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- PDB-9c8x: X-ray crystal structure of Methylorubrum extorquens La(III)-bound LanD -

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Basic information

Entry
Database: PDB / ID: 9c8x
TitleX-ray crystal structure of Methylorubrum extorquens La(III)-bound LanD
Componentslandiscernin
KeywordsMETAL BINDING PROTEIN / lanthanide / lanthanum / methanol dehydrogenase / chaperone
Function / homologyLANTHANUM (III) ION / Histidine kinase
Function and homology information
Biological speciesMethylorubrum extorquens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 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)6,7412
Polymers6,6031
Non-polymers1391
Water72140
1
A: landiscernin
hetero molecules

A: landiscernin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,4834
Polymers13,2052
Non-polymers2782
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation15_555-x+1/2,y,-z1
Buried area700 Å2
ΔGint-12 kcal/mol
Surface area7600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.710, 77.710, 77.710
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-

LA

21A-202-

HOH

31A-208-

HOH

41A-237-

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-LA / LANTHANUM (III) ION


Mass: 138.905 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: La / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 40 / 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: 2.96 Å3/Da / Density % sol: 58.47 %
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: APS / Beamline: 21-ID-G / Wavelength: 0.97857 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 15, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 1.9→38.86 Å / Num. obs: 11068 / % possible obs: 94.1 % / Redundancy: 33.6 % / CC1/2: 1 / Net I/σ(I): 14.7
Reflection shellResolution: 1.9→1.98 Å / Num. unique obs: 281 / CC1/2: 0.659

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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: 1.9→38.86 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 29.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2552 539 4.87 %
Rwork0.215 --
obs0.217 11068 92.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9→38.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms452 0 1 40 493
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009
X-RAY DIFFRACTIONf_angle_d0.86
X-RAY DIFFRACTIONf_dihedral_angle_d14.66191
X-RAY DIFFRACTIONf_chiral_restr0.04171
X-RAY DIFFRACTIONf_plane_restr0.00988
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-2.090.2548990.2152024X-RAY DIFFRACTION70
2.09-2.390.23111470.23242816X-RAY DIFFRACTION100
2.39-3.010.32631520.22922832X-RAY DIFFRACTION100
3.02-38.860.23261410.18742857X-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)
11.1466-0.2633-0.24540.3536-0.1650.21980.07380.2622-0.12050.0169-0.07260.1855-0.0182-0.19220.1530.1901-0.01640.10530.358-0.16220.45683.827111.0447-10.3389
21.0383-0.5334-0.5581.11160.09580.4520.05650.2558-0.27970.1192-0.16060.38320.1502-0.2320.21480.14310.01250.0420.1353-0.07840.191713.69946.143-11.827
31.7579-0.28270.27731.97191.34137.59620.03270.18580.1473-0.1716-0.21780.1356-0.26220.09030.13770.15450.00470.04680.1678-0.03520.168212.749915.1226-10.8543
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 75 )
3X-RAY DIFFRACTION3chain 'A' and (resid 76 through 91 )

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