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- PDB-7wh1: structure of C elegans BCMO-2 -

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Basic information

Entry
Database: PDB / ID: 7wh1
Titlestructure of C elegans BCMO-2
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
: / IMIDAZOLE / Beta,beta-carotene 9',10'-oxygenase
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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 / pdbx_initial_refinement_model

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,73611
Polymers62,8461
Non-polymers88910
Water10,124562
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area220 Å2
ΔGint-17 kcal/mol
Surface area19880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)148.756, 148.756, 136.294
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 62846.289 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: bcmo-2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9TXT9

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Non-polymers , 5 types, 572 molecules

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


Mass: 55.845 Da / Num. of mol.: 1 / 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.: 1 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 562 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.01 Å3/Da / Density % sol: 59.13 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN I/F_PLUS/MINUS COLUMNS.
Crystal growTemperature: 289 K / Method: evaporation / pH: 7.5 / Details: ammonium acetate, ammonium sulfate

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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: 1.9→50 Å / Num. obs: 58459 / % possible obs: 100 % / Redundancy: 26.4 % / Biso Wilson estimate: 19.83 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.093 / Rpim(I) all: 0.018 / Net I/σ(I): 41.7
Reflection shellResolution: 1.9→1.97 Å / Mean I/σ(I) obs: 2.3 / Num. unique obs: 4402 / CC1/2: 0.733 / Rpim(I) all: 0.409 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4RSE

4rse


Resolution: 1.9→39.488 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 17.28 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1864 2944 5.04 %
Rwork0.1584 55509 -
obs0.1598 58453 97.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 111.53 Å2 / Biso mean: 27.0159 Å2 / Biso min: 9.13 Å2
Refinement stepCycle: final / Resolution: 1.9→39.488 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4004 0 47 562 4613
Biso mean--48.09 39.9 -
Num. residues----499
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074177
X-RAY DIFFRACTIONf_angle_d0.8435653
X-RAY DIFFRACTIONf_chiral_restr0.058591
X-RAY DIFFRACTIONf_plane_restr0.005729
X-RAY DIFFRACTIONf_dihedral_angle_d16.7111534
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.9-1.93110.26371090.2529148757
1.9311-1.96440.26371090.2287241589
1.9644-2.00010.26361410.2121262898
2.0001-2.03860.22451530.1958266699
2.0386-2.08020.20441540.17282665100
2.0802-2.12540.20541520.17242695100
2.1254-2.17480.1881400.16072654100
2.1748-2.22920.19371480.16532703100
2.2292-2.28950.18781460.15872702100
2.2895-2.35690.18341540.16032680100
2.3569-2.43290.20911380.15652683100
2.4329-2.51990.2031450.16662714100
2.5199-2.62070.22061430.16472704100
2.6207-2.740.19161280.16312714100
2.74-2.88440.22361430.1672713100
2.8844-3.06510.20111310.1632745100
3.0651-3.30160.1841420.15652733100
3.3016-3.63360.16941430.14342736100
3.6336-4.15890.14491270.12892770100
4.1589-5.23790.12731480.11762794100
5.2379-39.480.18631500.1782908100
Refinement TLS params.Method: refined / Origin x: 83.5346 Å / Origin y: 52.2698 Å / Origin z: 39.9636 Å
111213212223313233
T0.0829 Å20.026 Å2-0.0061 Å2-0.1607 Å20.0568 Å2--0.1345 Å2
L0.5205 °20.1644 °2-0.1799 °2-1.5485 °2-0.0501 °2--1.1522 °2
S-0.0022 Å °-0.0834 Å °-0.0989 Å °0.0155 Å °0.0311 Å °-0.1156 Å °0.0755 Å °0.0593 Å °-0.0283 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1 - 709
2X-RAY DIFFRACTION1allA710
3X-RAY DIFFRACTION1allS1 - 568

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