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- PDB-1oq9: The Crystal Structure of the Complex between Stearoyl Acyl Carrie... -

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Basic information

Entry
Database: PDB / ID: 1oq9
TitleThe Crystal Structure of the Complex between Stearoyl Acyl Carrier Protein Desaturase from Ricinus Communis (Castor Bean) and Acetate.
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
ACETATE ION / : / Stearoyl-[acyl-carrier-protein] 9-desaturase, chloroplastic
Similarity search - Component
Biological speciesRicinus communis (castor bean)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 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: Advisory / Derived calculations ...Advisory / Derived calculations / Refinement description / Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,8744
Polymers41,7031
Non-polymers1713
Water1,31573
1
A: Acyl-[acyl-carrier protein] desaturase
hetero molecules

A: Acyl-[acyl-carrier protein] desaturase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,7488
Polymers83,4072
Non-polymers3416
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555x,x-y,-z1
Buried area6860 Å2
ΔGint-71 kcal/mol
Surface area27100 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)94.110, 94.110, 81.783
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number151
Space group name H-MP3112

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Components

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


Mass: 41703.312 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ricinus communis (castor bean) / Plasmid: pET9d / Production host: Escherichia coli (E. coli)
References: UniProt: P22337, stearoyl-[acyl-carrier-protein] 9-desaturase
#2: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 73 / 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: 2.65 Å3/Da / Density % sol: 53.15 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: 12-15% Peg4000, 80mM Cacodylate, 200mM Magnesium Acetate, 75mM Ammonium Sulphate, 0.2% Octyl glucoside, 20% Glycerol, pH 6.2, 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: NSLS / Beamline: X12B / Wavelength: 0.987 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 18, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.4→25 Å / Num. all: 16342 / Num. obs: 16245 / % possible obs: 99.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rsym value: 0.043 / Net I/σ(I): 13.5
Reflection shellResolution: 2.4→2.53 Å / Mean I/σ(I) obs: 2.8 / Rsym value: 0.283 / % possible all: 98.9
Reflection
*PLUS
Lowest resolution: 253 Å / Rmerge(I) obs: 0.043
Reflection shell
*PLUS
% possible obs: 98.9 % / Rmerge(I) obs: 0.283

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→25 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.911 / SU B: 9.161 / SU ML: 0.211 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.436 / ESU R Free: 0.277 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26447 819 5 %RANDOM
Rwork0.21582 ---
all0.21812 16342 --
obs0.21812 15426 99.42 %-
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: 44.845 Å2
Baniso -1Baniso -2Baniso -3
1-1.02 Å20.51 Å20 Å2
2--1.02 Å20 Å2
3----1.52 Å2
Refinement stepCycle: LAST / Resolution: 2.4→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2743 0 6 73 2822
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0212813
X-RAY DIFFRACTIONr_angle_refined_deg1.0241.9473809
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6915336
X-RAY DIFFRACTIONr_chiral_restr0.0690.2408
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022159
X-RAY DIFFRACTIONr_nbd_refined0.1890.21259
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1470.291
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1490.261
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.20.220
X-RAY DIFFRACTIONr_mcbond_it0.3411.51692
X-RAY DIFFRACTIONr_mcangle_it0.65822738
X-RAY DIFFRACTIONr_scbond_it1.05931121
X-RAY DIFFRACTIONr_scangle_it1.7444.51071
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.282 59
Rwork0.274 1098
Refinement TLS params.Method: refined / Origin x: 76.978 Å / Origin y: 27.904 Å / Origin z: 0.375 Å
111213212223313233
T0.0193 Å20.06 Å20.0581 Å2-0.3744 Å20.1334 Å2--0.1867 Å2
L3.8359 °20.4257 °20.4678 °2-0.7245 °2-0.173 °2--2.7417 °2
S-0.0374 Å °-0.3512 Å °0.1439 Å °-0.417 Å °-0.5604 Å °-0.1123 Å °0.1827 Å °1.1304 Å °0.5978 Å °
Refinement
*PLUS
Highest resolution: 2.4 Å / Rfactor Rfree: 0.264 / Rfactor Rwork: 0.216
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.009
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.02
LS refinement shell
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 2.453 Å

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