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- PDB-9c8z: X-ray crystal structure of Methylorubrum extorquens Eu(III)-bound LanD -

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Basic information

Entry
Database: PDB / ID: 9c8z
TitleX-ray crystal structure of Methylorubrum extorquens Eu(III)-bound LanD
Componentslandiscernin
KeywordsMETAL BINDING PROTEIN / lanthanide / europium / methanol dehydrogenase / chaperone
Function / homologyEUROPIUM ION / Histidine kinase
Function and homology information
Biological speciesMethylorubrum extorquens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.41 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)6,7552
Polymers6,6031
Non-polymers1521
Water18010
1
A: landiscernin
hetero molecules

A: landiscernin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,5094
Polymers13,2052
Non-polymers3042
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation14_665-x+1,-y+3/2,z1
Buried area730 Å2
ΔGint-11 kcal/mol
Surface area7410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.334, 78.334, 78.334
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-

EU

21A-202-

HOH

31A-210-

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-EU / EUROPIUM ION


Mass: 151.964 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Eu / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / 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: 3.03 Å3/Da / Density % sol: 59.45 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 100 mM MES, pH 6.5, 25% w/v PEG200

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.92011 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: May 28, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92011 Å / Relative weight: 1
ReflectionResolution: 1.41→31.98 Å / Num. obs: 14522 / % possible obs: 93.3 % / Redundancy: 7.6 % / CC1/2: 0.997 / Net I/σ(I): 24.7
Reflection shellResolution: 1.41→1.46 Å / Num. unique obs: 575 / CC1/2: 0.634

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
HKL-2000data scaling
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.41→31.98 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.02 / Phase error: 22.77 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2047 1422 9.98 %
Rwork0.1968 --
obs0.1976 14248 91.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.41→31.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms452 0 1 10 463
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008
X-RAY DIFFRACTIONf_angle_d0.957
X-RAY DIFFRACTIONf_dihedral_angle_d15.169213
X-RAY DIFFRACTIONf_chiral_restr0.05475
X-RAY DIFFRACTIONf_plane_restr0.00793
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.41-1.460.2617590.2552515X-RAY DIFFRACTION38
1.46-1.520.2061310.20621237X-RAY DIFFRACTION88
1.52-1.590.21481440.1821334X-RAY DIFFRACTION97
1.59-1.670.18511500.17571383X-RAY DIFFRACTION98
1.67-1.780.17861550.17271353X-RAY DIFFRACTION98
1.78-1.910.18151490.16891362X-RAY DIFFRACTION98
1.91-2.110.16721590.17481375X-RAY DIFFRACTION99
2.11-2.410.1751520.17711407X-RAY DIFFRACTION99
2.41-3.040.20081540.19191407X-RAY DIFFRACTION99
3.04-31.980.24071690.22951453X-RAY DIFFRACTION99
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)
12.77380.70350.82710.54540.5633.08940.08880.0894-0.3255-0.33670.06930.52690.3411-0.2212-0.12060.2635-0.005-0.1150.13530.04130.327229.573743.658850.1911
20.91681.21490.28492.32590.6820.21790.0343-0.0298-0.0485-0.1931-0.05360.21510.067-0.38420.10260.2124-0.0159-0.14680.3372-0.05010.342915.074449.470641.3836
34.169-0.3560.28131.7524-0.12791.80840.16510.1091-0.029-0.1509-0.09970.17810.05270.0037-0.04960.11310.0102-0.0280.09840.02280.110930.031554.713246.1232
45.7906-0.01861.04272.9850.12073.39590.0944-0.4620.10720.29020.15520.2819-0.0349-0.4344-0.13180.18640.02380.01620.18970.05770.161428.415752.289654.2223
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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