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- PDB-2j2f: The T199D Mutant of Stearoyl Acyl Carrier Protein Desaturase from... -

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Basic information

Entry
Database: PDB / ID: 2j2f
TitleThe T199D Mutant of Stearoyl Acyl Carrier Protein Desaturase from Ricinus Communis (Castor Bean)
ComponentsACYL-[ACYL-CARRIER-PROTEIN] DESATURASE
KeywordsOXIDOREDUCTASE / ELECTRON TRANSFER / FOUR-HELIX BUNDLE / LIPID SYNTHESIS / TRANSIT PEPTIDE / FATTY ACID BIOSYNTHESIS / NADP / CHLOROPLAST / DI-RON ENZYME
Function / homology
Function and homology information


stearoyl-[acyl-carrier-protein] 9-desaturase / stearoyl-[acp] desaturase activity / acyl-[acyl-carrier-protein] desaturase activity / stearoyl-CoA 9-desaturase activity / chloroplast stroma / fatty acid biosynthetic process / defense response / metal ion binding / cytosol
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: 2.65 Å
AuthorsGuy, J.E. / Abreu, I.A. / Moche, M. / Lindqvist, Y. / Whittle, E. / Shanklin, J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2006
Title: A Single Mutation in the Castor {Delta}9-18:0- Desaturase Changes Reaction Partitioning from Desaturation to Oxidase Chemistry.
Authors: Guy, J.E. / Abreu, I.A. / Moche, M. / Lindqvist, Y. / Whittle, E. / Shanklin, J.
History
DepositionAug 16, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 23, 2006Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / 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_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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_asym_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
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)250,97418
Polymers250,3046
Non-polymers67012
Water2,846158
1
A: ACYL-[ACYL-CARRIER-PROTEIN] DESATURASE
F: ACYL-[ACYL-CARRIER-PROTEIN] DESATURASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,6586
Polymers83,4352
Non-polymers2234
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: ACYL-[ACYL-CARRIER-PROTEIN] DESATURASE
C: ACYL-[ACYL-CARRIER-PROTEIN] DESATURASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,6586
Polymers83,4352
Non-polymers2234
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
D: ACYL-[ACYL-CARRIER-PROTEIN] DESATURASE
E: ACYL-[ACYL-CARRIER-PROTEIN] DESATURASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,6586
Polymers83,4352
Non-polymers2234
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)82.049, 145.768, 193.245
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
11C
21B
31A
41D
51E
61F

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111C18 - 363
2111B18 - 363
3111A18 - 363
4111D18 - 363
5111E18 - 363
6111F18 - 363
1211C370 - 371
2211B370 - 371
3211A370 - 371
4211D370 - 371
5211E370 - 371
6211F370 - 371
1311C373 - 374
2311B373 - 374
3311A373 - 374
4311D373 - 374
5311E373 - 374
6311F373 - 374

NCS oper:
IDCodeMatrixVector
1given(-0.99992, -0.01121, 0.00623), (-0.01154, 0.99845, -0.05437), (-0.00561, -0.05443, -0.9985)-74.23451, -2.06941, -53.65149
2given(0.99991, 0.01311, -0.00051), (0.00702, -0.50213, 0.86477), (0.01108, -0.86469, -0.50218)54.66861, 28.85051, -36.5457
3given(-0.99975, -0.0139, 0.01767), (-0.00775, -0.52444, -0.85141), (0.0211, -0.85133, 0.5242)-101.28857, -18.0007, -8.26376
4given(0.99975, 0.02158, 0.00494), (0.0154, -0.5176, -0.85548), (-0.01591, 0.85535, -0.51781)27.38794, -16.59148, -44.3969
5given(-0.99997, -0.00806, -0.00213), (0.00182, -0.46076, 0.88752), (-0.00813, 0.88749, 0.46076)-129.26241, 28.91237, -18.00307

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Components

#1: Protein
ACYL-[ACYL-CARRIER-PROTEIN] DESATURASE / STEAROYL ACP DESATURASE / DELTA 9 STEAROYL-ACYL CARRIER PROTEIN DESATURASE


Mass: 41717.297 Da / Num. of mol.: 6 / Fragment: RESIDUES 34-396 / Mutation: YES
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(DE3) / References: UniProt: P22337, EC: 1.14.99.6
#2: Chemical
ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Fe
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 158 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, THR 232 TO ASP ENGINEERED RESIDUE IN CHAIN B, THR 232 TO ASP ...ENGINEERED RESIDUE IN CHAIN A, THR 232 TO ASP ENGINEERED RESIDUE IN CHAIN B, THR 232 TO ASP ENGINEERED RESIDUE IN CHAIN C, THR 232 TO ASP ENGINEERED RESIDUE IN CHAIN D, THR 232 TO ASP ENGINEERED RESIDUE IN CHAIN E, THR 232 TO ASP ENGINEERED RESIDUE IN CHAIN F, THR 232 TO ASP
Sequence detailsMUTANT - T199D

