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- PDB-2biw: Crystal structure of apocarotenoid cleavage oxygenase from Synech... -

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Basic information

Entry
Database: PDB / ID: 2biw
TitleCrystal structure of apocarotenoid cleavage oxygenase from Synechocystis, native enzyme
ComponentsAPOCAROTENOID-CLEAVING OXYGENASE
KeywordsOXIDOREDUCTASE / OXYGENASE / NON-HEME IRON / CAROTENOID CLEAVAGE / RETINAL FORMATION / DIOXYGENASE
Function / homology
Function and homology information


all-trans-8'-apo-beta-carotenal 15,15'-oxygenase / all-trans-8'-apo-beta-carotenal 15,15'-oxygenase activity / 9-cis-epoxycarotenoid dioxygenase activity / carotenoid dioxygenase activity / carotene catabolic process / metal ion binding
Similarity search - Function
Carotenoid oxygenase / Retinal pigment epithelial membrane protein
Similarity search - Domain/homology
(3R)-3-HYDROXY-8'-APOCAROTENOL / : / Apocarotenoid-15,15'-oxygenase
Similarity search - Component
Biological speciesSYNECHOCYSTIS SP. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.39 Å
AuthorsKloer, D.P. / Ruch, S. / Al-Babili, S. / Beyer, P. / Schulz, G.E.
CitationJournal: Science / Year: 2005
Title: The Structure of a Retinal-Forming Carotenoid Oxygenase
Authors: Kloer, D.P. / Ruch, S. / Al-Babili, S. / Beyer, P. / Schulz, G.E.
History
DepositionJan 26, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 14, 2005Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2May 1, 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
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
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: APOCAROTENOID-CLEAVING OXYGENASE
B: APOCAROTENOID-CLEAVING OXYGENASE
C: APOCAROTENOID-CLEAVING OXYGENASE
D: APOCAROTENOID-CLEAVING OXYGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)219,33912
Polymers217,3774
Non-polymers1,9628
Water9,764542
1
A: APOCAROTENOID-CLEAVING OXYGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,8353
Polymers54,3441
Non-polymers4902
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: APOCAROTENOID-CLEAVING OXYGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,8353
Polymers54,3441
Non-polymers4902
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
C: APOCAROTENOID-CLEAVING OXYGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,8353
Polymers54,3441
Non-polymers4902
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
4
D: APOCAROTENOID-CLEAVING OXYGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,8353
Polymers54,3441
Non-polymers4902
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)119.046, 125.278, 203.086
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
31C
41D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLN / Beg label comp-ID: GLN / End auth comp-ID: THR / End label comp-ID: THR / Refine code: 4 / Auth seq-ID: 12 - 490 / Label seq-ID: 12 - 490

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD

NCS oper:
IDCodeMatrixVector
1given(0.022157, -0.99968, -0.012234), (0.999754, 0.022171, -0.000999), (0.00127, -0.012209, 0.999925)29.3029, -30.1669, 50.6999
2given(0.38794, 0.220637, -0.894887), (-0.567825, -0.707574, -0.420611), (-0.726001, 0.671311, -0.149213)93.7767, 30.8166, 166.3703
3given(0.23525, -0.362409, -0.901841), (-0.756169, 0.514705, -0.404088), (0.610627, 0.777006, -0.152957)52.9647, 13.9851, 118.8693

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Components

#1: Protein
APOCAROTENOID-CLEAVING OXYGENASE / LIGNOSTILBENE-ALPHA / BETA-DIOXYGENASE


Mass: 54344.191 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SYNECHOCYSTIS SP. (bacteria) / Strain: PCC 6803 / Plasmid: PET3B-ACO / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA / References: UniProt: P74334
#2: Chemical
ChemComp-3ON / (3R)-3-HYDROXY-8'-APOCAROTENOL / (1R)-4-[(1E,3E,5E,7Z,9E,11Z,13E,15E)-17-HYDROXY-3,7,12,16-TETRAMETHYLHEPTADECA-1,3,5,7,9,11,13,15-OCTAEN-1-YL]-3,5,5-TRIMETHYLCYCLOHEX-3-EN-1-OL


Mass: 434.653 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C30H42O2
#3: Chemical
ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 542 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE NAME OF THE MOLECULE IN THE UNIPROT DATABASE WITH ACCESSION NUMBER P74334 IS LIGNOSTILBENE- ...THE NAME OF THE MOLECULE IN THE UNIPROT DATABASE WITH ACCESSION NUMBER P74334 IS LIGNOSTILBENE-ALPHA,BETA- DIOXYGENASE BUT THE DEPOSITOR MAINTAINS THAT THIS IS A DATABASE ERROR

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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: 3.6 Å3/Da / Density % sol: 66 %
Crystal growpH: 5.7 / Details: pH 5.70

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.2399
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2399 Å / Relative weight: 1
ReflectionResolution: 2.39→44 Å / Num. obs: 111472 / % possible obs: 93.3 % / Redundancy: 2.7 % / Biso Wilson estimate: 55.8 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 10.8
Reflection shellResolution: 2.39→2.5 Å / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 2.1 / % possible all: 80.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: ACO APO FORM

Resolution: 2.39→44.41 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.938 / SU B: 12.241 / SU ML: 0.152 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.251 / ESU R Free: 0.206 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.224 5864 5 %RANDOM
Rwork0.18 ---
obs0.182 111472 97.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 64.26 Å2
Baniso -1Baniso -2Baniso -3
1-1.11 Å20 Å20 Å2
2---0.84 Å20 Å2
3----0.26 Å2
Refinement stepCycle: LAST / Resolution: 2.39→44.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15068 0 132 542 15742
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.02215648
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6091.96221308
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.99751912
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.54823.838740
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.092152384
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.761592
X-RAY DIFFRACTIONr_chiral_restr0.1060.22236
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212400
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2180.26945
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3160.210314
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1450.2988
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2320.271
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2140.215
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6711.59740
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.113215372
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.75836724
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.7544.55936
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: 3766 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Amedium positional0.340.5
2Bmedium positional0.340.5
3Cmedium positional0.310.5
4Dmedium positional0.320.5
1Amedium thermal0.862
2Bmedium thermal0.892
3Cmedium thermal0.862
4Dmedium thermal0.822
LS refinement shellResolution: 2.39→2.45 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.317 382
Rwork0.253 7640
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)
12.17370.3018-0.76052.1154-0.72982.8130.0846-0.0586-0.0248-0.13-0.1177-0.13870.02780.10520.0331-0.23350.05230.0352-0.19040.0372-0.242424.45950.871491.7002
22.057-0.0243-0.54832.19260.49512.5763-0.14790.0352-0.05940.0990.07540.07350.2074-0.05170.0725-0.1698-0.05820.0921-0.1887-0.0477-0.235230.97515.020541.0197
31.8507-0.5579-0.16662.12890.0522.4173-0.00430.0441-0.1478-0.0381-0.02680.3180.0839-0.34930.0311-0.28330.07030.0069-0.1112-0.001-0.049144.3183-44.226585.7755
42.36980.67040.00891.9680.10672.1585-0.07850.08730.244-0.19020.1230.1724-0.3824-0.0327-0.0446-0.0369-0.09880.0331-0.24580.0226-0.087-13.3793-17.531835.1802
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A12 - 490
2X-RAY DIFFRACTION2B12 - 490
3X-RAY DIFFRACTION3C12 - 490
4X-RAY DIFFRACTION4D12 - 490

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