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- PDB-4iql: Crystal Structure of Porphyromonas gingivalis Enoyl-ACP Reductase... -

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Basic information

Entry
Database: PDB / ID: 4iql
TitleCrystal Structure of Porphyromonas gingivalis Enoyl-ACP Reductase II (FabK) with cofactors NADPH and FMN
ComponentsEnoyl-(Acyl-carrier-protein) reductase II
KeywordsOXIDOREDUCTASE / TIM Barrel / Fatty Acid Binding / Reduction
Function / homology
Function and homology information


nitronate monooxygenase activity / nucleotide binding
Similarity search - Function
Nitronate monooxygenase / Nitronate monooxygenase / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / Chem-NDP / Enoyl-(Acyl-carrier-protein) reductase II
Similarity search - Component
Biological speciesPorphyromonas gingivalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.938 Å
AuthorsHevener, K.E. / Santarsiero, B.D. / Su, P.-C. / Boci, T. / Truong, K. / Johnson, M.E. / Mehboob, S.
CitationJournal: Acta Crystallogr F Struct Biol Commun / Year: 2018
Title: Structural characterization of Porphyromonas gingivalis enoyl-ACP reductase II (FabK).
Authors: Hevener, K.E. / Santarsiero, B.D. / Lee, H. / Jones, J.A. / Boci, T. / Johnson, M.E. / Mehboob, S.
History
DepositionJan 11, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 29, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2018Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Apr 18, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.page_first ..._citation.journal_abbrev / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed
Revision 1.3Sep 20, 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_ref_seq_dif / 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_auth_seq_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.pdbx_leaving_atom_flag / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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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 II
B: Enoyl-(Acyl-carrier-protein) reductase II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,75515
Polymers70,6312
Non-polymers4,12413
Water5,747319
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9660 Å2
ΔGint-100 kcal/mol
Surface area22880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.652, 86.652, 150.505
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 35315.258 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Porphyromonas gingivalis (bacteria) / Strain: W83 / Gene: fabK, PG_1416 / Plasmid: pET15B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Gold
References: UniProt: Q7MAW0, enoyl-[acyl-carrier-protein] reductase (NADH)

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Non-polymers , 5 types, 332 molecules

#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Chemical
ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 319 / 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: 2.25 Å3/Da / Density % sol: 45.23 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 20% PEG 3350, 0.2M sodium formate, 5mM MOPS (pH 7.0), 1mM DTT. 3uL(protein stock):3uL(Index 90):1uL Seed stock. (Seed Stock From: 10% PEG 3350, 0.15M Na Citrate pH 5.6), VAPOR DIFFUSION, ...Details: 20% PEG 3350, 0.2M sodium formate, 5mM MOPS (pH 7.0), 1mM DTT. 3uL(protein stock):3uL(Index 90):1uL Seed stock. (Seed Stock From: 10% PEG 3350, 0.15M Na Citrate pH 5.6), VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.9787 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Aug 10, 2012
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 1.938→20 Å / Num. all: 90851 / Num. obs: 90851 / % possible obs: 99.5 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 7.1 % / Biso Wilson estimate: 20.56 Å2 / Rmerge(I) obs: 0.134 / Rsym value: 0.134 / Net I/σ(I): 15.2
Reflection shellResolution: 1.938→2.05 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.538 / Mean I/σ(I) obs: 4.19 / Num. unique all: 14235 / % possible all: 97.5

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.5.0110refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2Z6J

2z6j


Resolution: 1.938→20 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.926 / SU B: 2.857 / SU ML: 0.084 / Cross valid method: THROUGHOUT / ESU R: 0.145 / ESU R Free: 0.138 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20695 2424 5.1 %RANDOM
Rwork0.161 ---
all0.16331 47951 --
obs0.16331 45527 99.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.324 Å2
Baniso -1Baniso -2Baniso -3
1--0.19 Å20 Å20 Å2
2--0.4 Å20 Å2
3----0.22 Å2
Refinement stepCycle: LAST / Resolution: 1.938→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4638 0 190 319 5147
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0214937
X-RAY DIFFRACTIONr_angle_refined_deg1.6062.0076714
X-RAY DIFFRACTIONr_dihedral_angle_1_deg12.8645.063634
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.27223.871186
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.3315807
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4731532
X-RAY DIFFRACTIONr_chiral_restr0.1230.2759
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0213618
X-RAY DIFFRACTIONr_mcbond_it1.2791.53103
X-RAY DIFFRACTIONr_mcangle_it2.16624952
X-RAY DIFFRACTIONr_scbond_it3.9631834
X-RAY DIFFRACTIONr_scangle_it6.4014.51761
LS refinement shellResolution: 1.938→1.988 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.272 175 -
Rwork0.21 3152 -
obs--96.3 %

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