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- PDB-4m86: Crystal Structure of Enoyl-Acyl Carrier Protein Reductase (FabI) ... -

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Basic information

Entry
Database: PDB / ID: 4m86
TitleCrystal Structure of Enoyl-Acyl Carrier Protein Reductase (FabI) from Neisseria meningitidis
ComponentsEnoyl-[acyl-carrier-protein] reductase [NADH]
KeywordsOXIDOREDUCTASE / Enoyl / acyl carrier protein / ACP / Neisseria / Rossmann Fold / Reductase
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 speciesNeisseria meningitidis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsNanson, J.D. / Forwood, J.K.
CitationJournal: TO BE PUBLISHED
Title: Crystal Structure of Enoyl-Acyl Carrier Protein Reductase (FabI) from Neisseria meningitidis
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 / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
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

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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]


Theoretical massNumber of molelcules
Total (without water)55,4432
Polymers55,4432
Non-polymers00
Water5,260292
1
A: Enoyl-[acyl-carrier-protein] reductase [NADH]
B: Enoyl-[acyl-carrier-protein] reductase [NADH]

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


Theoretical massNumber of molelcules
Total (without water)110,8874
Polymers110,8874
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_565x,x-y+1,-z+1/61
Buried area15050 Å2
ΔGint-100 kcal/mol
Surface area33340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.609, 91.609, 241.500
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
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: THR / End label comp-ID: THR / Refine code: _ / Auth seq-ID: 2 - 259 / Label seq-ID: 2 - 259

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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 292 / 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: 2.64 Å3/Da / Density % sol: 53.38 %
Crystal growTemperature: 296.15 K / Method: vapor diffusion, hanging drop
Details: 2.0M 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: 2.15→36.58 Å / Num. all: 33897 / Num. obs: 33863 / % possible obs: 99.9 %
Reflection shell
Resolution (Å)Diffraction-ID% possible all
2.15-2.231100
8.33-36.58197.3

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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: 2.15→30.65 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.934 / SU B: 7.337 / SU ML: 0.102 / Cross valid method: THROUGHOUT / ESU R: 0.216 / ESU R Free: 0.168 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20327 2000 6.3 %RANDOM
Rwork0.17603 ---
obs0.17776 29598 94.13 %-
all-31443 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.91 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å2-0 Å2
2--0 Å2-0 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.15→30.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3738 0 0 292 4030
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0193794
X-RAY DIFFRACTIONr_bond_other_d0.0030.023694
X-RAY DIFFRACTIONr_angle_refined_deg1.1571.9665113
X-RAY DIFFRACTIONr_angle_other_deg0.85838474
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6575495
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.85923.503157
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.77415647
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8721528
X-RAY DIFFRACTIONr_chiral_restr0.0630.2581
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024333
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02855
X-RAY DIFFRACTIONr_mcbond_it1.1892.0881992
X-RAY DIFFRACTIONr_mcbond_other1.1882.0861991
X-RAY DIFFRACTIONr_mcangle_it2.0423.1162483
X-RAY DIFFRACTIONr_mcangle_other2.0423.1182484
X-RAY DIFFRACTIONr_scbond_it1.4582.3981802
X-RAY DIFFRACTIONr_scbond_other1.4572.3991803
X-RAY DIFFRACTIONr_scangle_other2.5363.4892631
X-RAY DIFFRACTIONr_long_range_B_refined4.80517.5164544
X-RAY DIFFRACTIONr_long_range_B_other4.61717.2534429
Refine LS restraints NCS

Ens-ID: 1 / Number: 14895 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.09 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.15→2.206 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.255 152 -
Rwork0.202 2258 -
obs--99.63 %
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)
10.1252-0.08770.00840.13290.0780.4911-0.05710.0733-0.02590.0076-0.05690.01920.0087-0.0630.1140.0407-0.03850.0250.068-0.04340.046-30.609232.1573-1.4486
20.2601-0.07020.120.0714-0.05290.387-0.0778-0.0160.0543-0.0069-0.03030.0013-0.096-0.02550.10810.05210.0295-0.04760.0395-0.04230.0701-36.449856.482216.5791
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 259
2X-RAY DIFFRACTION2B2 - 259

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