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- PDB-4v0j: The channel-block Ser202Glu, Thr104Lys double mutant of Stearoyl-... -

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Basic information

Entry
Database: PDB / ID: 4v0j
TitleThe channel-block Ser202Glu, Thr104Lys double mutant of Stearoyl-ACP- Desaturase from Castor bean (Ricinus communis)
ComponentsACYL-[ACYL-CARRIER-PROTEIN] DESATURASE, CHLOROPLASTIC
KeywordsOXIDOREDUCTASE
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. / Guy, J. / Whittle, E. / Lindqvist, Y. / Shanklin, J.
CitationJournal: Plant Physiol. / Year: 2015
Title: Half-of-the-Sites Reactivity of the Castor Delta9-18:0-Acp Desaturase.
Authors: Liu, Q. / Chai, J. / Moche, M. / Guy, J. / Lindqvist, Y. / Shanklin, J.
History
DepositionSep 17, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 26, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 23, 2015Group: Database references
Revision 1.2Jan 10, 2024Group: 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_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_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_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 / _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

Downloads & links

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Assembly

Deposited unit
A: ACYL-[ACYL-CARRIER-PROTEIN] DESATURASE, CHLOROPLASTIC
B: ACYL-[ACYL-CARRIER-PROTEIN] DESATURASE, CHLOROPLASTIC
C: ACYL-[ACYL-CARRIER-PROTEIN] DESATURASE, CHLOROPLASTIC
D: ACYL-[ACYL-CARRIER-PROTEIN] DESATURASE, CHLOROPLASTIC
E: ACYL-[ACYL-CARRIER-PROTEIN] DESATURASE, CHLOROPLASTIC
F: ACYL-[ACYL-CARRIER-PROTEIN] DESATURASE, CHLOROPLASTIC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)230,09421
Polymers229,1486
Non-polymers94615
Water34219
1
C: ACYL-[ACYL-CARRIER-PROTEIN] DESATURASE, CHLOROPLASTIC
D: ACYL-[ACYL-CARRIER-PROTEIN] DESATURASE, CHLOROPLASTIC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,6987
Polymers76,3832
Non-polymers3155
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5990 Å2
ΔGint-65.7 kcal/mol
Surface area25140 Å2
MethodPISA
2
E: ACYL-[ACYL-CARRIER-PROTEIN] DESATURASE, CHLOROPLASTIC
F: ACYL-[ACYL-CARRIER-PROTEIN] DESATURASE, CHLOROPLASTIC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,6987
Polymers76,3832
Non-polymers3155
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5910 Å2
ΔGint-66.4 kcal/mol
Surface area24890 Å2
MethodPISA
3
A: ACYL-[ACYL-CARRIER-PROTEIN] DESATURASE, CHLOROPLASTIC
B: ACYL-[ACYL-CARRIER-PROTEIN] DESATURASE, CHLOROPLASTIC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,6987
Polymers76,3832
Non-polymers3155
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5900 Å2
ΔGint-64.9 kcal/mol
Surface area24860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)139.719, 139.719, 86.871
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15A
25F
16B
26C
17B
27D
18B
28E
19B
29F
110C
210D
111C
211E
112C
212F
113D
213E
114D
214F
115E
215F

