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- PDB-2xz0: The Structure of the 2:1 (Partially Occupied) Complex Between Ste... -

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Basic information

Entry
Database: PDB / ID: 2xz0
TitleThe Structure of the 2:1 (Partially 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 / stearoyl-CoA 9-desaturase activity / chloroplast stroma / phosphopantetheine binding / acyl carrier activity / chloroplast / defense response / fatty acid biosynthetic process ...stearoyl-[acyl-carrier-protein] 9-desaturase / : / stearoyl-[ACP] desaturase activity / stearoyl-CoA 9-desaturase activity / chloroplast stroma / phosphopantetheine binding / acyl carrier activity / chloroplast / defense response / fatty acid biosynthetic process / metal ion binding / cytosol
Similarity search - Function
Fatty acid desaturase type 2, conserved site / Fatty acid desaturases family 2 signature. / Acyl carrier protein, chloroplastic / Fatty acid desaturase, type 2 / Fatty acid desaturase / 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. / Acyl carrier protein, chloroplastic / Fatty acid desaturase, type 2 / Fatty acid desaturase / 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
: / 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 Å
AuthorsMoche, M. / Guy, J.E. / 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 1.1Sep 14, 2011Group: Other
Revision 1.2Oct 26, 2011Group: Database references
Revision 1.3Jul 17, 2019Group: Data collection / Derived calculations / Category: diffrn_source / struct_conn
Item: _diffrn_source.pdbx_synchrotron_site / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Dec 20, 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_conn_type / 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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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

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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 CARRIER PROTEIN 1, CHLOROPLASTIC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,62814
Polymers134,0354
Non-polymers59310
Water41423
1
C: ACYL-[ACYL-CARRIER-PROTEIN] DESATURASE, CHLOROPLASTIC
hetero molecules

C: ACYL-[ACYL-CARRIER-PROTEIN] DESATURASE, CHLOROPLASTIC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,7618
Polymers83,4072
Non-polymers3546
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+1/31
Buried area6350 Å2
ΔGint-23.3 kcal/mol
Surface area35030 Å2
MethodPISA
2
A: ACYL-[ACYL-CARRIER-PROTEIN] DESATURASE, CHLOROPLASTIC
B: ACYL-[ACYL-CARRIER-PROTEIN] DESATURASE, CHLOROPLASTIC
D: ACYL CARRIER PROTEIN 1, CHLOROPLASTIC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,74810
Polymers92,3313
Non-polymers4167
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7210 Å2
ΔGint-19.8 kcal/mol
Surface area41370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)188.274, 188.274, 81.315
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: PHE / Beg label comp-ID: PHE / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: 1 / Auth seq-ID: 18 - 363 / Label seq-ID: 18 - 363

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC

NCS oper:
IDCodeMatrixVector
1given(0.5685, -0.88227, -0.003608), (-0.8227, -0.5684, -0.08182), (0.00468, 0.0072, -1)-89.34, -170.5, 21.79
2given(-0.8505, -0.5258, 0.01109), (0.5259, -0.8505, 0.008639), (0.004889, 0.01318, 0.9999)-165.8, -206.9, 4.942

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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.: 3
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.: 1
Source method: isolated from a genetically manipulated source
Details: SER38 (SEP IN SEQUENCE) IS A PHOSPHOSERINE / Source: (gene. exp.) SPINACIA OLERACEA (spinach) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P07854

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Non-polymers , 4 types, 33 molecules

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


Mass: 55.845 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Fe
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 23 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.1 Å3/Da / Density % sol: 60.37 % / Description: NONE
Crystal growpH: 5.62
Details: 4-5% PEG 20000, 8% PEG 550MME, 180MM SODIUM BROMIDE, 100MM SODIUM ACETATE PH 5.62, 15% GLYCEROL.

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.811
DetectorType: MAR555 FLAT PANEL / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.811 Å / Relative weight: 1
ReflectionResolution: 3→30 Å / Num. obs: 33376 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 11.1 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 21.9
Reflection shellResolution: 3→3.16 Å / Redundancy: 9.6 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 4.3 / % possible all: 100

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Processing

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

1afr


Resolution: 3→29.28 Å / Cor.coef. Fo:Fc: 0.919 / Cor.coef. Fo:Fc free: 0.887 / SU B: 46.969 / SU ML: 0.389 / Cross valid method: THROUGHOUT / ESU R Free: 0.45 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED.
RfactorNum. reflection% reflectionSelection details
Rfree0.27744 1363 4.1 %RANDOM
Rwork0.24292 ---
obs0.24434 32013 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 98.175 Å2
Baniso -1Baniso -2Baniso -3
1-2.88 Å21.44 Å20 Å2
2--2.88 Å20 Å2
3----4.33 Å2
Refinement stepCycle: LAST / Resolution: 3→29.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9044 0 13 23 9080
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0229252
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2991.95812526
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.84351116
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.1624.06463
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.58215.0091632
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1761572
X-RAY DIFFRACTIONr_chiral_restr0.0780.21350
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0217093
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_it1.6291.55596
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.84829054
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.54333656
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it7.1874.53472
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: 2807 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Atight positional0.070.05
2Btight positional0.090.05
3Ctight positional0.070.05
1Atight thermal0.251
2Btight thermal0.261
3Ctight thermal0.251
LS refinement shellResolution: 3→3.077 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.395 93 -
Rwork0.314 2321 -
obs--100 %
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)
12.6230.126-0.35171.63450.2163.79670.06160.2249-0.24490.0817-0.03230.79420.2615-1.9392-0.02930.053-0.09110.04021.05090.07390.4429-29.4568-110.484910.4569
21.5724-0.87330.73812.8723-0.34032.1694-0.03570.06870.58250.17140.00140.2664-1.1238-0.57920.03420.68930.36570.1820.31450.10760.3997-15.4788-83.403710.6003
31.5195-0.0209-0.36942.72990.41132.2529-0.23330.0601-0.7681-0.0157-0.06310.17911.37570.03260.29640.89910.04520.16890.016-0.03350.4151-0.3176-29.577313.7109
43.8820.5186-2.04551.93610.73211.68330.402-1.51-0.32540.1458-0.4777-0.10940.08090.71070.07571.5256-0.10970.32640.717-0.07020.6635-15.6472-53.644732.6085
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A18 - 363
2X-RAY DIFFRACTION1A401 - 402
3X-RAY DIFFRACTION1A501
4X-RAY DIFFRACTION2B18 - 363
5X-RAY DIFFRACTION2B401 - 402
6X-RAY DIFFRACTION2B501
7X-RAY DIFFRACTION2B601
8X-RAY DIFFRACTION3C18 - 363
9X-RAY DIFFRACTION3C401 - 402
10X-RAY DIFFRACTION3C501
11X-RAY DIFFRACTION4D1 - 82

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