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- PDB-9c90: X-ray crystal structure of Methylorubrum extorquens Ho(III)-bound LanD -

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Basic information

Entry
Database: PDB / ID: 9c90
TitleX-ray crystal structure of Methylorubrum extorquens Ho(III)-bound LanD
Componentslandiscernin
KeywordsMETAL BINDING PROTEIN / lanthanide / holmium / methanol dehydrogenase / chaperone
Function / homologyHOLMIUM (III) ATOM / Histidine kinase
Function and homology information
Biological speciesMethylorubrum extorquens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.38 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)6,7672
Polymers6,6031
Non-polymers1651
Water1448
1
A: landiscernin
hetero molecules

A: landiscernin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,5354
Polymers13,2052
Non-polymers3302
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation14_665-x+1,-y+3/2,z1
Buried area720 Å2
ΔGint-12 kcal/mol
Surface area7410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.164, 78.164, 78.164
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-

HO3

21A-208-

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-HO3 / HOLMIUM (III) ATOM


Mass: 164.930 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ho / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / 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: 3.01 Å3/Da / Density % sol: 59.19 %
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: BL12-1 / Wavelength: 0.97949 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 28, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.38→39.08 Å / Num. obs: 31728 / % possible obs: 100 % / Redundancy: 39.3 % / CC1/2: 1 / Net I/σ(I): 21.8
Reflection shellResolution: 1.38→1.42 Å / Num. unique obs: 1210 / CC1/2: 0.477

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata scaling
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.38→39.08 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.36 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2234 3150 9.93 %
Rwork0.221 --
obs0.2212 31728 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.38→39.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms452 0 1 8 461
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008
X-RAY DIFFRACTIONf_angle_d0.917
X-RAY DIFFRACTIONf_dihedral_angle_d16.432195
X-RAY DIFFRACTIONf_chiral_restr0.05272
X-RAY DIFFRACTIONf_plane_restr0.00691
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.38-1.40.32621250.3141217X-RAY DIFFRACTION100
1.4-1.420.34541460.29791270X-RAY DIFFRACTION100
1.42-1.450.29351310.29091231X-RAY DIFFRACTION100
1.45-1.470.27591460.27691267X-RAY DIFFRACTION100
1.47-1.50.25841400.25641215X-RAY DIFFRACTION100
1.5-1.530.2341300.25691231X-RAY DIFFRACTION100
1.53-1.560.22271340.25031239X-RAY DIFFRACTION100
1.56-1.590.24481340.2311264X-RAY DIFFRACTION100
1.59-1.630.2331380.21711254X-RAY DIFFRACTION100
1.63-1.670.23171360.21541236X-RAY DIFFRACTION100
1.67-1.710.20961300.19161222X-RAY DIFFRACTION100
1.71-1.760.20881440.2041265X-RAY DIFFRACTION100
1.77-1.820.21681300.19221254X-RAY DIFFRACTION100
1.82-1.890.21361400.21751226X-RAY DIFFRACTION100
1.89-1.960.21261400.21251230X-RAY DIFFRACTION100
1.96-2.050.19561430.1911273X-RAY DIFFRACTION100
2.05-2.160.17051360.20821246X-RAY DIFFRACTION100
2.16-2.290.24981400.20781209X-RAY DIFFRACTION100
2.3-2.470.19371320.20121242X-RAY DIFFRACTION100
2.47-2.720.2131340.2041245X-RAY DIFFRACTION100
2.72-3.110.22461440.21631249X-RAY DIFFRACTION100
3.12-3.920.2151370.22161249X-RAY DIFFRACTION100
3.93-39.080.24241400.24151244X-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)
12.69920.8994-1.14422.2129-1.23775.16550.31740.4756-0.2749-0.6468-0.00140.63561.11140.2143-0.08540.52860.041-0.17790.19080.04450.457428.847643.466549.9585
23.8865-1.10854.6920.3353-1.38226.02420.9469-1.0667-0.9455-1.1754-0.35161.42621.4311-1.5039-0.97030.4635-0.1218-0.34480.3990.00480.484515.171549.368541.1395
36.71470.3247-1.11653.1297-0.75294.29790.2693-0.0289-0.1988-0.3803-0.15360.09560.22750.3003-0.13890.22550.0343-0.04640.15920.02480.142231.045354.318746.3025
48.13243.45822.49185.881-0.91477.690.1201-0.55640.62130.39770.12760.2659-0.0805-0.4427-0.30610.21270.03430.02040.22760.06230.222528.396552.292754.117
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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