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PROPROLEULEUAA33 - 3631 - 331
21PROPROLEULEUBB33 - 3631 - 331
12GLNGLNLEULEUAA35 - 3633 - 331
22GLNGLNLEULEUCC35 - 3633 - 331
13PROPROLYSLYSAA34 - 3622 - 330
23PROPROLYSLYSDD34 - 3622 - 330
14PROPROLEULEUAA34 - 3632 - 331
24PROPROLEULEUEE34 - 3632 - 331
15PROPROLEULEUAA34 - 3632 - 331
25PROPROLEULEUFF34 - 3632 - 331
16GLNGLNLYSLYSBB35 - 3623 - 330
26GLNGLNLYSLYSCC35 - 3623 - 330
17PROPROLEULEUBB34 - 3632 - 331
27PROPROLEULEUDD34 - 3632 - 331
18PROPROLYSLYSBB34 - 3622 - 330
28PROPROLYSLYSEE34 - 3622 - 330
19PROPROLEULEUBB34 - 3632 - 331
29PROPROLEULEUFF34 - 3632 - 331
110GLNGLNLEULEUCC35 - 3633 - 331
210GLNGLNLEULEUDD35 - 3633 - 331
111GLNGLNLYSLYSCC35 - 3623 - 330
211GLNGLNLYSLYSEE35 - 3623 - 330
112GLNGLNLEULEUCC35 - 3633 - 331
212GLNGLNLEULEUFF35 - 3633 - 331
113PROPROLEULEUDD34 - 3632 - 331
213PROPROLEULEUEE34 - 3632 - 331
114PROPROLEULEUDD34 - 3632 - 331
214PROPROLEULEUFF34 - 3632 - 331
115PROPROLEULEUEE34 - 3632 - 331
215PROPROLEULEUFF34 - 3632 - 331

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15

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Components

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


Mass: 38191.273 Da / Num. of mol.: 6 / Fragment: RESIDUES 66-396 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) RICINUS COMMUNIS (castor bean) / Production host: ESCHERICHIA COLI (E. coli)
References: UniProt: P22337, stearoyl-[acyl-carrier-protein] 9-desaturase
#2: Chemical
ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 19 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsSER202GLU AND THR104LYS DOUBLE MUTANT. RESIDUES 1-65 OF P22337 IS NOT PRESENT IN THE CONSTRUCT.

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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: 2.14 Å3/Da / Density % sol: 42.43 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1
DetectorType: Brandeis B4 / Detector: CCD / Date: Jul 9, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→120 Å / Num. obs: 41961 / % possible obs: 93.6 % / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Biso Wilson estimate: 68.83 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 12.1
Reflection shellResolution: 2.8→2.95 Å / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 2.1 / % possible all: 71.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1AFR

1afr


Resolution: 2.8→119.52 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.9 / SU B: 20.137 / SU ML: 0.386 / Cross valid method: THROUGHOUT / ESU R Free: 0.473 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.26418 1772 4.1 %RANDOM
Rwork0.21183 ---
obs0.21399 41961 93.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 62.753 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å20.02 Å20 Å2
2--0.05 Å20 Å2
3----0.15 Å2
Refinement stepCycle: LAST / Resolution: 2.8→119.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15910 0 30 19 15959
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01916295
X-RAY DIFFRACTIONr_bond_other_d0.0070.0215377
X-RAY DIFFRACTIONr_angle_refined_deg1.3861.95522038
X-RAY DIFFRACTIONr_angle_other_deg1.304335418
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.02551952
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.97723.947826
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.511152866
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.01315130
X-RAY DIFFRACTIONr_chiral_restr0.0710.22351
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02118335
X-RAY DIFFRACTIONr_gen_planes_other0.0060.023779
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_it5.126.0557835
X-RAY DIFFRACTIONr_mcbond_other5.1196.0557834
X-RAY DIFFRACTIONr_mcangle_it7.8899.079778
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it5.0956.3988460
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A206200.07
12B206200.07
21A204950.07
22C204950.07
31A202990.07
32D202990.07
41A205620.07
42E205620.07
51A206100.08
52F206100.08
61B208200.06
62C208200.06
71B204550.08
72D204550.08
81B210070.06
82E210070.06
91B206460.07
92F206460.07
101C202350.09
102D202350.09
111C207300.07
112E207300.07
121C204580.07
122F204580.07
131D204630.08
132E204630.08
141D205210.07
142F205210.07
151E206770.07
152F206770.07
LS refinement shellResolution: 2.8→2.873 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.355 90 -
Rwork0.335 2223 -
obs--67.3 %

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