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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: 2.42 Å3/Da / Density % sol: 48.77 %
Crystal growpH: 5.4
Details: 0.08M CACODYLATE PH 5.4 0.2M MAGNESIUM ACETATE 75MM AMMONIUM SULFATE 16-18% PEG 4000 0.2% BOG

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.931
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.931 Å / Relative weight: 1
ReflectionResolution: 2.65→40 Å / Num. obs: 68082 / % possible obs: 98.4 % / Observed criterion σ(I): 2 / Redundancy: 3.3 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 9.6
Reflection shellResolution: 2.65→2.79 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 2.3 / % possible all: 98.4

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1AFR

1afr


Resolution: 2.65→40 Å / Cor.coef. Fo:Fc: 0.915 / Cor.coef. Fo:Fc free: 0.891 / SU B: 31.663 / SU ML: 0.321 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.383 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.272 3388 5.1 %RANDOM
Rwork0.24 ---
obs0.242 68033 98.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.87 Å2
Baniso -1Baniso -2Baniso -3
1--2.51 Å20 Å20 Å2
2---1.08 Å20 Å2
3---3.59 Å2
Refinement stepCycle: LAST / Resolution: 2.65→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16885 0 12 158 17055
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.02217290
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3711.95523417
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.50752075
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.92923.771875
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.554153015
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.90715144
X-RAY DIFFRACTIONr_chiral_restr0.090.22489
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213343
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2420.29149
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3160.212099
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1850.2611
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3760.2118
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3190.210
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3881.510644
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.483216842
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.84437513
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.0994.56575
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 2801 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Ctight positional0.060.05
2Btight positional0.050.05
3Atight positional0.050.05
4Dtight positional0.060.05
5Etight positional0.050.05
6Ftight positional0.050.05
1Ctight thermal0.120.5
2Btight thermal0.120.5
3Atight thermal0.10.5
4Dtight thermal0.120.5
5Etight thermal0.110.5
6Ftight thermal0.110.5
LS refinement shellResolution: 2.65→2.72 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.328 246
Rwork0.316 4669
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 °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.87970.0175-0.17412.77681.75061.9560.2119-0.61791.5781-0.34760.1572-0.3715-0.86290.1274-0.3692-0.0173-0.04070.1502-0.0798-0.34490.5891-63.993929.7572-12.2226
21.7466-0.24790.73732.719-1.96632.0082-0.21110.28620.75770.325-0.0693-0.0116-0.62720.18450.2805-0.1603-0.0314-0.1123-0.22560.0527-0.0543-10.654729.0617-42.6778
31.7951-0.16230.70081.1537-0.68512.62950.18180.813-0.1454-0.7256-0.15850.10290.72940.3972-0.02340.07440.141-0.0611-0.0192-0.0677-0.258-8.92122.8778-56.8619
42.25710.42180.03733.74651.20070.735-0.11140.4971-0.5972-0.69670.0349-0.16940.0398-0.04720.0765-0.1228-0.03550.0789-0.1562-0.1113-0.1613-37.9508-22.6826-41.3969
51.90780.91330.14262.8866-0.35071.03360.2673-0.8491-0.57811.0385-0.3501-0.28050.3394-0.06330.08280.1275-0.1268-0.02770.0560.1109-0.1161-36.0182-22.5172-11.6049
63.46960.0292-0.20342.08820.91872.60560.0049-1.83180.05751.09890.2116-0.32410.71080.2129-0.21640.16380.1-0.11140.5793-0.0916-0.1877-65.44034.17053.3204
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A19 - 363
2X-RAY DIFFRACTION1A370 - 371
3X-RAY DIFFRACTION2B19 - 363
4X-RAY DIFFRACTION2B370 - 371
5X-RAY DIFFRACTION3C19 - 363
6X-RAY DIFFRACTION3C370 - 371
7X-RAY DIFFRACTION4D19 - 363
8X-RAY DIFFRACTION4D370 - 371
9X-RAY DIFFRACTION5E19 - 363
10X-RAY DIFFRACTION5E370 - 371
11X-RAY DIFFRACTION6F19 - 363
12X-RAY DIFFRACTION6F370 - 371

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