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- PDB-2xz1: The Structure of the 2:2 (Fully Occupied) Complex Between Stearoy... -

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Basic information

Entry
Database: PDB / ID: 2xz1
TitleThe Structure of the 2:2 (Fully Occupied) Complex Between Stearoyl Acyl Carrier Protein Desaturase from Ricinus Communis (Castor Bean) and Acyl Carrier Protein.
Components
  • ACYL CARRIER PROTEIN 1, CHLOROPLASTIC
  • ACYL-[ACYL-CARRIER-PROTEIN] DESATURASE, CHLOROPLASTIC
KeywordsOXIDOREDUCTASE/LIPID BINDING PROTEIN / OXIDOREDUCTASE-LIPID BINDING PROTEIN COMPLEX
Function / homology
Function and homology information


stearoyl-[acyl-carrier-protein] 9-desaturase / stearoyl-[ACP] desaturase activity / acyl carrier activity / phosphopantetheine binding / 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 / Acyl carrier protein, chloroplastic / ACP-like / Ribonucleotide Reductase, subunit A / Ribonucleotide Reductase, subunit A / Ribonucleotide reductase-like / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A ...Fatty acid desaturase type 2, conserved site / Fatty acid desaturases family 2 signature. / Fatty acid desaturase, type 2 / Fatty acid desaturase / Acyl carrier protein, chloroplastic / ACP-like / Ribonucleotide Reductase, subunit A / Ribonucleotide Reductase, subunit A / Ribonucleotide reductase-like / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / Acyl carrier protein (ACP) / Phosphopantetheine attachment site / Phosphopantetheine attachment site. / Ferritin-like superfamily / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
CACODYLATE ION / : / Chem-PNY / Acyl carrier protein 1, chloroplastic / Stearoyl-[acyl-carrier-protein] 9-desaturase, chloroplastic
Similarity search - Component
Biological speciesRICINUS COMMUNIS (castor bean)
SPINACIA OLERACEA (spinach)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.35 Å
AuthorsGuy, J.E. / Moche, M. / Whittle, E. / Lengqvist, J. / Shanklin, J. / Lindqvist, Y.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2011
Title: Remote Control of Regioselectivity in Acyl-Acyl Carrier Protein-Desaturases.
Authors: Guy, J.E. / Whittle, E. / Moche, M. / Lengqvist, J. / Lindqvist, Y. / Shanklin, J.
History
DepositionNov 22, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 7, 2011Provider: repository / Type: Initial release
Revision 1.1Oct 26, 2011Group: Database references
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_ncs_dom_lim / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _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.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_conn_type.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
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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 CARRIER PROTEIN 1, CHLOROPLASTIC
D: ACYL CARRIER PROTEIN 1, CHLOROPLASTIC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,11213
Polymers101,2564
Non-polymers8569
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9200 Å2
ΔGint-25.5 kcal/mol
Surface area45310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.404, 76.404, 403.372
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number95
Space group name H-MP4322
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21A
12C
22D

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111PROPROLEULEU1BB17 - 36317 - 363
211PROPROLEULEU1AA17 - 36317 - 363
121FEFEFEFE1BI - J401 - 402
221FEFEFEFE1AE - F401 - 402
112ALAALAASPASP6CC1 - 371 - 37
212ALAALAASPASP6DD1 - 371 - 37
122LEULEUALAALA4CC39 - 8239 - 82
222LEULEUALAALA4DD39 - 8239 - 82

NCS ensembles :
ID
1
2

NCS oper:
IDCodeMatrixVector
1given(-0.6935, -0.7205, -0.005791), (-0.7205, 0.6935, -0.001873), (0.005366, 0.002873, -1)53.32, 22.63, -50.99
2given(0.9894, 0.01811, 0.1444), (-0.02697, 0.9979, 0.05963), (-0.143, -0.06289, 0.9877)8.442, 5.173, 6.836

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Components

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Protein , 2 types, 4 molecules ABCD

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


Mass: 41703.312 Da / Num. of mol.: 2
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: Protein ACYL CARRIER PROTEIN 1, CHLOROPLASTIC / ACP I / ACYL CARRIER PROTEIN I


