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- PDB-5i7e: Crystal structure of B. pseudomallei FabI in apo form -

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Basic information

Entry
Database: PDB / ID: 5i7e
TitleCrystal structure of B. pseudomallei FabI in apo form
ComponentsEnoyl-[acyl-carrier-protein] reductase [NADH]
KeywordsOXIDOREDUCTASE / enoyl-ACP reductase / Burkholderia pseudomallei
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] / Enoyl-[acyl-carrier-protein] reductase [NADH]
Similarity search - Component
Biological speciesBurkholderia pseudomallei (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsHirschbeck, M.W. / Eltschkner, S. / Tonge, P.J. / Kisker, C.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationSFB 630 Germany
CitationJournal: Biochemistry / Year: 2017
Title: Rationalizing the Binding Kinetics for the Inhibition of the Burkholderia pseudomallei FabI1 Enoyl-ACP Reductase.
Authors: Neckles, C. / Eltschkner, S. / Cummings, J.E. / Hirschbeck, M. / Daryaee, F. / Bommineni, G.R. / Zhang, Z. / Spagnuolo, L. / Yu, W. / Davoodi, S. / Slayden, R.A. / Kisker, C. / Tonge, P.J.
History
DepositionFeb 17, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Feb 22, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 8, 2017Group: Database references
Revision 1.2Apr 19, 2017Group: Database references
Revision 2.0Sep 6, 2017Group: Atomic model / Author supporting evidence / Category: atom_site / pdbx_audit_support
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _pdbx_audit_support.funding_organization
Revision 2.1Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)29,3251
Polymers29,3251
Non-polymers00
Water4,089227
1
A: Enoyl-[acyl-carrier-protein] reductase [NADH]

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

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

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


Theoretical massNumber of molelcules
Total (without water)117,3024
Polymers117,3024
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
crystal symmetry operation3_655-x+1,y,-z1
crystal symmetry operation4_555x,-y,-z1
Buried area13420 Å2
ΔGint-94 kcal/mol
Surface area34510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.686, 75.243, 85.706
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-411-

HOH

21A-482-

HOH

31A-499-

HOH

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Components

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


Mass: 29325.391 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia pseudomallei (bacteria)
Gene: fabI, fabI_2, ACT79_25590, AM256_11615, AM257_11635, AMS56_08605, DP46_2957, DP49_6839, ERS012314_03793, ERS012372_03823, SY87_14645, TR70_1075, VU09_13745
Production host: Escherichia coli (E. coli)
References: UniProt: A0A069B9A4, UniProt: A0A0H3HP34*PLUS, enoyl-[acyl-carrier-protein] reductase (NADH)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 227 / 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: 1.99 Å3/Da / Density % sol: 38.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1 M MES, pH 6.5, 30 % PEG 400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.849999 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 27, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.849999 Å / Relative weight: 1
ReflectionResolution: 1.65→37.62 Å / Num. obs: 28203 / % possible obs: 96.6 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.061 / Net I/σ(I): 13.1
Reflection shellResolution: 1.65→1.74 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.702 / Mean I/σ(I) obs: 2.2 / % possible all: 98.3

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Processing

Software
NameVersionClassification
PHENIX1.7.3_928refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ek2

3ek2


Resolution: 1.65→33.325 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.78
RfactorNum. reflection% reflection
Rfree0.1861 1421 5.04 %
Rwork0.1585 --
obs0.1599 28188 95.81 %
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Bsol: 51.777 Å2 / ksol: 0.367 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--4.1508 Å20 Å20 Å2
2--3.5551 Å20 Å2
3---0.5957 Å2
Refinement stepCycle: LAST / Resolution: 1.65→33.325 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1900 0 0 227 2127
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061979
X-RAY DIFFRACTIONf_angle_d1.0422693
X-RAY DIFFRACTIONf_dihedral_angle_d9.98718
X-RAY DIFFRACTIONf_chiral_restr0.074314
X-RAY DIFFRACTIONf_plane_restr0.004349
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.7090.27911540.22062694X-RAY DIFFRACTION98
1.709-1.77740.23681450.20182684X-RAY DIFFRACTION98
1.7774-1.85830.21141530.17072685X-RAY DIFFRACTION98
1.8583-1.95620.1971430.16632681X-RAY DIFFRACTION97
1.9562-2.07880.21671350.1592697X-RAY DIFFRACTION97
2.0788-2.23930.18741370.15742660X-RAY DIFFRACTION96
2.2393-2.46450.19041290.15412686X-RAY DIFFRACTION96
2.4645-2.8210.18061300.16182659X-RAY DIFFRACTION95
2.821-3.55350.18111520.15592632X-RAY DIFFRACTION93
3.5535-33.33170.16261430.14662689X-RAY DIFFRACTION92
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)
12.5514-0.1265-0.30871.4963-0.18063.62850.1439-0.11360.25310.0839-0.00670.0007-0.3247-0.3694-0.12390.19340.05280.04310.22990.02310.209110.90685.186616.8731
22.2724-0.0057-0.1060.4417-0.54892.2031-0.0262-0.32180.16120.13830.09290.0775-0.1893-0.2026-0.07460.21290.01430.01470.26080.01160.218912.80510.218224.3239
36.9632-0.2393-2.40981.0822-0.68341.50650.0274-0.44320.95140.2193-0.0053-0.0813-0.2943-0.1646-0.01120.30530.036-0.00580.2884-0.09880.337839.052614.371322.1688
41.71430.5744-0.22110.6426-0.10040.8526-0.0041-0.09220.0115-0.01140.0614-0.0119-0.0046-0.0313-0.05450.15190.01850.01890.1369-0.00430.149328.46980.575217.8933
50.8556-0.0655-0.05590.55620.50580.97370.0033-0.0580.01320.02880.02640.0030.0393-0.051-0.03430.1730.0060.00420.15030.0260.167828.5709-4.211212.4767
60.86270.7486-0.21771.5981-0.25480.0723-0.2819-0.67810.1201-0.12310.27190.1018-0.35110.23960.05470.29430.09040.01780.3014-0.0580.240825.742818.527113.7442
72.1996-0.3263-0.73972.41730.91795.0870.1383-0.13890.3010.2929-0.0254-0.3601-0.6580.4134-0.13760.3495-0.0277-0.01170.1617-0.01140.251228.212320.29421.4431
80.76320.07350.00920.9076-0.28481.2288-0.0174-0.03870.03270.05170.0746-0.0059-0.0695-0.1354-0.04630.16170.0233-0.00330.17140.01040.159721.17424.82732.6984
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 2:45)
2X-RAY DIFFRACTION2(chain A and resid 46:93)
3X-RAY DIFFRACTION3(chain A and resid 94:108)
4X-RAY DIFFRACTION4(chain A and resid 109:156)
5X-RAY DIFFRACTION5(chain A and resid 157:187)
6X-RAY DIFFRACTION6(chain A and resid 188:202)
7X-RAY DIFFRACTION7(chain A and resid 203:217)
8X-RAY DIFFRACTION8(chain A and resid 218:256)

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