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- PDB-7wh0: structure of C elegans BCMO-1 -

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Basic information

Entry
Database: PDB / ID: 7wh0
Titlestructure of C elegans BCMO-1
ComponentsBeta-Carotene 15,15'-MonoOxygenase
KeywordsMETAL BINDING PROTEIN / nonheme iron / dioxygenase / Caenorhabditis elegans / retinoid / beta-carotene
Function / homology
Function and homology information


The canonical retinoid cycle in rods (twilight vision) / Retinoid metabolism and transport / beta-carotene 15,15'-dioxygenase activity / carotenoid dioxygenase activity / carotene catabolic process / retinal metabolic process / metal ion binding
Similarity search - Function
Carotenoid oxygenase / Retinal pigment epithelial membrane protein
Similarity search - Domain/homology
: / OXALIC ACID / Beta,beta-carotene 9',10'-oxygenase
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsPan, W. / Liu, L.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Front Mol Biosci / Year: 2022
Title: Structural and Functional Analysis of Nonheme Iron Enzymes BCMO-1 and BCMO-2 from Caenorhabditis elegans .
Authors: Pan, W. / Zhou, Y.L. / Wang, J. / Dai, H.E. / Wang, X. / Liu, L.
History
DepositionDec 29, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 2, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 16, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-Carotene 15,15'-MonoOxygenase
B: Beta-Carotene 15,15'-MonoOxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,0588
Polymers125,5822
Non-polymers4766
Water16,214900
1
A: Beta-Carotene 15,15'-MonoOxygenase
hetero molecules

B: Beta-Carotene 15,15'-MonoOxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,0588
Polymers125,5822
Non-polymers4766
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y+1/2,-z1
Buried area3040 Å2
ΔGint-50 kcal/mol
Surface area40360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.204, 104.733, 76.438
Angle α, β, γ (deg.)90.000, 102.160, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 1 through 10 or resid 12...
21(chain B and (resid 1 through 10 or resid 12...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETPHEPHE(chain A and (resid 1 through 10 or resid 12...AA1 - 1021 - 30
12ASNASNPROPRO(chain A and (resid 1 through 10 or resid 12...AA12 - 1732 - 37
13GLUGLUGLUGLU(chain A and (resid 1 through 10 or resid 12...AA1838
14METMETASNASN(chain A and (resid 1 through 10 or resid 12...AA1 - 52921 - 549
15METMETASNASN(chain A and (resid 1 through 10 or resid 12...AA1 - 52921 - 549
16METMETASNASN(chain A and (resid 1 through 10 or resid 12...AA1 - 52921 - 549
17METMETASNASN(chain A and (resid 1 through 10 or resid 12...AA1 - 52921 - 549
21METMETPHEPHE(chain B and (resid 1 through 10 or resid 12...BB1 - 1021 - 30
22ASNASNTYRTYR(chain B and (resid 1 through 10 or resid 12...BB12 - 8332 - 103
23METMETASNASN(chain B and (resid 1 through 10 or resid 12...BB1 - 52921 - 549
24METMETASNASN(chain B and (resid 1 through 10 or resid 12...BB1 - 52921 - 549
25ALAALAALAALA(chain B and (resid 1 through 10 or resid 12...BB168 - 381188 - 401
26GLYGLYASNASN(chain B and (resid 1 through 10 or resid 12...BB383 - 529403 - 549

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Components

#1: Protein Beta-Carotene 15,15'-MonoOxygenase


Mass: 62790.883 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: bcmo-1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9U2E4
#2: Chemical ChemComp-FE / FE (III) ION


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


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-OXD / OXALIC ACID


Mass: 90.035 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H2O4 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 900 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.28 Å3/Da / Density % sol: 46.08 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN I/F_PLUS/MINUS COLUMNS.
Crystal growTemperature: 289 K / Method: evaporation / pH: 5.5 / Details: ammonium sulfate, PEG 3350.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 31, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 102764 / % possible obs: 98.2 % / Redundancy: 6.7 % / Biso Wilson estimate: 28.25 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.066 / Rpim(I) all: 0.027 / Net I/σ(I): 29.1
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.621 / Mean I/σ(I) obs: 3 / Num. unique obs: 9990 / CC1/2: 0.887 / Rpim(I) all: 0.259 / % possible all: 96.6

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
HKL-3000data scaling
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4RSE

4rse


Resolution: 1.8→31.63 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.189 5112 4.97 %
Rwork0.166 97652 -
obs0.1671 102764 98.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 68.28 Å2 / Biso mean: 35.1648 Å2 / Biso min: 19.02 Å2
Refinement stepCycle: final / Resolution: 1.8→31.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8524 0 26 900 9450
Biso mean--34.5 40.2 -
Num. residues----1058
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A5053X-RAY DIFFRACTION9.125TORSIONAL
12B5053X-RAY DIFFRACTION9.125TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.8-1.820.29561490.2764311893
1.82-1.840.29491530.2522316196
1.84-1.860.27991580.251321297
1.86-1.880.25611590.2366323897
1.88-1.910.31471710.225326198
1.91-1.940.24421590.2225318097
1.94-1.960.26951720.214323398
1.96-1.990.23151810.2092318497
1.99-2.020.2361720.2001319898
2.02-2.060.2521790.2017325598
2.06-2.090.20821760.1928322197
2.09-2.130.22541790.1936323798
2.13-2.170.20611490.1945322797
2.17-2.220.21051640.1879322898
2.22-2.260.22311790.1915326299
2.26-2.320.22481770.1837329498
2.32-2.370.21381730.1877321698
2.37-2.440.21281930.1828322999
2.44-2.510.22691630.1825327199
2.51-2.590.18591610.1786328799
2.59-2.680.20321470.1846332499
2.68-2.790.21661750.1812327199
2.79-2.920.20511640.1841330399
2.92-3.070.2081620.1802332799
3.07-3.260.20231810.1727329099
3.26-3.520.15191600.1519332499
3.52-3.870.17632150.1446327199
3.87-4.430.14891560.1263348100
4.43-5.570.13441820.12073349100
5.57-31.630.15812030.1403333399
Refinement TLS params.Method: refined / Origin x: 16.8011 Å / Origin y: 4.5187 Å / Origin z: -14.3814 Å
111213212223313233
T0.2286 Å2-0.018 Å20.0117 Å2-0.1844 Å2-0.0222 Å2--0.202 Å2
L0.4037 °2-0.2464 °20.3359 °2-0.3043 °2-0.3404 °2--0.6305 °2
S-0.0175 Å °-0.0382 Å °0.0376 Å °0.0494 Å °-0.0256 Å °-0.0398 Å °-0.0019 Å °0.0036 Å °0.0431 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1 - 529
2X-RAY DIFFRACTION1allA600 - 701
3X-RAY DIFFRACTION1allB1 - 529
4X-RAY DIFFRACTION1allB600 - 701
5X-RAY DIFFRACTION1allS1 - 903

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