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- PDB-4alm: Crystal structure of S. aureus FabI (P43212) -

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Basic information

Entry
Database: PDB / ID: 4alm
TitleCrystal structure of S. aureus FabI (P43212)
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
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: 2.45 Å
AuthorsSchiebel, 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)125,82617
Polymers124,5774
Non-polymers1,24913
Water3,855214
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15060 Å2
ΔGint-243.1 kcal/mol
Surface area41190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.490, 87.490, 307.180
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

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


Mass: 31144.240 Da / Num. of mol.: 4 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STAPHYLOCOCCUS AUREUS (bacteria) / Strain: N315 / Plasmid: PETM-11 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q7A6D8, UniProt: A0A0H3JLH9*PLUS, EC: 1.3.1.10
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 214 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, LEU 2 TO VAL ENGINEERED RESIDUE IN CHAIN B, LEU 2 TO VAL ENGINEERED ...ENGINEERED RESIDUE IN CHAIN A, LEU 2 TO VAL ENGINEERED RESIDUE IN CHAIN B, LEU 2 TO VAL ENGINEERED RESIDUE IN CHAIN C, LEU 2 TO VAL ENGINEERED RESIDUE IN CHAIN D, LEU 2 TO VAL

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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: 2.68 Å3/Da / Density % sol: 53.82 % / Description: NONE
Crystal growpH: 5
Details: 1.15 M (NH4)2SO4, 0.1 M SODIUM ACETATE PH 5.0, 1% ETHANOL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.919
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 6, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.919 Å / Relative weight: 1
ReflectionResolution: 2.45→50 Å / Num. obs: 44583 / % possible obs: 98.9 % / Observed criterion σ(I): -3 / Redundancy: 7.2 % / Biso Wilson estimate: 45.97 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 16.4
Reflection shellResolution: 2.45→2.6 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.78 / Mean I/σ(I) obs: 2.8 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE: 1.6.4_486)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4ALL

