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- PDB-3oec: Crystal structure of carveol dehydrogenase from Mycobacterium the... -

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Basic information

Entry
Database: PDB / ID: 3oec
TitleCrystal structure of carveol dehydrogenase from Mycobacterium thermoresistibile
ComponentsCarveol dehydrogenase (MythA.01326.c, A0R518 homolog)
KeywordsOXIDOREDUCTASE / SSGCID / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / DEHYDROGENASE
Function / homology
Function and homology information


flavanone 4-reductase activity / flavanone 4-reductase
Similarity search - Function
Mycofactocin-dependent oxidoreductase / short chain dehydrogenase / 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
Carveol dehydrogenase (MythA.01326.c, A0R518 homolog)
Similarity search - Component
Biological speciesMycobacterium thermoresistibile (bacteria)
MethodX-RAY DIFFRACTION / 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
DepositionAug 12, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 1, 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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 (MythA.01326.c, A0R518 homolog)
B: Carveol dehydrogenase (MythA.01326.c, A0R518 homolog)
C: Carveol dehydrogenase (MythA.01326.c, A0R518 homolog)
D: Carveol dehydrogenase (MythA.01326.c, A0R518 homolog)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,1948
Polymers137,1034
Non-polymers924
Water14,790821
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13150 Å2
ΔGint-123 kcal/mol
Surface area35180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.860, 120.570, 134.560
Angle α, β, γ (deg.)90.00, 94.05, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-326-

HOH

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Components

#1: Protein
Carveol dehydrogenase (MythA.01326.c, A0R518 homolog)


Mass: 34275.633 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium thermoresistibile (bacteria)
Strain: ATCC 19527 / NCTC 10409 / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: E1C9L4*PLUS, flavanone 4-reductase
#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 821 / 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: 2.01 Å3/Da / Density % sol: 38 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 80MM NA-CACOCYLATE PH 6.5, 14.4% PEG 8000, 20% GLYCEROL, protein AT 29.5MG/ML, VAPOR DIFFUSION, SITTING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Jul 12, 2010 / Details: RIGAKU VARIMAX HF
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. all: 78522 / Num. obs: 77636 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Biso Wilson estimate: 20.88 Å2 / Rmerge(I) obs: 0.089 / Net I/σ(I): 10.23
Reflection shellResolution: 1.95→2 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.316 / Mean I/σ(I) obs: 2.9 / Num. unique all: 5832 / Rsym value: 0.316 / % possible all: 96.8

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Processing

Software
NameVersionClassification
StructureStudiodata collection
PHASERphasing
REFMAC5.5.0109refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1iy8

1iy8


Resolution: 1.95→45.74 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.892 / SU B: 8.806 / SU ML: 0.113 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.163 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE
RfactorNum. reflection% reflectionSelection details
Rfree0.233 3898 5 %RANDOM
Rwork0.176 ---
obs0.179 77535 98.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.8 Å2
Baniso -1Baniso -2Baniso -3
1--0.69 Å20 Å2-0.14 Å2
2---0.05 Å20 Å2
3---0.72 Å2
Refinement stepCycle: LAST / Resolution: 1.95→45.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8145 0 4 821 8970
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0218367
X-RAY DIFFRACTIONr_bond_other_d0.0010.025428
X-RAY DIFFRACTIONr_angle_refined_deg1.5361.94811411
X-RAY DIFFRACTIONr_angle_other_deg0.969313256
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.67251116
X-RAY DIFFRACTIONr_dihedral_angle_2_deg43.05924.289380
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.361151314
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3351569
X-RAY DIFFRACTIONr_chiral_restr0.0930.21332
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.029632
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021629
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8021.55465
X-RAY DIFFRACTIONr_mcbond_other0.2451.52259
X-RAY DIFFRACTIONr_mcangle_it1.34928705
X-RAY DIFFRACTIONr_scbond_it2.33232902
X-RAY DIFFRACTIONr_scangle_it3.7564.52693
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.95→2 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.292 274 -
Rwork0.228 5356 -
obs--96.59 %
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)
10.4537-0.03740.11120.20070.04660.30580.02140.069-0.007-0.0285-0.0036-0.03390.00510.0683-0.01780.02030.01280.01820.0377-0.0040.02759.88275.0318.197
20.4692-0.1032-0.16670.1656-0.03170.49010.02370.09810.0159-0.0449-0.01370.0635-0.0112-0.1075-0.00990.01930.0164-0.01730.04950.0030.0502-19.31587.50918.952
30.2276-0.0525-0.00730.24720.01620.1951-0.009-0.02140.02060.0020.0064-0.0099-0.0447-0.01750.00270.0121-0.00110.00180.0363-0.0070.0535-14.96293.07749.469
40.1871-0.06150.05860.25720.03650.2720.0028-0.0174-0.03520.01450.00240.00230.04470.0197-0.00520.00870.00090.00510.03510.00880.04945.43168.22949.556
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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