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- PDB-9c8w: X-ray crystal structure of Methylorubrum extorquens apo LanD -

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Basic information

Entry
Database: PDB / ID: 9c8w
TitleX-ray crystal structure of Methylorubrum extorquens apo LanD
Componentslandiscernin
KeywordsMETAL BINDING PROTEIN / lanthanide / chaperone / methanol dehydrogenase / metal-centered dimer
Function / homologyHistidine kinase
Function and homology information
Biological speciesMethylorubrum extorquens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 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
B: landiscernin


Theoretical massNumber of molelcules
Total (without water)13,2052
Polymers13,2052
Non-polymers00
Water3,351186
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area530 Å2
ΔGint-1 kcal/mol
Surface area7580 Å2
Unit cell
Length a, b, c (Å)76.776, 23.507, 76.446
Angle α, β, γ (deg.)90.00, 120.02, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein landiscernin


Mass: 6602.546 Da / Num. of mol.: 2
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 186 / Source method: isolated from a natural source / Formula: H2O
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: 2.26 Å3/Da / Density % sol: 45.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2 M potassium fluoride, 20% w/v PEG3350

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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: Feb 5, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 1.65→38.39 Å / Num. obs: 21758 / % possible obs: 96.5 % / Redundancy: 7.2 % / Biso Wilson estimate: 13.29 Å2 / CC1/2: 1 / Net I/σ(I): 28.4
Reflection shellResolution: 1.65→1.71 Å / Num. unique obs: 1073 / CC1/2: 0.9

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
HKL-2000data scaling
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.65→38.39 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.257 1070 4.92 %
Rwork0.2119 --
obs0.2141 21758 78.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.65→38.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms889 0 0 186 1075
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005
X-RAY DIFFRACTIONf_angle_d0.816
X-RAY DIFFRACTIONf_dihedral_angle_d12.071357
X-RAY DIFFRACTIONf_chiral_restr0.042134
X-RAY DIFFRACTIONf_plane_restr0.007164
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.730.3208700.25351340X-RAY DIFFRACTION40
1.73-1.820.2941900.26891724X-RAY DIFFRACTION52
1.82-1.930.24541140.24152031X-RAY DIFFRACTION63
1.93-2.080.24251360.21882660X-RAY DIFFRACTION80
2.08-2.290.24711670.19873149X-RAY DIFFRACTION96
2.29-2.620.28061640.21233310X-RAY DIFFRACTION100
2.62-3.310.28521760.21413276X-RAY DIFFRACTION99
3.31-38.390.22361530.19883198X-RAY DIFFRACTION97
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.98791.09011.20892.8620.64542.93030.1082-0.8058-0.31960.8439-0.17570.28180.45-0.4124-0.32920.44580.01790.15710.48280.1780.32862.03530.414328.011
24.69952.59410.02614.5598-0.19432.10330.0857-0.28480.03250.1487-0.1226-0.1620.0108-0.13170.04540.0620.00020.00130.07030.03010.062412.1428.900212.9986
34.31251.91350.6613.43390.00482.54-0.14630.42250.0975-0.31010.1256-0.1253-0.16050.06870.04570.10840.00910.04430.08150.03890.066412.46498.23442.0255
45.45771.05752.5172.2740.35694.30430.07160.0634-0.0437-0-0.0893-0.41930.29060.0901-0.08810.09350.01120.01240.07210.0280.148915.56281.96457.1547
56.1283-1.43611.13663.6645-0.05772.1549-0.2917-0.1509-0.22310.2766-0.06990.37520.0991-0.3160.06050.1373-0.00730.04920.2347-0.00250.10941.03296.250119.9628
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resid 58 through 90 )
2X-RAY DIFFRACTION2chain 'A' and (resid 32 through 57 )
3X-RAY DIFFRACTION3chain 'A' and (resid 58 through 75 )
4X-RAY DIFFRACTION4chain 'A' and (resid 76 through 91 )
5X-RAY DIFFRACTION5chain 'B' and (resid 33 through 57 )

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