20.1199.626597965190.4
2-2.090.09911.525502920089.8
2.09-2.190.07813.824530874489.2
2.19-2.310.06516.123270820988.2
2.31-2.450.0561822168774187.4
2.45-2.620.0492020774716286.3
2.62-2.830.04222.919327661985.2
2.83-3.10.03526.217853604084.3
3.1-3.470.02931.516062536683.1
3.47-40.02436.314088469181.8
4-4.90.02139.812108393780.9
4.9-6.930.02336.89304300479.2
6.930.02138.74910160474.3

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å48.8 Å
Translation2.5 Å48.8 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
REFMAC5.6.0117refinement
PDB_EXTRACT3.004data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 3T7C

3t7c


Resolution: 1.55→50 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.97 / SU B: 2.118 / SU ML: 0.037 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.066 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16 8057 5 %RANDOM
Rwork0.146 ---
obs0.146 161312 89.25 %-
all-180725 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.798 Å2
Baniso -1Baniso -2Baniso -3
1--0.32 Å20 Å2-0.11 Å2
2---0.03 Å20 Å2
3---0.35 Å2
Refinement stepCycle: LAST / Resolution: 1.55→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8326 0 236 893 9455
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0198933
X-RAY DIFFRACTIONr_bond_other_d0.0060.025905
X-RAY DIFFRACTIONr_angle_refined_deg1.5341.98412204
X-RAY DIFFRACTIONr_angle_other_deg1.147314499
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3451186
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.20123.908348
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.165151402
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8851556
X-RAY DIFFRACTIONr_chiral_restr0.0910.21406
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02110011
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021737
LS refinement shellResolution: 1.55→1.59 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.247 579 -
Rwork0.234 11549 -
all-12128 -
obs--93.42 %
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)
10.2731-0.0021-0.08130.30780.00510.3389-0.0027-0.01510.01690.0147-0.00790.0379-0.0264-0.0140.01050.0156-0.00130.00770.0029-0.00540.01619.0544.16742.569
20.31610.00470.09050.29320.00080.31850.0025-0.024-0.02020.0126-0.0041-0.01310.02940.05550.00160.01870.0018-0.00760.02920.00920.00739.607-5.542.963
30.30040.0167-0.05080.24860.01160.3243-0.00270.02440.0201-0.0131-0.0038-0.0044-0.03190.05620.00650.016-0.00230.00130.02630.00990.004939.643.14911.317
40.2852-0.00760.1110.32510.02420.33520.00250.0146-0.0138-0.0107-0.00970.0390.0245-0.01540.00720.02010.0014-0.01520.0033-0.00470.01779.066-6.69711.783
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 282
2X-RAY DIFFRACTION1A300 - 310
3X-RAY DIFFRACTION1A286 - 931
4X-RAY DIFFRACTION2B2 - 282
5X-RAY DIFFRACTION2B286 - 310
6X-RAY DIFFRACTION2B287 - 936
7X-RAY DIFFRACTION3C2 - 282
8X-RAY DIFFRACTION3C300 - 310
9X-RAY DIFFRACTION3C286 - 937
10X-RAY DIFFRACTION4D2 - 282
11X-RAY DIFFRACTION4D300 - 310
12X-RAY DIFFRACTION4D286 - 934

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