4all


Resolution: 2.45→48.177 Å / SU ML: 0.31 / σ(F): 2 / Phase error: 23.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2516 2228 5 %
Rwork0.1847 --
obs0.188 44548 98.89 %
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 61.03 Å2 / ksol: 0.36 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-3.3064 Å20 Å20 Å2
2--3.3064 Å20 Å2
3----6.6128 Å2
Refinement stepCycle: LAST / Resolution: 2.45→48.177 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7541 0 65 214 7820
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0077688
X-RAY DIFFRACTIONf_angle_d0.98110373
X-RAY DIFFRACTIONf_dihedral_angle_d15.2672836
X-RAY DIFFRACTIONf_chiral_restr0.0651185
X-RAY DIFFRACTIONf_plane_restr0.0041339
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4501-2.53760.31892200.2494170X-RAY DIFFRACTION100
2.5376-2.63920.31932210.22394196X-RAY DIFFRACTION100
2.6392-2.75930.30962200.20674165X-RAY DIFFRACTION100
2.7593-2.90480.25582200.18524210X-RAY DIFFRACTION100
2.9048-3.08680.27492210.18124189X-RAY DIFFRACTION99
3.0868-3.32510.2432220.17414206X-RAY DIFFRACTION99
3.3251-3.65960.23492230.16634241X-RAY DIFFRACTION99
3.6596-4.18880.21652230.15094244X-RAY DIFFRACTION99
4.1888-5.27650.20442240.1554257X-RAY DIFFRACTION98
5.2765-48.18610.28882340.22644442X-RAY DIFFRACTION96
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)
11.39950.07981.68490.3881.06846.4559-0.39241.2222-0.16850.2173-0.18990.20790.28560.47380.54930.89390.30320.07640.8227-0.0530.2279-31.5264-12.3457-6.2088
22.3912-1.35090.26022.5522-1.02592.46610.05690.26510.1903-0.4911-0.11940.2121-0.6498-0.43540.07830.37210.1307-0.05410.3667-0.00260.2269-56.248418.75879.1168
30.312-0.6016-0.3451.3613-0.32333.2438-0.04150.09470.11170.07820.0456-0.0484-0.59820.3784-0.0070.30620.05060.01540.44760.00440.2233-49.383516.221826.1681
41.2390.0023-0.45452.02690.10610.29690.0523-0.2863-0.0792-0.0364-0.2093-0.14910.19170.18540.1310.27420.05220.00630.3545-0.02580.1575-43.35527.680914.3306
52.6289-1.5223-0.73612.66470.04010.3116-0.0671-0.5955-0.09770.45390.12230.2295-0.3338-0.6149-0.03230.39380.11030.05890.5067-0.02430.1783-58.821612.966360.4291
61.357-0.77390.21561.2247-0.26573.42650.0930.05780.1518-0.0001-0.06440.0563-0.2688-0.4497-0.11260.27360.11250.09170.26750.00450.1871-55.490913.609842.8522
71.05911.59780.3963.88422.54062.44130.17180.08620.01160.5967-0.3031-0.04670.8281-0.88070.23810.702-0.3651-0.06380.7136-0.02390.3689-57.3144-15.343145.5491
81.59470.7567-0.2031.8719-0.82350.54590.1895-0.3128-0.1207-0.09-0.203-0.04290.10160.05630.04410.30510.0416-0.03230.2710.00550.1838-45.73253.153.0771
95.2055-3.4325-0.22963.47180.96370.5176-0.587-1.1108-0.00911.06860.70370.10191.23590.16970.13010.58710.11820.05430.50680.10570.1244-42.5954-3.593969.542
101.5192-0.56410.70881.50410.62170.84060.0986-0.13090.13560.3567-0.0944-0.26840.50760.97560.01450.42220.2155-0.10050.83140.00210.2269-20.0942-7.745359.7449
112.24870.1657-0.42130.38790.09112.35220.1761-0.0004-0.12140.1284-0.11160.00020.82420.7664-0.12830.58790.3276-0.06810.4455-0.05340.2152-28.9251-11.33645.3827
123.42653.7792-2.66657.3717-0.39234.05390.0937-0.21271.0869-1.0646-0.0697-0.2867-0.33170.9671-0.22930.3587-0.14510.24380.41640.11940.8719-22.243914.698247.5799
131.10930.35560.25252.25390.9650.40080.04820.17480.1639-0.42610.03040.2707-0.00840.29740.00690.43190.09070.01190.3869-0.00870.1476-35.61071.557853.474
141.8414-0.9759-0.99371.43931.42682.2327-0.11120.2739-0.0416-0.03270.0341-0.11670.51490.51680.06030.34970.22810.03540.5055-0.04120.1952-28.2535-12.15267.4807
151.1311-0.07990.77981.43711.06242.5098-0.2042-0.1248-0.0790.30520.28040.01280.47370.1412-0.08240.26390.23710.01040.3716-0.0470.121-36.0436-7.486222.1347
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID -17:0)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 1:100)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 101:220)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 221:252)
5X-RAY DIFFRACTION5(CHAIN B AND RESID 1:95)
6X-RAY DIFFRACTION6(CHAIN B AND RESID 96:187)
7X-RAY DIFFRACTION7(CHAIN B AND RESID 188:220)
8X-RAY DIFFRACTION8(CHAIN B AND RESID 221:250)
9X-RAY DIFFRACTION9(CHAIN C AND RESID -6:9)
10X-RAY DIFFRACTION10(CHAIN C AND RESID 10:71)
11X-RAY DIFFRACTION11(CHAIN C AND RESID 72:189)
12X-RAY DIFFRACTION12(CHAIN C AND RESID 190:219)
13X-RAY DIFFRACTION13(CHAIN C AND RESID 220:253)
14X-RAY DIFFRACTION14(CHAIN D AND RESID -3:100)
15X-RAY DIFFRACTION15(CHAIN D AND RESID 101:256)

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