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- PDB-2uw1: Ivy Desaturase Structure -

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Basic information

Entry
Database: PDB / ID: 2uw1
TitleIvy Desaturase Structure
Components(PLASTID DELTA4 MULTIFUNCTIONAL ACYL-ACYL CARRIER PROTEIN ...) x 2
KeywordsOXIDOREDUCTASE / ELECTRON TRANSFER / LIPID SYNTHESIS / FATTY ACID BIOSYNTHESIS
Function / homologyRibonucleotide Reductase, subunit A / Ribonucleotide Reductase, subunit A / Orthogonal Bundle / Mainly Alpha / : / (3R)-3-HYDROXY-5,5-DIMETHYLHEXANOIC ACID
Function and homology information
Biological speciesHEDERA HELIX (English ivy)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsGuy, J.E. / Whittle, E. / Kumaran, D. / Lindqvist, Y. / Shanklin, J.
CitationJournal: J.Biol.Chem. / Year: 2007
Title: The Crystal Structure of the Ivy {Delta}4-16:0-Acp Desaturase Reveals Structural Details of the Oxidized Active Site and Potential Determinants of Regioselectivity.
Authors: Guy, J.E. / Whittle, E. / Kumaran, D. / Lindqvist, Y. / Shanklin, J.
History
DepositionMar 15, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 8, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / 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
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_asym_id / _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_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.pdbx_dist_value / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PLASTID DELTA4 MULTIFUNCTIONAL ACYL-ACYL CARRIER PROTEIN DESATURASE
B: PLASTID DELTA4 MULTIFUNCTIONAL ACYL-ACYL CARRIER PROTEIN DESATURASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,55710
Polymers77,9672
Non-polymers5908
Water9,782543
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7330 Å2
ΔGint-98.8 kcal/mol
Surface area25600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.122, 61.863, 201.002
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
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1115A33 - 336
2115B33 - 336
1216A401 - 402
2216B401 - 402
1316A337 - 353
2316B337 - 353
1415A354 - 358
2415B354 - 358

NCS oper: (Code: given
Matrix: (-0.17958, 0.98338, 0.02669), (0.98341, 0.17875, 0.03093), (0.02565, 0.0318, -0.99917)
Vector: 11.46227, -10.9528, 50.88496)

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Components

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PLASTID DELTA4 MULTIFUNCTIONAL ACYL-ACYL CARRIER PROTEIN ... , 2 types, 2 molecules AB

#1: Protein PLASTID DELTA4 MULTIFUNCTIONAL ACYL-ACYL CARRIER PROTEIN DESATURASE / DESATURASE


Mass: 38986.441 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HEDERA HELIX (English ivy) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: EC: 1.14.99.6
#2: Protein PLASTID DELTA4 MULTIFUNCTIONAL ACYL-ACYL CARRIER PROTEIN DESATURASE / DESATURASE


Mass: 38980.371 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HEDERA HELIX (English ivy) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: EC: 1.14.99.6

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Non-polymers , 4 types, 551 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-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-GVM / (3R)-3-HYDROXY-5,5-DIMETHYLHEXANOIC ACID


Mass: 160.211 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H16O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 543 / 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: 2.24 Å3/Da / Density % sol: 44.64 %
Crystal growpH: 7 / Details: pH 7.00

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 56078 / % possible obs: 98.7 % / Observed criterion σ(I): 2 / Redundancy: 8.1 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 27.4
Reflection shellResolution: 1.95→2 Å / Redundancy: 5 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 2.96 / % possible all: 90.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1AFR

1afr


Resolution: 1.95→30 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.922 / SU B: 6.338 / SU ML: 0.097 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.166 / ESU R Free: 0.153 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.229 2838 5.1 %RANDOM
Rwork0.184 ---
obs0.186 53042 98.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.96 Å2
Baniso -1Baniso -2Baniso -3
1--0.09 Å20 Å20 Å2
2--0.5 Å20 Å2
3----0.41 Å2
Refinement stepCycle: LAST / Resolution: 1.95→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5382 0 28 543 5953
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0225588
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1241.9597584
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7725694
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.57924.051274
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.642151008
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.5591540
X-RAY DIFFRACTIONr_chiral_restr0.0890.2817
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024268
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1970.23139
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2970.23948
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2510.2499
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1760.236
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1140.223
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3581.53350
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.71325424
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.35732340
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.2364.52144
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 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1198medium positional0.180.5
2B1198medium positional0.180.5
1A1272loose positional0.515
2B1272loose positional0.515
1A1198medium thermal0.652
2B1198medium thermal0.652
1A1272loose thermal1.1210
2B1272loose thermal1.1210
LS refinement shellResolution: 1.95→2 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.303 178
Rwork0.232 3494
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)
11.26020.23910.36690.58820.08530.93060.01440.0710.1339-0.0509-0.00180.0711-0.0439-0.0893-0.0126-0.12070.0170.0317-0.10730.007-0.1276-15.9721-13.079115.4941
20.9640.1326-0.28881.1544-0.25240.9437-0.0283-0.148-0.14630.1829-0.0055-0.15020.17120.11340.0337-0.05030.0335-0.019-0.0733-0.0135-0.11350.8395-28.832234.4256
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A32 - 358
2X-RAY DIFFRACTION2B21 - 358

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