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- PDB-3pgx: Crystal structure of a putative carveol dehydrogenase from Mycoba... -

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Basic information

Entry
Database: PDB / ID: 3pgx
TitleCrystal structure of a putative carveol dehydrogenase from Mycobacterium paratuberculosis bound to nicotinamide adenine dinucleotide
Componentscarveol dehydrogenase
KeywordsOXIDOREDUCTASE / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID / carveol dehydrogenase / short chain dehydrogenase/reductase superfamily / nicotinamide adenine dinucleotide / NAD / putative uncharacterized protein
Function / homology
Function and homology information


Oxidoreductases / oxidoreductase activity
Similarity search - Function
Mycofactocin-dependent oxidoreductase / PKS_KR / 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 NAD-dependent oxidoreductase MAP_4146
Similarity search - Component
Biological speciesMycobacterium avium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.85 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
DepositionNov 2, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 24, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 11, 2015Group: Database references
Revision 1.3Apr 15, 2015Group: Database references
Revision 1.4Feb 8, 2017Group: Database references
Revision 1.5Sep 6, 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)120,1068
Polymers117,4524
Non-polymers2,6544
Water17,457969
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17550 Å2
ΔGint-115 kcal/mol
Surface area30990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)130.030, 57.920, 131.740
Angle α, β, γ (deg.)90.000, 91.350, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
carveol dehydrogenase


Mass: 29363.045 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium avium (bacteria) / Strain: paratuberculosis / Gene: MAP_4146 / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / References: UniProt: Q73SC8
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 969 / 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: 2.11 Å3/Da / Density % sol: 41.74 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: protein at 23.8 mg/mL in 20 mM Hepes pH 7, 300 mM NaCl, 5% glycerol, DTT, 0.2 M MgCl2, 0.1 M Bis Tris, 25% PEG 3350 with 25% ethylene glycol as cryo-protectant, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 0.97946 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 18, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. all: 84005 / Num. obs: 82274 / % possible obs: 97.9 % / Observed criterion σ(I): -3 / Redundancy: 4.6 % / Biso Wilson estimate: 21.352 Å2 / Rmerge(I) obs: 0.093 / Net I/σ(I): 14.15
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
1.85-1.94.70.4713.6279016159597697
1.9-1.950.3884.427309586597.3
1.95-2.010.3065.526595571297.4
2.01-2.070.2616.425811554197.5
2.07-2.140.2197.724860536097.5
2.14-2.210.184924214522497.6
2.21-2.290.16310.123279504197.8
2.29-2.390.13911.322493485997.9
2.39-2.490.1191321465465398
2.49-2.620.11213.320650449298.3
2.62-2.760.09714.919615428298.4
2.76-2.930.08117.718303401998.2
2.93-3.130.06720.517211381298.5
3.13-3.380.05624.315994356898.6
3.38-3.70.04427.814296325898.5
3.7-4.140.03831.312849297498.5
4.14-4.780.03435.211834265099.1
4.78-5.850.03631.810059223699
5.85-8.270.03330.87859176598.8
8.270.02434.5421898797.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 57.1 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å48.93 Å
Translation2.5 Å48.93 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
Starting model: PDB ENTRY 3oec

3oec


Resolution: 1.85→50 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.941 / WRfactor Rfree: 0.1795 / WRfactor Rwork: 0.1312 / Occupancy max: 1 / Occupancy min: 0.4 / FOM work R set: 0.8948 / SU B: 5.788 / SU ML: 0.079 / SU R Cruickshank DPI: 0.1288 / SU Rfree: 0.1265 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.126 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1949 4114 5 %RANDOM
Rwork0.1446 ---
obs0.1471 82151 97.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 44.57 Å2 / Biso mean: 15.0129 Å2 / Biso min: 2.12 Å2
Baniso -1Baniso -2Baniso -3
1-0.97 Å20 Å20.11 Å2
2---0.56 Å20 Å2
3----0.4 Å2
Refinement stepCycle: LAST / Resolution: 1.85→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7942 0 176 969 9087
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0218356
X-RAY DIFFRACTIONr_angle_refined_deg1.4841.97911456
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.78751094
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.86223.62326
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.349151218
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.071560
X-RAY DIFFRACTIONr_chiral_restr0.10.21332
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0216356
X-RAY DIFFRACTIONr_mcbond_it0.7191.55371
X-RAY DIFFRACTIONr_mcangle_it1.18928610
X-RAY DIFFRACTIONr_scbond_it2.03932985
X-RAY DIFFRACTIONr_scangle_it3.144.52837
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.266 293 -
Rwork0.2 5666 -
all-5959 -
obs--96.97 %
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)
10.31810.00040.02810.00940.03260.1747-0.02440.0293-0.03020.0121-0.00460.00620.002-0.0280.0290.0430.00440.0070.0182-0.00940.041281.470118.939217.4412
20.3840.01860.07760.0546-0.04120.0890.0085-0.0813-0.0538-0.0216-0.0278-0.022-0.01730.01640.01930.0488-0.0061-0.00880.03840.03260.0297111.854217.621947.9993
30.2982-0.03670.03270.0448-0.02110.1981-0.0030.06040.03640.0263-0.0297-0.00770.01070.04160.03270.03520.00270.00990.03970.02660.0395110.528728.169416.3096
40.4075-0.13030.06390.0484-0.0260.055-0.0581-0.1139-0.01230.00290.04-0.0009-0.0278-0.03670.01810.0680.01840.00080.0431-0.00270.015382.650926.370649.8325
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

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