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- PDB-3ek2: Crystal structure of eonyl-(acyl carrier protein) reductase from ... -

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Basic information

Entry
Database: PDB / ID: 3ek2
TitleCrystal structure of eonyl-(acyl carrier protein) reductase from burkholderia pseudomallei 1719b
ComponentsEnoyl-(Acyl-carrier-protein) reductase (NADH)
KeywordsOXIDOREDUCTASE / SSGCID / enoyl-(acyl carrier protein) reductase / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
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
Enoyl-[acyl-carrier-protein] reductase [NADH]
Similarity search - Component
Biological speciesBurkholderia pseudomallei 1710b (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / molecular replacement, molecular replacement / Resolution: 1.9 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: Plos One / Year: 2013
Title: Combining functional and structural genomics to sample the essential Burkholderia structome.
Authors: Baugh, L. / Gallagher, L.A. / Patrapuvich, R. / Clifton, M.C. / Gardberg, A.S. / Edwards, T.E. / Armour, B. / Begley, D.W. / Dieterich, S.H. / Dranow, D.M. / Abendroth, J. / Fairman, J.W. / ...Authors: Baugh, L. / Gallagher, L.A. / Patrapuvich, R. / Clifton, M.C. / Gardberg, A.S. / Edwards, T.E. / Armour, B. / Begley, D.W. / Dieterich, S.H. / Dranow, D.M. / Abendroth, J. / Fairman, J.W. / Fox, D. / Staker, B.L. / Phan, I. / Gillespie, A. / Choi, R. / Nakazawa-Hewitt, S. / Nguyen, M.T. / Napuli, A. / Barrett, L. / Buchko, G.W. / Stacy, R. / Myler, P.J. / Stewart, L.J. / Manoil, C. / Van Voorhis, W.C.
History
DepositionSep 18, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 30, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 23, 2013Group: Database references
Revision 1.3Apr 4, 2018Group: Data collection / Source and taxonomy / Category: diffrn_source / entity_src_gen
Item: _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.type ..._diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.type / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name
Revision 1.4Aug 30, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Enoyl-(Acyl-carrier-protein) reductase (NADH)
B: Enoyl-(Acyl-carrier-protein) reductase (NADH)
C: Enoyl-(Acyl-carrier-protein) reductase (NADH)
D: Enoyl-(Acyl-carrier-protein) reductase (NADH)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,3555
Polymers115,3194
Non-polymers351
Water14,772820
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14540 Å2
ΔGint-121 kcal/mol
Surface area32630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.195, 122.195, 139.255
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1116A1 - 260
2116B1 - 260
3116C1 - 260
4116D1 - 260

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Components

#1: Protein
Enoyl-(Acyl-carrier-protein) reductase (NADH)


Mass: 28829.838 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia pseudomallei 1710b (bacteria)
Strain: 1719B / Gene: fabI, BURPS1710b_2636 / Plasmid: BG1861 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q3JQY0, enoyl-[acyl-carrier-protein] reductase (NADH)
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 820 / 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: 2.37 Å3/Da / Density % sol: 48.06 %
Crystal growTemperature: 298 K / pH: 7
Details: JCSG+ SCREEN: 10% PEG 6000, 100MM HEPES PH 7.0, VAPOR DIFFUSION, TEMPERATURE 298K, pH 7.00, VAPOR DIFFUSION, SITTING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.9793
DetectorType: MAR 300 / Detector: CCD / Date: Aug 1, 2008
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.8→69.673 Å / Num. obs: 82541 / % possible obs: 95.5 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.142 / Rsym value: 0.142 / Net I/σ(I): 3.7
Reflection shellResolution: 1.9→2 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.598 / Mean I/σ(I) obs: 1 / Rsym value: 0.598 / % possible all: 97.7

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Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.5.0046refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: molecular replacement, molecular replacement
Starting model: pdb entry 1qsg, tetramer, modified

1qsg


Resolution: 1.9→69.673 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.932 / SU B: 3.19 / SU ML: 0.092 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.148 / ESU R Free: 0.14 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE
RfactorNum. reflection% reflectionSelection details
Rfree0.218 4094 5 %RANDOM
Rwork0.176 ---
obs0.178 82036 94.6 %-
all-82036 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.54 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å20 Å20 Å2
2---0.69 Å20 Å2
3---0.74 Å2
Refinement stepCycle: LAST / Resolution: 1.9→69.673 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7399 0 1 820 8220
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0227527
X-RAY DIFFRACTIONr_bond_other_d0.0010.024927
X-RAY DIFFRACTIONr_angle_refined_deg1.5071.96610195
X-RAY DIFFRACTIONr_angle_other_deg0.985312014
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.175995
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.04723.887301
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.12151173
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5871540
X-RAY DIFFRACTIONr_chiral_restr0.0960.21184
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.028569
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021575
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_it0.891.54942
X-RAY DIFFRACTIONr_mcbond_other0.2421.52067
X-RAY DIFFRACTIONr_mcangle_it1.57127799
X-RAY DIFFRACTIONr_scbond_it2.53432585
X-RAY DIFFRACTIONr_scangle_it4.0714.52396
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Number: 3021 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDTypeRms dev position (Å)Weight position
Aloose positional0.265
Bloose positional0.365
Cloose positional0.355
Dloose positional0.295
Aloose thermal3.5310
Bloose thermal2.5610
Cloose thermal3.0910
Dloose thermal2.6810
LS refinement shellResolution: 1.9→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.36 327 -
Rwork0.325 5703 -
obs--94.9 %

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