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- PDB-4z9r: Crystal structure of PfaD from Shewanella oneidensis in complex w... -

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Basic information

Entry
Database: PDB / ID: 4z9r
TitleCrystal structure of PfaD from Shewanella oneidensis in complex with NAD+ determined by in-situ diffraction.
ComponentsOmega-3 polyunsaturated fatty acid synthase subunit PfaD
KeywordsOXIDOREDUCTASE / PfaD / NAD+ / In-situ
Function / homology
Function and homology information


nucleotide binding / metal ion binding
Similarity search - Function
Fatty acid synthase subunit PfaD, N-terminal / Fatty acid synthase subunit PfaD N-terminal domain / PfaD family protein / : / [Acyl-carrier-protein] S-malonyltransferase, inserted helical domain / Nitronate monooxygenase / Aldolase-type TIM barrel
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Omega-3 polyunsaturated fatty acid synthase subunit PfaD
Similarity search - Component
Biological speciesShewanella oneidensis MR-1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsBaker, G.E. / Race, P.R.
CitationJournal: To Be Published
Title: Crystal structure of PfaD from Shewanella oneidensis in complex with NAD+ determined by in-situ diffraction.
Authors: Baker, G.E. / Race, P.R.
History
DepositionApr 11, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Apr 6, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Omega-3 polyunsaturated fatty acid synthase subunit PfaD
B: Omega-3 polyunsaturated fatty acid synthase subunit PfaD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,5816
Polymers119,3422
Non-polymers2,2404
Water1,08160
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7200 Å2
ΔGint-45 kcal/mol
Surface area38740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.680, 106.680, 217.477
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: PRO / Beg label comp-ID: PRO / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: _ / Auth seq-ID: 20 - 544 / Label seq-ID: 20 - 544

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Omega-3 polyunsaturated fatty acid synthase subunit PfaD


Mass: 59670.934 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shewanella oneidensis MR-1 (bacteria) / Gene: pfaD, SO_1597 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8EGK4
#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-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 60 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.59 Å3/Da / Density % sol: 52.55 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2 M potassium/sodium tartate, 0.1 M Bis tris propane at pH 8.5 and 20 % (w/v) polyethylene glycol.

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 3, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 2.8→48.44 Å / Num. obs: 30357 / % possible obs: 95.9 % / Observed criterion σ(I): 9.6 / Redundancy: 4.7 % / Rmerge(I) obs: 0.278 / Net I/σ(I): 9.6
Reflection shellRmerge(I) obs: 0.971 / Mean I/σ(I) obs: 3.4 / % possible all: 95.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
PHASERphasing
Cootmodel building
XDSdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4YX6

4yx6


Resolution: 2.8→48.44 Å / Cor.coef. Fo:Fc: 0.909 / Cor.coef. Fo:Fc free: 0.871 / SU B: 15.415 / SU ML: 0.298 / Cross valid method: THROUGHOUT / ESU R Free: 0.374 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2527 1477 4.9 %RANDOM
Rwork0.2122 ---
obs0.21418 28792 95.33 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.51 Å2
Baniso -1Baniso -2Baniso -3
1-1.26 Å20 Å20 Å2
2--1.26 Å20 Å2
3----2.52 Å2
Refinement stepCycle: 1 / Resolution: 2.8→48.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7315 0 150 60 7525
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0197605
X-RAY DIFFRACTIONr_bond_other_d0.0010.027075
X-RAY DIFFRACTIONr_angle_refined_deg0.8051.98210351
X-RAY DIFFRACTIONr_angle_other_deg0.583316146
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.125981
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.98623.979289
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.312151124
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5221541
X-RAY DIFFRACTIONr_chiral_restr0.0440.21186
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.028651
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021704
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_it2.4393.2423972
X-RAY DIFFRACTIONr_mcbond_other2.4373.2423971
X-RAY DIFFRACTIONr_mcangle_it3.9434.8344937
X-RAY DIFFRACTIONr_mcangle_other3.9444.8354938
X-RAY DIFFRACTIONr_scbond_it2.8063.5393633
X-RAY DIFFRACTIONr_scbond_other2.8063.543632
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.5045.2155415
X-RAY DIFFRACTIONr_long_range_B_refined6.49125.9128640
X-RAY DIFFRACTIONr_long_range_B_other6.49125.9118641
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 49690 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.14 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.8→2.873 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.332 99 -
Rwork0.283 2069 -
obs--94.59 %

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