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- PDB-4jro: Crystal structure of 3-oxoacyl-[acyl-carrier protein]reductase (F... -

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Basic information

Entry
Database: PDB / ID: 4jro
TitleCrystal structure of 3-oxoacyl-[acyl-carrier protein]reductase (FabG)from Listeria monocytogenes in complex with NADP+
ComponentsFabG protein
KeywordsOXIDOREDUCTASE / STRUCTURAL GENOMICS / CENTER FOR STRUCTURAL GENOMICS OF INFECTIOUS DISEASES / CSGID / short chain dehydrogenase / FabG / beta-ketoacyl-acyl carrier protein reductase
Function / homology
Function and homology information


: / : / 3-oxoacyl-[acyl-carrier-protein] reductase / 3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity / fatty acid biosynthetic process / NAD binding
Similarity search - Function
3-oxoacyl-(acyl-carrier-protein) reductase / Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / 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 / 3-oxoacyl-[acyl-carrier-protein] reductase
Similarity search - Component
Biological speciesListeria monocytogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.92 Å
AuthorsHou, J. / Zheng, H. / Cooper, D.R. / Osinski, T. / Shatsman, S. / Anderson, W.F. / Minor, W. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: Crystal structure of 3-oxoacyl-[acyl-carrier protein]reductase (FabG)from Listeria monocytogenes in complex with NADP+
Authors: Hou, J. / Zheng, H. / Cooper, D.R. / Osinski, T. / Shatsman, S. / Anderson, W.F. / Minor, W. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionMar 21, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 3, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software
Revision 1.2Apr 13, 2022Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / database_2 / struct_ref_seq_dif / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _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
Revision 1.3Feb 28, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: FabG protein
B: FabG protein
C: FabG protein
D: FabG protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,3067
Polymers116,0764
Non-polymers2,2303
Water10,521584
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16190 Å2
ΔGint-85 kcal/mol
Surface area33340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.977, 93.695, 89.079
Angle α, β, γ (deg.)90.000, 103.840, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
FabG protein


Mass: 29019.068 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria monocytogenes (bacteria) / Strain: EGD-e / Gene: fabG, lmo1807, NT01LM1948 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL / References: UniProt: Q8Y690
#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE / Nicotinamide adenine dinucleotide phosphate


Mass: 743.405 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 584 / 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: 2.27 Å3/Da / Density % sol: 45.77 %
Crystal growTemperature: 289 K / Method: vapor diffusion / pH: 8.5
Details: 0.200M Trimethylamine N-oxide, 0.100M Tris, 20% w/v PEG 2K MME, pH 8.5, vapor diffusion, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.9792 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 6, 2013 / Details: MIRRORS
RadiationMonochromator: SI 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.92→50 Å / Num. obs: 77534 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.1 % / Biso Wilson estimate: 25.6 Å2 / Rmerge(I) obs: 0.094 / Net I/σ(I): 22.8
Reflection shellResolution: 1.92→1.95 Å / Redundancy: 3 % / Rmerge(I) obs: 0.432 / Mean I/σ(I) obs: 3 / Num. unique all: 3889 / % possible all: 99.2

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.11data extraction
HKL-3000data collection
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.92→46.89 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.944 / WRfactor Rfree: 0.1989 / WRfactor Rwork: 0.1614 / Occupancy max: 1 / Occupancy min: 0.2 / FOM work R set: 0.88 / SU B: 2.942 / SU ML: 0.086 / SU R Cruickshank DPI: 0.1395 / SU Rfree: 0.1298 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.139 / ESU R Free: 0.13 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2013 3887 5 %RANDOM
Rwork0.1633 ---
obs0.1652 77508 98.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 70.66 Å2 / Biso mean: 25.5825 Å2 / Biso min: 11.94 Å2
Baniso -1Baniso -2Baniso -3
1-1.08 Å2-0 Å2-0.77 Å2
2---1.68 Å20 Å2
3---0.7 Å2
Refinement stepCycle: LAST / Resolution: 1.92→46.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7161 0 144 584 7889
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0197415
X-RAY DIFFRACTIONr_bond_other_d0.0010.027253
X-RAY DIFFRACTIONr_angle_refined_deg1.3241.98410052
X-RAY DIFFRACTIONr_angle_other_deg0.752316594
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4195976
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.40825.406283
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.243151262
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9551537
X-RAY DIFFRACTIONr_chiral_restr0.0750.21202
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.028478
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021590
LS refinement shellResolution: 1.92→1.974 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.28 270 -
Rwork0.213 5310 -
all-5580 -
obs--96.16 %

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