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- PDB-1oqb: The Crystal Structure of the one-iron form of the di-iron center ... -

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Basic information

Entry
Database: PDB / ID: 1oqb
TitleThe Crystal Structure of the one-iron form of the di-iron center in Stearoyl Acyl Carrier Protein Desaturase from Ricinus Communis (Castor Bean).
ComponentsAcyl-[acyl-carrier protein] desaturase
KeywordsOXIDOREDUCTASE / di-iron enzyme / four-helix bundle / fatty acid biosynthesis / electron transfer
Function / homology
Function and homology information


stearoyl-[acyl-carrier-protein] 9-desaturase / stearoyl-[ACP] desaturase activity / chloroplast / fatty acid biosynthetic process / metal ion binding
Similarity search - Function
Fatty acid desaturase type 2, conserved site / Fatty acid desaturases family 2 signature. / Fatty acid desaturase, type 2 / Fatty acid desaturase / Ribonucleotide Reductase, subunit A / Ribonucleotide Reductase, subunit A / Ribonucleotide reductase-like / Ferritin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
: / Stearoyl-[acyl-carrier-protein] 9-desaturase, chloroplastic
Similarity search - Component
Biological speciesRicinus communis (castor bean)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsMoche, M. / Shanklin, J. / Ghoshal, A.K. / Lindqvist, Y.
CitationJournal: J.Biol.Chem. / Year: 2003
Title: Azide and Acetate Complexes plus two iron-depleted Crystal Structures of the Di-iron Enzyme delta9 Stearoyl-ACP Desaturase-Implications for Oxygen Activation and Catalytic Intermediates
Authors: Moche, M. / Shanklin, J. / Ghoshal, A. / Lindqvist, Y.
History
DepositionMar 7, 2003Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 13, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 23, 2018Group: Advisory / Data collection
Category: diffrn_source / pdbx_unobs_or_zero_occ_atoms / struct_biol
Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Mar 13, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _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

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Assembly

Deposited unit
A: Acyl-[acyl-carrier protein] desaturase
B: Acyl-[acyl-carrier protein] desaturase
C: Acyl-[acyl-carrier protein] desaturase
D: Acyl-[acyl-carrier protein] desaturase
E: Acyl-[acyl-carrier protein] desaturase
F: Acyl-[acyl-carrier protein] desaturase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)250,55512
Polymers250,2206
Non-polymers3356
Water905
1
A: Acyl-[acyl-carrier protein] desaturase
B: Acyl-[acyl-carrier protein] desaturase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,5184
Polymers83,4072
Non-polymers1122
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5830 Å2
ΔGint-39 kcal/mol
Surface area26600 Å2
MethodPISA
2
C: Acyl-[acyl-carrier protein] desaturase
D: Acyl-[acyl-carrier protein] desaturase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,5184
Polymers83,4072
Non-polymers1122
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5870 Å2
ΔGint-40 kcal/mol
Surface area26590 Å2
MethodPISA
3
E: Acyl-[acyl-carrier protein] desaturase
F: Acyl-[acyl-carrier protein] desaturase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,5184
Polymers83,4072
Non-polymers1122
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5780 Å2
ΔGint-40 kcal/mol
Surface area26670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.908, 145.791, 192.424
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: PHE / Beg label comp-ID: PHE / End auth comp-ID: FE2 / End label comp-ID: FE2 / Refine code: 1 / Auth seq-ID: 18 - 364 / Label seq-ID: 18

Dom-IDAuth asym-IDLabel asym-ID
1AA - G
2BB - H
3CC - I
4DD - J
5EE - K
6FF - L
DetailsThe enzyme is dimeric and the unit cell contains three of these dimers giving six protein chains

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Components

#1: Protein
Acyl-[acyl-carrier protein] desaturase / Stearoyl Acyl Carrier Protein Desaturase


Mass: 41703.312 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ricinus communis (castor bean) / Plasmid: pET9d / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 gold
References: UniProt: P22337, stearoyl-[acyl-carrier-protein] 9-desaturase
#2: Chemical
ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Fe
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / 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: 2.44 Å3/Da / Density % sol: 49.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 8-12% Peg8000, 50mM Potassium Dihydrogen Phosphate and 20% Glycerol as cryoprotectant, pH 4, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
pH: 5.4
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
170 mMsodium azide1drop
20.08 Mcacodylate1reservoirpH5.4
3200 mMmagnesium acetate1reservoir
475 mMammonium sulfate1reservoir
50.2 %octyl-glucoside1reservoir
612-15 %PEG40001reservoir

