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- PDB-5ej2: Crystal structure of Carveol dehydrogenase from Mycobacterium avi... -

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Basic information

Entry
Database: PDB / ID: 5ej2
TitleCrystal structure of Carveol dehydrogenase from Mycobacterium avium in complex with NAD
ComponentsCarveol dehydrogenase
KeywordsOXIDOREDUCTASE / SSGCID / Carveol dehydrogenase / NAD / dehydrogenase / Mycobacterium avium / 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 / 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 / PHOSPHATE ION / Carveol dehydrogenase
Similarity search - Component
Biological speciesMycobacterium avium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 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
DepositionOct 31, 2015Deposition site: RCSB / Processing site: RCSB
SupersessionDec 2, 2015ID: 3UWR
Revision 1.0Dec 2, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 8, 2017Group: Database references
Revision 1.2Sep 27, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)134,70214
Polymers131,3854
Non-polymers3,31610
Water9,818545
1
A: Carveol dehydrogenase
B: Carveol dehydrogenase
hetero molecules

A: Carveol dehydrogenase
B: Carveol dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,70214
Polymers131,3854
Non-polymers3,31610
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_557x,-y,-z+21
Buried area19410 Å2
ΔGint-173 kcal/mol
Surface area33140 Å2
MethodPISA
2
C: Carveol dehydrogenase
D: Carveol dehydrogenase
hetero molecules

C: Carveol dehydrogenase
D: Carveol dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,70214
Polymers131,3854
Non-polymers3,31610
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_567x,-y+1,-z+21
Buried area19300 Å2
ΔGint-171 kcal/mol
Surface area33090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.820, 132.210, 155.050
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number17
Space group name H-MP2221
Components on special symmetry positions
IDModelComponents
11C-528-

HOH

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Components

#1: Protein
Carveol dehydrogenase / MyavA.01326.q


Mass: 32846.352 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium avium (bacteria) / Strain: 104 / Gene: MAV_2983 / Plasmid: MyavA.01326.q.A1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: A0A0H2ZYS9, (+)-trans-carveol dehydrogenase
#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


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


Mass: 18.015 Da / Num. of mol.: 545 / 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: 2.38 Å3/Da / Density % sol: 48 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: JCSG+ A11 optimized: 50% MPD, 200mM Ammonium phosphate, 100mM Tris pH 8.5; MyavA.01326.q.A1.PS00712 at 26.9mg/ml; cryo: 15% EG; tray: 220331a8; puck dzb3-1

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.9774 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 16, 2011
RadiationMonochromator: Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9774 Å / Relative weight: 1
ReflectionResolution: 2.15→50 Å / Num. obs: 68679 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 5.76 % / Biso Wilson estimate: 21.97 Å2 / Rmerge F obs: 0.997 / Rmerge(I) obs: 0.11 / Rrim(I) all: 0.121 / Χ2: 0.939 / Net I/σ(I): 15.17 / Num. measured all: 395887
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
2.15-2.215.80.8730.5363.2129290503850350.58799.9
2.21-2.270.9010.4443.8728371490248960.48799.9
2.27-2.330.9110.4074.2927769476947650.44699.9
2.33-2.40.9470.3345.1526923464046380.365100
2.4-2.480.9450.3215.3326003447244680.35299.9
2.48-2.570.9560.2656.5225304436943620.2999.8
2.57-2.670.9630.247.2224466422742210.26399.9
2.67-2.780.9730.1959.0423518406640630.21499.9
2.78-2.90.9820.16510.4222608390038930.1899.8
2.9-3.040.990.12413.6621640376037540.13699.8
3.04-3.210.9940.10116.3720295352435150.11199.7
3.21-3.40.9950.08519.5619441338933780.09399.7
3.4-3.630.9980.05927.118115316231480.06499.6
3.63-3.930.9980.05329.7616906296929490.05899.3
3.93-4.30.9990.04434.5915523274827220.04899.1
4.3-4.810.9990.03640.513858249024640.0499
4.81-5.550.9990.04135.6812213223522090.04598.8
5.55-6.80.9990.04631.9310795190318770.0598.6
6.8-9.620.9990.02551.38320150014670.02797.8
9.62-5010.0254.6645299078550.02294.3

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHASERphasing
ARPmodel building
Cootmodel building
PHENIXdev_2210refinement
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3uve

