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- PDB-4m89: Crystal Structure of Enoyl-Acyl Carrier Protein Reductase (FabI) ... -

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Basic information

Entry
Database: PDB / ID: 4m89
TitleCrystal Structure of Enoyl-Acyl Carrier Protein Reductase (FabI) from Neisseria meningitidis in complex with NAD+ and Triclosan
ComponentsEnoyl-[acyl-carrier-protein] reductase [NADH]
KeywordsOXIDOREDUCTASE/ANTIBIOTIC / Enoyl / acyl carrier protein / ACP / Neisseria / Inhibitor / Rossmann Fold / Reductase / NAD / Triclosan / OXIDOREDUCTASE-ANTIBIOTIC complex
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 / TRICLOSAN / Enoyl-[acyl-carrier-protein] reductase [NADH]
Similarity search - Component
Biological speciesNeisseria meningitidis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsNanson, J.D. / Forwood, J.K.
CitationJournal: TO BE PUBLISHED
Title: Crystal Structure of Enoyl-Acyl Carrier Protein Reductase (FabI) from Neisseria meningitidis in complex with NAD+ and Triclosan
Authors: Nanson, J.D. / Forwood, J.K.
History
DepositionAug 13, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 2, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: 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 / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_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

Downloads & links

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Assembly

Deposited unit
A: Enoyl-[acyl-carrier-protein] reductase [NADH]
B: Enoyl-[acyl-carrier-protein] reductase [NADH]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,3496
Polymers55,4432
Non-polymers1,9064
Water5,657314
1
A: Enoyl-[acyl-carrier-protein] reductase [NADH]
B: Enoyl-[acyl-carrier-protein] reductase [NADH]
hetero molecules

A: Enoyl-[acyl-carrier-protein] reductase [NADH]
B: Enoyl-[acyl-carrier-protein] reductase [NADH]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,69912
Polymers110,8874
Non-polymers3,8128
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_545x,x-y-1,-z+1/61
Buried area14360 Å2
ΔGint-90 kcal/mol
Surface area32800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.770, 90.770, 241.270
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-512-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: SER / End label comp-ID: SER / Refine code: _ / Auth seq-ID: 2 - 258 / Label seq-ID: 2 - 258

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Enoyl-[acyl-carrier-protein] reductase [NADH]


Mass: 27721.664 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria meningitidis (bacteria) / Strain: FAM18 / Gene: fabI, NMC1834 / Production host: Escherichia coli (E. coli)
References: UniProt: A1KVU8, enoyl-[acyl-carrier-protein] reductase (NADH)
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical ChemComp-TCL / TRICLOSAN


Mass: 289.542 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H7Cl3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 314 / 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: 2.59 Å3/Da / Density % sol: 52.46 %
Crystal growTemperature: 296.15 K / Method: vapor diffusion, hanging drop
Details: 1.8M ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 296.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 5, 2013
RadiationMonochromator: Silicon Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.9→34.47 Å / Num. all: 47383 / Num. obs: 47336 / % possible obs: 99.9 %
Reflection shellResolution: 1.9→2 Å / % possible all: 100

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
REFMAC5.7.0032refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→33.06 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.94 / SU B: 3.784 / SU ML: 0.064 / Cross valid method: THROUGHOUT / ESU R: 0.128 / ESU R Free: 0.112 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18613 2383 5.1 %RANDOM
Rwork0.16747 ---
obs0.16841 44797 99.78 %-
all-44895 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.932 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3----0 Å2
Refinement stepCycle: LAST / Resolution: 1.9→33.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3828 0 122 314 4264
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0194060
X-RAY DIFFRACTIONr_bond_other_d0.0040.023882
X-RAY DIFFRACTIONr_angle_refined_deg1.49825500
X-RAY DIFFRACTIONr_angle_other_deg1.00838906
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6835520
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.28323.333162
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.87115666
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.561530
X-RAY DIFFRACTIONr_chiral_restr0.070.2618
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024610
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02934
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_it0.6411.1742068
X-RAY DIFFRACTIONr_mcbond_other0.6391.1732067
X-RAY DIFFRACTIONr_mcangle_it1.1331.7582586
X-RAY DIFFRACTIONr_mcangle_other1.1331.7592587
X-RAY DIFFRACTIONr_scbond_it0.8951.3491990
X-RAY DIFFRACTIONr_scbond_other0.8941.3491989
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.571.9572913
X-RAY DIFFRACTIONr_long_range_B_refined3.37810.1524892
X-RAY DIFFRACTIONr_long_range_B_other3.2139.9144766
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 15286 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.08 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2 195 -
Rwork0.193 3203 -
obs--99.91 %
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)
10.1187-0.0945-0.00360.1619-0.13540.352-0.0360.04410.01770.0018-0.0448-0.02560.02380.01830.08080.0323-0.0285-0.01190.04080.01280.036430.2861-31.5227-1.4763
20.2461-0.03570.01160.0327-0.02390.3295-0.0468-0.0331-0.0126-0.0198-0.00530.00040.10210.01430.05210.06180.01280.03210.02220.01380.043935.6333-56.485516.6043
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 258
2X-RAY DIFFRACTION2B2 - 258

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