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 0.8423 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 29, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8423 Å / Relative weight: 1
ReflectionResolution: 2.8→20 Å / Num. all: 57328 / Num. obs: 45472 / % possible obs: 79.3 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Rsym value: 0.058 / Net I/σ(I): 12.1
Reflection shellResolution: 2.8→2.85 Å / Rsym value: 0.252 / % possible all: 32
Reflection
*PLUS
Lowest resolution: 20 Å / Rmerge(I) obs: 0.058
Reflection shell
*PLUS
% possible obs: 32 % / Rmerge(I) obs: 0.252

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→20 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.904 / SU B: 20.931 / SU ML: 0.384 / TLS residual ADP flag: UNVERIFIED / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.465 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24803 935 2.1 %RANDOM
Rwork0.22428 ---
all0.22477 57328 --
obs0.22477 44537 79.32 %-
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: 27.124 Å2
Baniso -1Baniso -2Baniso -3
1--3.53 Å20 Å20 Å2
2---1.92 Å20 Å2
3---5.45 Å2
Refinement stepCycle: LAST / Resolution: 2.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16836 0 6 5 16847
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.02117244
X-RAY DIFFRACTIONr_angle_refined_deg1.2391.94623352
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.35652070
X-RAY DIFFRACTIONr_chiral_restr0.0810.22490
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0213278
X-RAY DIFFRACTIONr_nbd_refined0.2310.28802
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1470.2537
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.4210.289
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2310.24
X-RAY DIFFRACTIONr_mcbond_it0.261.510374
X-RAY DIFFRACTIONr_mcangle_it0.546216788
X-RAY DIFFRACTIONr_scbond_it1.15236870
X-RAY DIFFRACTIONr_scangle_it1.9434.56564
Refine LS restraints NCS

Ens-ID: 1 / Number: 2807 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Atight positional0.030.05
2Btight positional0.040.05
3Ctight positional0.040.05
4Dtight positional0.040.05
5Etight positional0.030.05
6Ftight positional0.030.05
1Atight thermal0.060.5
2Btight thermal0.070.5
3Ctight thermal0.070.5
4Dtight thermal0.070.5
5Etight thermal0.060.5
6Ftight thermal0.060.5
LS refinement shellResolution: 2.8→2.872 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.326 31
Rwork0.315 1323
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 °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.0738-0.64160.17433.095-0.18761.1166-0.20680.0191.00810.828-0.2313-0.7459-0.3585-0.0390.25440.00260.01450.40320.20010.2393-35.41295.74511.247
22.8144-0.32940.21483.2910.8290.68710.265-0.2397-0.48870.7638-0.07750.4918-0.1532-0.00740.11540.0587-0.070.1819-0.08210.2349-37.996.50640.729
32.13780.2976-0.44211.3782-0.59142.7187-0.41960.0901-0.88780.1298-0.00090.7195-0.51150.34470.2844-0.1063-0.01210.3228-0.05840.1636-8.4570.44356.919
42.36140.3145-0.5842.0574-1.81562.19540.0826-0.4896-0.304-0.9538-0.1381-0.16850.52460.23650.11620.04680.09730.11520.04570.4037-10.8144.52742.912
52.80390.14630.24532.22980.97951.80790.08070.22610.5596-1.2019-0.2995-0.02850.71860.09120.2728-0.01190.00660.2613-0.15140.609518.7343.8112.236
63.1526-0.1228-0.4231.84050.70762.48510.03950.06491.4250.0522-0.1922-0.9566-0.3841-0.080.3958-0.09390.06010.65240.05350.214316.09369.005-3.247
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA - G18 - 36418 - 1
2X-RAY DIFFRACTION2BB - H18 - 36418 - 1
3X-RAY DIFFRACTION3CC - I18 - 36418 - 1
4X-RAY DIFFRACTION4DD - J18 - 36418 - 1
5X-RAY DIFFRACTION5EE - K18 - 36418 - 1
6X-RAY DIFFRACTION6FF - L18 - 36418 - 1
Refinement
*PLUS
Highest resolution: 2.8 Å / Rfactor Rfree: 0.248 / Rfactor Rwork: 0.224
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.013
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.24
LS refinement shell
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 2.85 Å

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