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- PDB-4d46: Crystal structure of E. coli FabI in complex with NAD and 5-bromo... -

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Basic information

Entry
Database: PDB / ID: 4d46
TitleCrystal structure of E. coli FabI in complex with NAD and 5-bromo-2-(4-chloro-2-hydroxyphenoxy)benzonitrile
ComponentsENOYL-[ACYL-CARRIER-PROTEIN] REDUCTASE [NADH]
KeywordsOXIDOREDUCTASE / ENOYL-ACP REDUCTASE / SHORT-CHAIN DEHYDROGENASE/REDUCTASE SUPERFAMILY / ESCHERICHIA COLI / FATTY ACID BIOSYNTHESIS / LIPID SYNTHESIS / ECFABI / FABI
Function / homology
Function and homology information


enoyl-[acyl-carrier-protein] reductase [NAD(P)H] activity / biotin biosynthetic process / 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
5-bromo-2-(4-chloro-2-hydroxyphenoxy)benzonitrile / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Enoyl-[acyl-carrier-protein] reductase [NADH] / Enoyl-[acyl-carrier-protein] reductase [NADH]
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsTareilus, M. / Schiebel, J. / Chang, A. / Tonge, P.J. / Sotriffer, C.A. / Kisker, C.
CitationJournal: Biochemistry / Year: 2015
Title: An Ordered Water Channel in Staphylococcus Aureus Fabi: Unraveling the Mechanism of Substrate Recognition and Reduction.
Authors: Schiebel, J. / Chang, A. / Merget, B. / Bommineni, G.R. / Yu, W. / Spagnuolo, L.A. / Baxter, M.V. / Tareilus, M. / Tonge, P.J. / Kisker, C. / Sotriffer, C.A.
History
DepositionOct 26, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 4, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 15, 2015Group: Database references
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 [NADH]
B: ENOYL-[ACYL-CARRIER-PROTEIN] REDUCTASE [NADH]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,9046
Polymers57,9282
Non-polymers1,9764
Water4,504250
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)119,80812
Polymers115,8564
Non-polymers3,9528
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_554-y,-x,-z-1/61
Buried area18590 Å2
ΔGint-83.9 kcal/mol
Surface area29800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.144, 79.144, 322.316
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-2149-

HOH

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Components

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


Mass: 28964.068 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: BL21(DE3) / Plasmid: PET23B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: C6EFU4, UniProt: A0A140NA83*PLUS, 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-J47 / 5-bromo-2-(4-chloro-2-hydroxyphenoxy)benzonitrile


Mass: 324.557 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H7BrClNO2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 250 / 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: 2.52 Å3/Da / Density % sol: 51.19 % / Description: NONE
Crystal growpH: 10.5 / Details: 0.08 M NH4AC, 0.1 M CAPS PH 10.5, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 10, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2→46.96 Å / Num. obs: 41818 / % possible obs: 100 % / Observed criterion σ(I): 6 / Redundancy: 19 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 16.2
Reflection shellResolution: 2→2.11 Å / Redundancy: 19.2 % / Rmerge(I) obs: 1.25 / Mean I/σ(I) obs: 2.4 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.5.0102refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QSG

1qsg


Resolution: 2→68.54 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.955 / SU B: 7.733 / SU ML: 0.1 / Cross valid method: THROUGHOUT / ESU R: 0.139 / ESU R Free: 0.133 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. VERY WEAK DENSITY FOR LOOP REGION 193-210 IN SUBUNIT A, WHICH WAS NOT INTERPRETED. VERY WEAK DENSITY FOR LOOP REGION 204-209 IN SUBUNIT B, ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. VERY WEAK DENSITY FOR LOOP REGION 193-210 IN SUBUNIT A, WHICH WAS NOT INTERPRETED. VERY WEAK DENSITY FOR LOOP REGION 204-209 IN SUBUNIT B, WHICH WAS NOT INTERPRETED. INHIBITOR DENSITY BETTER FOR SUBUNIT A, BUT STILL SUFFICIENT FOR B
RfactorNum. reflection% reflectionSelection details
Rfree0.20643 2099 5 %RANDOM
Rwork0.16563 ---
obs0.16766 39588 99.98 %-
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: 41.565 Å2
Baniso -1Baniso -2Baniso -3
1-2.06 Å21.03 Å20 Å2
2--2.06 Å20 Å2
3----3.08 Å2
Refinement stepCycle: LAST / Resolution: 2→68.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3604 0 124 250 3978
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0213818
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7521.9525181
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2345489
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.79424.183153
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.215597
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4381521
X-RAY DIFFRACTIONr_chiral_restr0.1070.2582
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.0213122
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_it1.6161.52419
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.31523839
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.85131399
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.594.51339
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
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.329 149 -
Rwork0.27 2849 -
obs--100 %
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)
10.87440.07010.50190.35990.39651.1727-0.0148-0.04770.0106-0.0130.176-0.1004-0.08160.3368-0.16130.008-0.0240.00670.1818-0.11570.1062-18.243429.5398-13.8584
20.68110.1646-0.16870.6520.63951.98350.0218-0.09210.0215-0.07310.03610.0156-0.09690.1263-0.0580.0197-0.0165-0.00980.0759-0.05730.0811-31.689428.9298-20.4672
318.38243.77873.64615.10312.70253.0186-0.2027-1.3484-0.49010.4074-0.05450.23870.80540.01870.25720.44890.08350.04350.23510.04640.1869-33.41619.3933-12.4633
40.68380.5573-0.1561.10020.71842.35890.09810.0741-0.06750.03650.0269-0.03420.1736-0.0172-0.1250.07360.0081-0.03910.0854-0.07070.1112-29.968717.1722-23.002
51.2882-0.01210.39982.23941.0632.8138-0.1901-0.09260.3671-0.3593-0.31990.2912-0.8598-0.51690.510.33510.2313-0.2260.1764-0.16230.2159-55.373254.04-17.1138
61.0753-0.105-0.1090.58210.82471.3763-0.0909-0.04020.1059-0.2211-0.07040.0563-0.3695-0.17240.16130.12950.0426-0.05870.0577-0.06950.105-41.89841.2031-18.9122
76.99824.7352-2.24053.2054-1.51550.7195-0.22011.08250.8858-0.11710.62770.60830.0082-0.3515-0.40761.28290.018-0.21370.35550.03710.5454-41.305549.0374-34.7352
82.23250.08390.68031.86881.36053.7065-0.1576-0.10920.1891-0.4045-0.19930.0411-0.5738-0.12520.35690.16850.0971-0.11510.0817-0.07990.141-52.912136.8469-32.2917
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 147
2X-RAY DIFFRACTION2A148 - 192
3X-RAY DIFFRACTION3A211 - 223
4X-RAY DIFFRACTION4A224 - 257
5X-RAY DIFFRACTION5B2 - 87
6X-RAY DIFFRACTION6B88 - 188
7X-RAY DIFFRACTION7B189 - 203
8X-RAY DIFFRACTION8B210 - 257

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