Mass: 8924.858 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: SER38 CHAIN D IS A PHOSPHOSERINE, IN CHAIN C IT IS ALSO LINKED TO A FRAGMENT OF PANTETHEINE
Source: (gene. exp.) SPINACIA OLERACEA (spinach) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P07854

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Non-polymers , 4 types, 9 molecules

#3: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-CAC / CACODYLATE ION / dimethylarsinate


Mass: 136.989 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6AsO2
#6: Chemical ChemComp-PNY / (2R)-2,4-dihydroxy-3,3-dimethyl-N-{3-oxo-3-[(2-sulfanylethyl)amino]propyl}butanamide / pantetheine / (R)-2,4-Dihydroxy-N-(3-((2-mercaptoethyl)amino)-3-oxopropyl)-3,3-dimethylbutanamide


Mass: 278.368 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H22N2O4S

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Details

Has protein modificationY
Sequence detailsSEQUENCE AS DESCRIBED IN BROADWATER AND FOX PROTEIN EXPRESSION AND PURIFICATION VOL 15, 314-326 (1999)

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.91 Å3/Da / Density % sol: 57.69 % / Description: NONE
Crystal growpH: 5.8
Details: 16-20% MPD,6-8% PEG20000, 0.1M SODIUM CACODYLATE PH 5.8, 4-6% ACETONITRILE

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 3.35→20 Å / Num. obs: 16101 / % possible obs: 92.7 % / Observed criterion σ(I): 2 / Redundancy: 2.6 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 9.7
Reflection shellResolution: 3.35→3.44 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 2.7 / % possible all: 96

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Processing

Software
NameVersionClassification
REFMAC5.5.0102refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1AFR

1afr


Resolution: 3.35→20 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.931 / SU B: 60.836 / SU ML: 0.445 / Cross valid method: THROUGHOUT / ESU R Free: 0.585 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.25451 857 5.1 %RANDOM
Rwork0.20933 ---
obs0.21155 16101 94.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 107.329 Å2
Baniso -1Baniso -2Baniso -3
1-2.51 Å20 Å20 Å2
2--2.51 Å20 Å2
3----5.01 Å2
Refinement stepCycle: LAST / Resolution: 3.35→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6923 0 25 0 6948
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0227084
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0941.9669593
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.5085861
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.68524.64347
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.48115.0121266
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9061548
X-RAY DIFFRACTIONr_chiral_restr0.0730.21058
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0215366
X-RAY DIFFRACTIONr_gen_planes_other
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
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

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
12A2815tight positional0.030.05
11B2815tight positional0.030.05
22A343medium positional0.490.5
22B343medium positional0.490.5
22A272loose positional0.515
22B272loose positional0.515
LS refinement shellResolution: 3.35→3.437 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.325 66 -
Rwork0.301 1164 -
obs--95.65 %
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)
12.02530.4873-0.7583.0386-0.19392.2152-0.0708-0.2671-0.10530.2380.00190.12810.1011-0.03220.06890.08950.05120.06160.1478-0.02870.115813.576717.8856-14.2148
23.3239-0.6489-1.10641.6956-0.25712.17210.01510.05390.0859-0.1723-0.11040.00530.01050.03110.09530.05720.0472-0.00690.04490.00720.039231.51725.7606-36.3897
38.8262-3.93091.53411.61863.51537.66960.20070.9544-0.3289-1.601-0.26390.7929-0.5676-0.8490.06320.76390.0869-0.01930.5329-0.00370.420739.492714.5488-71.1199
43.3866-3.09044.53362.8898-4.14486.1477-0.0538-0.07390.05040.143-0.0135-0.38140.08650.20.06731.53030.0248-0.04041.31570.02091.881913.63472.823421.2458
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A11 - 363
2X-RAY DIFFRACTION1A401 - 403
3X-RAY DIFFRACTION1A501
4X-RAY DIFFRACTION2B16 - 363
5X-RAY DIFFRACTION2B401 - 403
6X-RAY DIFFRACTION2B501
7X-RAY DIFFRACTION3C1 - 1138
8X-RAY DIFFRACTION4D1 - 82

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