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- PDB-2wyv: High resolution structure of Thermus thermophilus enoyl-acyl carr... -

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Basic information

Entry
Database: PDB / ID: 2wyv
TitleHigh resolution structure of Thermus thermophilus enoyl-acyl carrier protein reductase NAD-form
ComponentsENOYL-[ACYL CARRIER PROTEIN] REDUCTASE
KeywordsOXIDOREDUCTASE / FATTY ACID BIOSYNTHESIS / OXIDATION REDUCTION
Function / homology
Function and homology information


enoyl-[acyl-carrier-protein] reductase (NADH) / enoyl-[acyl-carrier-protein] reductase (NADH) activity / fatty acid biosynthetic process / nucleotide binding
Similarity search - Function
Enoyl-[acyl-carrier-protein] reductase (NADH) / 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 / Enoyl-[acyl-carrier-protein] reductase [NADH]
Similarity search - Component
Biological speciesTHERMUS THERMOPHILUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.86 Å
AuthorsOtero, J.M. / Noel, A.J. / Guardado-Calvo, P. / Llamas-Saiz, A.L. / van Raaij, M.J.
CitationJournal: Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun.
Year: 2012
Title: High-resolution structures of Thermus thermophilus enoyl-acyl carrier protein reductase in the apo form, in complex with NAD+ and in complex with NAD+ and triclosan.
Authors: Otero, J.M. / Noel, A.J. / Guardado-Calvo, P. / Llamas-Saiz, A.L. / Wende, W. / Schierling, B. / Pingoud, A. / van Raaij, M.J.
History
DepositionNov 20, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 24, 2010Provider: repository / Type: Initial release
Revision 1.1Oct 10, 2012Group: Database references / Other
Revision 1.2Oct 17, 2012Group: Database references
Revision 1.3Jan 31, 2018Group: Database references / Source and taxonomy / Category: citation / citation_author / entity_src_gen
Item: _citation.journal_abbrev / _citation.page_last ..._citation.journal_abbrev / _citation.page_last / _citation.title / _citation_author.name / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_variant
Revision 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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_database_status.status_code_sf / _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_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_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_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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_conn.ptnr2_label_seq_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

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Assembly

Deposited unit
A: ENOYL-[ACYL CARRIER PROTEIN] REDUCTASE
B: ENOYL-[ACYL CARRIER PROTEIN] REDUCTASE
C: ENOYL-[ACYL CARRIER PROTEIN] REDUCTASE
D: ENOYL-[ACYL CARRIER PROTEIN] REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,9629
Polymers112,5664
Non-polymers1,3965
Water9,818545
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19770 Å2
ΔGint-155.8 kcal/mol
Surface area33530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.270, 107.800, 85.980
Angle α, β, γ (deg.)90.00, 95.89, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
ENOYL-[ACYL CARRIER PROTEIN] REDUCTASE


Mass: 28141.432 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) THERMUS THERMOPHILUS (bacteria) / Strain: HB8
Description: THERMUS THERMOPHILUS DNA OBTAINED FROM PROF. WOLFGANG LIEBL, GOETTINGEN.
Plasmid: PET30A / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Variant (production host): ROSETTA / References: UniProt: Q5SLI9, EC: 1.3.1.10
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: 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: 2.2 Å3/Da / Density % sol: 44.7 % / Description: NONE
Crystal growpH: 5.4
Details: 20% (W/V) POLYETHYLENE GLYCOL 4000, 100 MM SODIUM CITRATE PH 5.4, 2 MM NAD

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.939
DetectorType: ADSC CCD / Detector: CCD / Date: Jul 19, 2008 / Details: TOROIDAL FOCUSING MIRROR
RadiationMonochromator: SINGLE SILICON (111) MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.939 Å / Relative weight: 1
ReflectionResolution: 1.85→40 Å / Num. obs: 77770 / % possible obs: 95.9 % / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Biso Wilson estimate: 21.5 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 10.1
Reflection shellResolution: 1.85→1.95 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 2.2 / % possible all: 89.2

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Processing

Software
NameVersionClassification
REFMAC5.5.0070refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2WYU

2wyu


Resolution: 1.86→39.75 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.927 / SU B: 4.043 / SU ML: 0.118 / Cross valid method: THROUGHOUT / ESU R: 0.151 / ESU R Free: 0.15 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.23926 1098 1.4 %RANDOM
Rwork0.18199 ---
obs0.18277 76657 95.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.445 Å2
Baniso -1Baniso -2Baniso -3
1-1.75 Å20 Å2-2.35 Å2
2---2.46 Å20 Å2
3---0.23 Å2
Refinement stepCycle: LAST / Resolution: 1.86→39.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7695 0 91 545 8331
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0227932
X-RAY DIFFRACTIONr_bond_other_d0.0010.025356
X-RAY DIFFRACTIONr_angle_refined_deg1.48210752
X-RAY DIFFRACTIONr_angle_other_deg1.016313009
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.94851008
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.53922.857322
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.185151331
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.8241571
X-RAY DIFFRACTIONr_chiral_restr0.0880.21244
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.028809
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021624
X-RAY DIFFRACTIONr_nbd_refined0.2070.21497
X-RAY DIFFRACTIONr_nbd_other0.1750.25097
X-RAY DIFFRACTIONr_nbtor_refined0.1670.23676
X-RAY DIFFRACTIONr_nbtor_other0.0810.23713
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1390.2366
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.1540.27
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2070.212
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1750.242
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1350.27
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8171.55011
X-RAY DIFFRACTIONr_mcbond_other0.1831.52080
X-RAY DIFFRACTIONr_mcangle_it1.4827952
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.21432921
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.7914.52800
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.858→1.958 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.337 150 -
Rwork0.304 9089 -
obs--88.14 %

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