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- PDB-4nk5: Crystal structure of FabI-NAD complex from Candidatus Liberibacte... -

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Basic information

Entry
Database: PDB / ID: 4nk5
TitleCrystal structure of FabI-NAD complex from Candidatus Liberibacter asiaticus
ComponentsEnoyl-[acyl-carrier-protein] reductase [NADH]
KeywordsOXIDOREDUCTASE / Enoyl-ACP Reductase I
Function / homologyNAD(P)-binding Rossmann-like Domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / :
Function and homology information
Biological speciesCandidatus Liberibacter asiaticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsJiang, L. / Gao, Z.Q. / Dong, Y.H.
CitationJournal: Protein Sci. / Year: 2014
Title: Crystal structures and kinetic properties of enoyl-acyl carrier protein reductase I from Candidatus Liberibacter asiaticus.
Authors: Jiang, L. / Gao, Z. / Li, Y. / Wang, S. / Dong, Y.
History
DepositionNov 12, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 12, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 9, 2014Group: Database references
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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]
C: Enoyl-[acyl-carrier-protein] reductase [NADH]
D: Enoyl-[acyl-carrier-protein] reductase [NADH]
E: Enoyl-[acyl-carrier-protein] reductase [NADH]
F: Enoyl-[acyl-carrier-protein] reductase [NADH]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)200,84910
Polymers198,1966
Non-polymers2,6544
Water4,216234
1
A: Enoyl-[acyl-carrier-protein] reductase [NADH]
B: Enoyl-[acyl-carrier-protein] reductase [NADH]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,7293
Polymers66,0652
Non-polymers6631
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4320 Å2
ΔGint-35 kcal/mol
Surface area21760 Å2
MethodPISA
2
C: Enoyl-[acyl-carrier-protein] reductase [NADH]
D: Enoyl-[acyl-carrier-protein] reductase [NADH]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,3924
Polymers66,0652
Non-polymers1,3272
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5510 Å2
ΔGint-41 kcal/mol
Surface area21520 Å2
MethodPISA
3
E: Enoyl-[acyl-carrier-protein] reductase [NADH]
F: Enoyl-[acyl-carrier-protein] reductase [NADH]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,7293
Polymers66,0652
Non-polymers6631
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4380 Å2
ΔGint-33 kcal/mol
Surface area21780 Å2
MethodPISA
4
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)133,4576
Polymers132,1304
Non-polymers1,3272
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area17480 Å2
ΔGint-133 kcal/mol
Surface area34670 Å2
MethodPISA
5
C: Enoyl-[acyl-carrier-protein] reductase [NADH]
D: Enoyl-[acyl-carrier-protein] reductase [NADH]
E: Enoyl-[acyl-carrier-protein] reductase [NADH]
F: Enoyl-[acyl-carrier-protein] reductase [NADH]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,1217
Polymers132,1304
Non-polymers1,9903
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18900 Å2
ΔGint-144 kcal/mol
Surface area34300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)203.272, 203.272, 82.432
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-410-

HOH

21B-301-

HOH

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Components

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


Mass: 33032.586 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candidatus Liberibacter asiaticus (bacteria)
Gene: WSI_01645 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: M4Q2P0, enoyl-[acyl-carrier-protein] reductase (NADH)
#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 234 / 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: 2.48 Å3/Da / Density % sol: 50.41 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 35% v/v 2-ethoxyethanol, 0.1 M cacodylate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 19, 2012
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. all: 52181 / Num. obs: 52181 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.6 % / Rmerge(I) obs: 0.134 / Net I/σ(I): 12.9
Reflection shellResolution: 2.7→2.75 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.464 / Mean I/σ(I) obs: 2.56 / Num. unique all: 2624 / % possible all: 97

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3GRK

3grk


Resolution: 2.7→47.804 Å / SU ML: 0.43 / σ(F): 1.33 / Phase error: 26.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2575 2646 5.08 %RANDOM
Rwork0.1867 ---
all0.1903 52181 --
obs0.1867 52096 96.7 %-
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 36.512 Å2 / ksol: 0.338 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-3.077 Å2-0 Å2-0 Å2
2--3.077 Å20 Å2
3----6.154 Å2
Refinement stepCycle: LAST / Resolution: 2.7→47.804 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11838 0 176 234 12248
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00812291
X-RAY DIFFRACTIONf_angle_d1.22416669
X-RAY DIFFRACTIONf_dihedral_angle_d16.1134543
X-RAY DIFFRACTIONf_chiral_restr0.0831871
X-RAY DIFFRACTIONf_plane_restr0.0052108
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.74910.40081120.29762628X-RAY DIFFRACTION97
2.7491-2.8020.33331530.25822589X-RAY DIFFRACTION98
2.802-2.85920.3441390.24472626X-RAY DIFFRACTION97
2.8592-2.92130.30391450.21872602X-RAY DIFFRACTION98
2.9213-2.98930.29231200.21952630X-RAY DIFFRACTION98
2.9893-3.0640.30881280.22562596X-RAY DIFFRACTION97
3.064-3.14690.3141490.20682617X-RAY DIFFRACTION98
3.1469-3.23940.29241490.21812602X-RAY DIFFRACTION98
3.2394-3.3440.3441360.2212603X-RAY DIFFRACTION97
3.344-3.46350.29231420.21382581X-RAY DIFFRACTION97
3.4635-3.60210.27641580.20682571X-RAY DIFFRACTION96
3.6021-3.7660.28381390.21382603X-RAY DIFFRACTION97
3.766-3.96440.2091320.17222591X-RAY DIFFRACTION96
3.9644-4.21270.23441410.15112606X-RAY DIFFRACTION97
4.2127-4.53770.19041530.14422552X-RAY DIFFRACTION96
4.5377-4.99390.22021500.13312589X-RAY DIFFRACTION96
4.9939-5.71550.2161520.1522596X-RAY DIFFRACTION96
5.7155-7.1970.23451290.18882618X-RAY DIFFRACTION95
7.197-47.81190.20281190.14972650X-RAY DIFFRACTION93
Refinement TLS params.Method: refined / Origin x: -76.542 Å / Origin y: -31.707 Å / Origin z: -2.82 Å
111213212223313233
T-0.213 Å20.0792 Å2-0.0419 Å2-0.0673 Å20.017 Å2---0.0085 Å2
L0.0684 °20.0061 °20.0711 °2--0.0053 °2-0.0263 °2--0.0498 °2
S-0.0207 Å °-0.0576 Å °0.0254 Å °0.0462 Å °-0.0953 Å °0.0312 Å °0.0039 Å °-0.1854 Å °-0.0885 Å °
Refinement TLS groupSelection details: all

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