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- PDB-4all: Crystal structure of S. aureus FabI in complex with NADP and tric... -

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Basic information

Entry
Database: PDB / ID: 4all
TitleCrystal structure of S. aureus FabI in complex with NADP and triclosan (P212121)
ComponentsENOYL-[ACYL-CARRIER-PROTEIN] REDUCTASE [NADPH]
KeywordsOXIDOREDUCTASE / SHORT-CHAIN DEHYDROGENASE/REDUCTASE SUPERFAMILY / FATTY ACID BIOSYNTHESIS / LIPID SYNTHESIS
Function / homology
Function and homology information


: / enoyl-[acyl-carrier-protein] reductase (NADPH, Re-specific) / enoyl-[acyl-carrier-protein] reductase (NADPH) activity / enoyl-[acyl-carrier-protein] reductase (NADH) activity / fatty acid biosynthetic process / nucleotide binding / identical protein 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
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / TRICLOSAN / Enoyl-[acyl-carrier-protein] reductase [NADPH] / Enoyl-[acyl-carrier-protein] reductase [NADPH]
Similarity search - Component
Biological speciesSTAPHYLOCOCCUS AUREUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsSchiebel, J. / Chang, A. / Tonge, P.J. / Kisker, C.
CitationJournal: Structure / Year: 2012
Title: Staphylococcus Aureus Fabi: Inhibition, Substrate Recognition and Potential Implications for in Vivo Essentiality
Authors: Schiebel, J. / Chang, A. / Lu, H. / Baxter, M.V. / Tonge, P.J. / Kisker, C.
History
DepositionMar 4, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 9, 2012Provider: repository / Type: Initial release
Revision 1.1May 23, 2012Group: Other
Revision 1.2Dec 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 / 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 / _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 [NADPH]
B: ENOYL-[ACYL-CARRIER-PROTEIN] REDUCTASE [NADPH]
C: ENOYL-[ACYL-CARRIER-PROTEIN] REDUCTASE [NADPH]
D: ENOYL-[ACYL-CARRIER-PROTEIN] REDUCTASE [NADPH]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,36612
Polymers122,2344
Non-polymers4,1328
Water1629
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22250 Å2
ΔGint-162.1 kcal/mol
Surface area32670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.520, 111.910, 111.640
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
1112A2 - 98
2112B2 - 98
3112C2 - 98
4112D2 - 98
1212A100 - 256
2212B100 - 256
3212C100 - 256
4212D100 - 256

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Components

#1: Protein
ENOYL-[ACYL-CARRIER-PROTEIN] REDUCTASE [NADPH] / ENR / ENOYL-ACP REDUCTASE


Mass: 30558.551 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STAPHYLOCOCCUS AUREUS (bacteria) / Strain: N315 / Plasmid: PET-16B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS
References: UniProt: Q7A6D8, UniProt: A0A0H3JLH9*PLUS, EC: 1.3.1.10
#2: Chemical
ChemComp-TCL / TRICLOSAN


Mass: 289.542 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C12H7Cl3O2 / Comment: antifungal, antibiotic, detergent*YM
#3: Chemical
ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / 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: 2.3 Å3/Da / Density % sol: 46.11 % / Description: NONE
Crystal growpH: 6.5 / Details: 0.1 M K/NA-PHOSPHATE PH 6.5, 35% MPD

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.976
DetectorType: MARRESEARCH / Detector: CCD / Date: Aug 19, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.8→42.91 Å / Num. obs: 22827 / % possible obs: 87.2 % / Observed criterion σ(I): 6 / Redundancy: 5.25 % / Rmerge(I) obs: 0.15 / Net I/σ(I): 6.49
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 5.16 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 2.51 / % possible all: 89.6

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2QIO

2qio


Resolution: 2.8→79.04 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.9 / SU B: 39.894 / SU ML: 0.384 / Cross valid method: THROUGHOUT / ESU R Free: 0.482 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.2624 1146 5.1 %RANDOM
Rwork0.21406 ---
obs0.21645 21537 85.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 66.354 Å2
Baniso -1Baniso -2Baniso -3
1--0.34 Å20 Å20 Å2
2---2.33 Å20 Å2
3---2.67 Å2
Refinement stepCycle: LAST / Resolution: 2.8→79.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7832 0 260 9 8101
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0228220
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5911.98211125
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.90851014
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.29925.055364
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.412151433
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4091544
X-RAY DIFFRACTIONr_chiral_restr0.1190.21255
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.026088
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.3591.55014
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.69628020
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.24433206
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.2444.53105
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
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1012tight positional0.050.05
2B1012tight positional0.050.05
3C1012tight positional0.050.05
4D1012tight positional0.050.05
1A934medium positional0.080.5
2B934medium positional0.060.5
3C934medium positional0.070.5
4D934medium positional0.070.5
1A1012tight thermal0.10.5
2B1012tight thermal0.090.5
3C1012tight thermal0.090.5
4D1012tight thermal0.080.5
1A934medium thermal0.12
2B934medium thermal0.092
3C934medium thermal0.092
4D934medium thermal0.092
LS refinement shellResolution: 2.8→2.873 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.346 99 -
Rwork0.323 1606 -
obs--88.76 %
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)
13.3134-0.82410.3323.3470.12342.07780.0827-0.11490.9493-0.1883-0.1477-0.8049-0.13690.36930.06510.3861-0.04990.06070.0923-0.01061.35067.8152-29.1101-25.2183
24.3745-0.19770.45893.3631-0.27022.39910.18570.56190.2859-0.9327-0.08360.24790.0618-0.3076-0.10210.60680.0237-0.07130.19470.02650.8623-21.4078-35.2356-39.5374
33.2835-0.6677-0.33323.3742-0.10411.9688-0.0231-0.66310.14010.40120.09880.6840.1825-0.4179-0.07580.3891-0.08790.08060.4041-0.0750.9734-30.5068-45.8456-10.8043
43.3782-0.3548-0.48272.5340.28652.93380.0288-0.9987-0.09260.4269-0.0532-0.18260.38150.30890.02440.5430.034-0.0630.3583-0.01060.85681.0677-54.0536-6.4677
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 256
2X-RAY DIFFRACTION2B3 - 256
3X-RAY DIFFRACTION3C3 - 256
4X-RAY DIFFRACTION4D3 - 256

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