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- PDB-9c8y: X-ray crystal structure of Methylorubrum extorquens Ce(III)-bound LanD -

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Basic information

Entry
Database: PDB / ID: 9c8y
TitleX-ray crystal structure of Methylorubrum extorquens Ce(III)-bound LanD
Componentslandiscernin
KeywordsMETAL BINDING PROTEIN / lanthanide / cerium / methanol dehydrogenase / chaperone
Function / homologyCERIUM (III) ION / Histidine kinase
Function and homology information
Biological speciesMethylorubrum extorquens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsJung, J.J. / Lin, C.-Y. / Boal, A.K.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2024
Title: Modulating metal-centered dimerization of a lanthanide chaperone protein for separation of light lanthanides.
Authors: Larrinaga, W.B. / Jung, J.J. / Lin, C.Y. / Boal, A.K. / Cotruvo Jr., J.A.
History
DepositionJun 13, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 16, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: landiscernin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,7432
Polymers6,6031
Non-polymers1401
Water66737
1
A: landiscernin
hetero molecules

A: landiscernin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,4854
Polymers13,2052
Non-polymers2802
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation14_555-x,-y+1/2,z1
Buried area700 Å2
ΔGint-12 kcal/mol
Surface area7510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.086, 78.086, 78.086
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number199
Space group name H-MI213
Components on special symmetry positions
IDModelComponents
11A-101-

CE

21A-203-

HOH

31A-205-

HOH

41A-235-

HOH

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Components

#1: Protein landiscernin


Mass: 6602.546 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methylorubrum extorquens (bacteria) / Gene: LanD / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: C5B159
#2: Chemical ChemComp-CE / CERIUM (III) ION


Mass: 140.116 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ce / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 37 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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 Å3/Da / Density % sol: 59.06 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 100 mM MES, pH 6.5, 50% w/v PEG200

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 5, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.8→31.88 Å / Num. obs: 14271 / % possible obs: 100 % / Redundancy: 40 % / CC1/2: 0.998 / Net I/σ(I): 21.8
Reflection shellResolution: 1.8→1.86 Å / Num. unique obs: 742 / CC1/2: 0.994

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata scaling
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.8→31.88 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 32.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2466 704 4.93 %
Rwork0.1878 --
obs0.1906 14271 100 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→31.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms452 0 1 37 490
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008
X-RAY DIFFRACTIONf_angle_d0.79
X-RAY DIFFRACTIONf_dihedral_angle_d13.482187
X-RAY DIFFRACTIONf_chiral_restr0.03969
X-RAY DIFFRACTIONf_plane_restr0.00687
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.940.26521380.24962731X-RAY DIFFRACTION100
1.94-2.130.24221400.19462695X-RAY DIFFRACTION100
2.14-2.440.24231460.19322722X-RAY DIFFRACTION100
2.45-3.080.2311340.19542716X-RAY DIFFRACTION100
3.08-31.880.25481460.16842703X-RAY DIFFRACTION100
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)
11.80231.5726-0.66932.6908-2.52954.39160.1099-0.2564-0.69280.01330.21470.44240.038-0.5434-0.19840.17690.0279-0.04910.34560.12490.4137-15.42539.1528.5537
21.12350.2741-0.29290.0669-0.07140.0763-0.0461-0.2535-0.24140.1622-0.01250.12360.2671-0.0603-0.00790.2859-0.04790.00150.36280.24340.5103-9.3609-4.514417.3809
34.5478-1.22031.09476.3104-0.74232.5266-0.1098-0.3292-0.27890.32780.21310.1689-0.0928-0.2638-0.17140.1060.0372-0.01460.14070.03640.0715-4.499611.39712.3258
43.54630.2558-0.21459.3163-2.15864.7429-0.03270.1481-0.3316-0.34990.164-0.1360.4684-0.1771-0.02390.17680.0096-0.02770.1847-0.0170.1919-6.49268.88944.5629
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 32 through 50 )
2X-RAY DIFFRACTION2chain 'A' and (resid 51 through 57 )
3X-RAY DIFFRACTION3chain 'A' and (resid 58 through 75 )
4X-RAY DIFFRACTION4chain 'A' and (resid 76 through 91 )

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