3uve


Resolution: 2.15→48.136 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.19 2000 2.91 %Random selection
Rwork0.148 66641 --
obs0.1492 68641 99.59 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 81.73 Å2 / Biso mean: 27.2262 Å2 / Biso min: 7.31 Å2
Refinement stepCycle: final / Resolution: 2.15→48.136 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8185 0 218 545 8948
Biso mean--27.19 33.32 -
Num. residues----1108
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0068602
X-RAY DIFFRACTIONf_angle_d0.83411760
X-RAY DIFFRACTIONf_chiral_restr0.0531374
X-RAY DIFFRACTIONf_plane_restr0.0051514
X-RAY DIFFRACTIONf_dihedral_angle_d10.3665034
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.15-2.20380.24131410.181847134854100
2.2038-2.26340.21991420.168447164858100
2.2634-2.330.2061410.166546914832100
2.33-2.40520.2061410.157347144855100
2.4052-2.49110.22471420.161947304872100
2.4911-2.59090.17761410.155947234864100
2.5909-2.70880.19861420.154647084850100
2.7088-2.85160.1851430.151647634906100
2.8516-3.03020.20641430.149947764919100
3.0302-3.26410.20071420.153747374879100
3.2641-3.59250.21251440.141247934937100
3.5925-4.11210.17491440.13024776492099
4.1121-5.17980.1461440.12214826497099
5.1798-48.14810.17291500.15564975512598
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)
11.27370.09190.05791.5233-0.22891.5724-0.0709-0.23960.0520.25170.06920.0989-0.2322-0.20420.00220.19770.05590.00920.1992-0.03410.111615.395314.5079183.8609
20.2453-0.29610.72651.0072-0.7473.0783-0.0683-0.18340.01710.12050.03910.1173-0.3649-0.20120.06550.16840.0592-0.01620.1675-0.03220.134519.457419.0153173.6871
32.0255-0.61140.63271.0896-0.41211.3452-0.0175-0.01010.0250.0260.0391-0.0236-0.17-0.017-0.01980.13890.01060.00060.1427-0.00840.08121.090914.0557166.5332
40.97810.4962-0.14241.50410.781.3166-0.0726-0.01420.1075-0.0681-0.07490.3207-0.1685-0.29840.07140.12380.0455-0.00090.1991-0.00580.13117.84323.8448170.1239
51.1250.0610.08681.08980.22061.2467-0.13380.22720.1262-0.25030.0536-0.0129-0.3256-0.00040.06860.2567-0.0429-0.04280.16520.0420.12523.345725.9872135.9109
60.13710.05630.67551.2058-0.79054.0863-0.06830.17870.1573-0.0045-0.00310.0302-0.3260.15210.11810.15680.0106-0.02610.11170.0140.169919.349425.292147.0752
71.4980.0750.2171.25610.05391.4412-0.08320.05160.10010.00840.05410.0245-0.2558-0.02220.03350.11980.0193-0.01120.10450.00440.095417.631317.7283151.1289
80.7991-0.1587-0.71892.1515-0.30810.9419-0.1043-0.07970.11770.1389-0.0017-0.3822-0.13240.17120.04850.1389-0.0355-0.03580.1561-0.00070.130531.022410.3538143.5073
91.5981-0.1564-0.32150.7819-0.31661.9471-0.1180.4228-0.1887-0.54340.1609-0.1510.2328-0.0613-0.05650.3901-0.09860.05830.2368-0.06570.249646.833447.1936128.847
100.37840.3696-0.28921.884-0.42763.4936-0.13280.2338-0.1464-0.32630.1522-0.11290.3909-0.02810.09650.2157-0.02730.03210.1437-0.03420.292950.576444.1152139.952
111.81070.2759-0.48892.0504-0.36931.7659-0.08290.0401-0.1362-0.14620.0924-0.19460.23510.1247-0.00820.15420.00650.02310.131-0.02180.242252.503450.3954145.894
120.9875-0.37310.76912.28620.68891.1738-0.15140.0849-0.1505-0.04990.07320.27140.2022-0.14560.04680.1963-0.06020.02460.17550.02840.193939.157759.7445140.947
131.3735-0.01250.23651.3879-0.51340.576-0.1715-0.3993-0.37150.5010.1736-0.13820.26830.1126-0.03970.36780.1738-0.04290.32190.10590.362454.779343.5239177.9396
140.1611-0.292-0.11571.30670.02163.1728-0.0967-0.2712-0.23240.13950.0929-0.07390.40190.21330.04160.2280.09180.00830.19290.07930.327749.93542.1132167.7441
151.6721-0.2769-0.92351.55870.30561.6111-0.1036-0.0805-0.18720.00630.1254-0.06390.22510.0823-0.03010.1560.0365-0.03250.13110.03730.250149.043549.2336161.7237
161.419-0.08340.43551.8294-0.51440.8757-0.1572-0.0554-0.14020.00390.0336-0.39680.13230.29380.09980.18860.0696-0.03510.25710.01280.276362.300457.8761168.1906
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 10 through 87 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 88 through 125 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 126 through 199 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 200 through 286 )A0
5X-RAY DIFFRACTION5chain 'B' and (resid 10 through 87 )B0
6X-RAY DIFFRACTION6chain 'B' and (resid 88 through 125 )B0
7X-RAY DIFFRACTION7chain 'B' and (resid 126 through 199 )B0
8X-RAY DIFFRACTION8chain 'B' and (resid 200 through 286 )B0
9X-RAY DIFFRACTION9chain 'C' and (resid 10 through 87 )C0
10X-RAY DIFFRACTION10chain 'C' and (resid 88 through 125 )C0
11X-RAY DIFFRACTION11chain 'C' and (resid 126 through 199 )C0
12X-RAY DIFFRACTION12chain 'C' and (resid 200 through 286 )C0
13X-RAY DIFFRACTION13chain 'D' and (resid 10 through 87 )D0
14X-RAY DIFFRACTION14chain 'D' and (resid 88 through 125 )D0
15X-RAY DIFFRACTION15chain 'D' and (resid 126 through 199 )D0
16X-RAY DIFFRACTION16chain 'D' and (resid 200 through 286 )D0

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