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- PDB-8fns: X-ray crystal structure of Methylorubrum extorquens AM1 lanmoduli... -

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Basic information

Entry
Database: PDB / ID: 8fns
TitleX-ray crystal structure of Methylorubrum extorquens AM1 lanmodulin (LanM) with neodymium (III) bound at pH 7
ComponentsEF-hand domain-containing protein
KeywordsMETAL BINDING PROTEIN
Function / homology
Function and homology information


periplasmic space / calcium ion binding
Similarity search - Function
EF hand / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair
Similarity search - Domain/homology
Biological speciesMethylorubrum extorquens AM1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.01 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: Nature / Year: 2023
Title: Enhanced rare-earth separation with a metal-sensitive lanmodulin dimer.
Authors: Mattocks, J.A. / Jung, J.J. / Lin, C.Y. / Dong, Z. / Yennawar, N.H. / Featherston, E.R. / Kang-Yun, C.S. / Hamilton, T.A. / Park, D.M. / Boal, A.K. / Cotruvo Jr., J.A.
History
DepositionDec 28, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 7, 2023Provider: repository / Type: Initial release
Revision 1.1Jul 26, 2023Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: EF-hand domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,6475
Polymers11,0701
Non-polymers5774
Water3,009167
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)24.099, 44.398, 82.316
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein EF-hand domain-containing protein


Mass: 11070.180 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methylorubrum extorquens AM1 (bacteria)
Gene: MexAM1_META1p1786 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: C5B164
#2: Chemical
ChemComp-ND / Neodymium Ion


Mass: 144.240 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Nd / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 167 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 1.99 Å3/Da / Density % sol: 38.16 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1 M ammonium sulfate, 0.1 M Tris pH 7.5, and 20 % (w/v) PEG 1500

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.9792 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Jul 30, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.01→50 Å / Num. obs: 42844 / % possible obs: 90.67 % / Redundancy: 11.9 % / CC1/2: 0.986 / Net I/σ(I): 26.7
Reflection shellResolution: 1.01→1.046 Å / Num. unique obs: 1876 / CC1/2: 0.752

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
HKL-2000data scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 1.01→30.18 Å / SU ML: 0.08 / Cross valid method: THROUGHOUT / σ(F): 1.16 / Phase error: 16.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1524 1939 4.52 %
Rwork0.1453 40914 -
obs0.1456 42843 90.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 59.47 Å2 / Biso mean: 24.5977 Å2 / Biso min: 14.16 Å2
Refinement stepCycle: final / Resolution: 1.01→30.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms778 0 4 167 949
Biso mean--19.3 33.49 -
Num. residues----105
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.01-1.030.2493420.22431016105832
1.03-1.060.1873960.19662028212464
1.06-1.090.17331270.19952684281184
1.09-1.130.16631460.19113049319596
1.13-1.170.21511420.17383076321896
1.17-1.220.1831500.16293121327198
1.22-1.270.15061520.15583179333199
1.27-1.340.15261500.15313191334199
1.34-1.420.1481540.147832013355100
1.42-1.530.1541530.135632183371100
1.53-1.690.1481540.138432233377100
1.69-1.930.15491550.140432613416100
1.93-2.430.13621580.136133173475100
2.43-30.180.15671600.14773350351097
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)
12.05030.8169-2.92647.9113-1.25485.8335-0.2840.2654-0.1998-0.44310.23780.72780.1077-0.3974-0.0170.3383-0.0227-0.03050.20950.02180.275713.79248.476953.8717
21.84521.3831-0.82953.0587-1.40241.9573-0.12570.0721-0.241-0.19390.041-0.2020.23570.13120.07710.166-0.00420.01090.1622-0.01150.201522.045811.783555.0453
31.72862.54150.98063.8191.61713.1525-0.10910.7122-0.2034-0.792-0.0328-0.59230.29730.2383-0.0120.5001-0.0910.09650.4339-0.05170.287729.090121.2238.0927
43.59540.77251.23061.62870.42523.3163-0.09670.59760.2673-0.6527-0.0255-0.1405-0.50830.08270.0730.3509-0.0677-0.0140.30510.03760.219625.04126.537342.0869
51.48110.1622-0.60131.33390.07071.8626-0.0610.3769-0.0990.1222-0.08830.3557-0.0308-0.62070.23720.41220.03280.00590.3658-0.00590.236316.874425.089842.3379
61.0824-0.94841.23960.8546-1.0871.44610.00830.38560.4819-0.070.00240.5211-0.4784-0.84660.01050.43580.07240.01680.37770.04320.346117.642232.999749.0016
74.00371.96130.54671.0160.69476.8345-0.44030.18210.5344-0.63180.2549-0.1676-0.80330.04430.09990.2873-0.0666-0.03360.25720.0450.205427.141232.728847.9662
81.28470.5903-0.42741.8363-0.62472.17820.0274-0.13310.05120.1572-0.0335-0.0145-0.14960.04830.0030.16340.0046-0.01410.158-0.00160.177519.368420.712460.4423
94.58580.50820.52632.4014-0.11090.7939-0.01220.1488-0.0947-0.0576-0.01240.07330.0457-0.10350.00280.15780.0009-0.00920.1559-0.01510.198111.326417.33655.3384
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 29 through 34 )A29 - 34
2X-RAY DIFFRACTION2chain 'A' and (resid 35 through 58 )A35 - 58
3X-RAY DIFFRACTION3chain 'A' and (resid 59 through 63 )A59 - 63
4X-RAY DIFFRACTION4chain 'A' and (resid 64 through 68 )A64 - 68
5X-RAY DIFFRACTION5chain 'A' and (resid 69 through 76 )A69 - 76
6X-RAY DIFFRACTION6chain 'A' and (resid 77 through 83 )A77 - 83
7X-RAY DIFFRACTION7chain 'A' and (resid 84 through 92 )A84 - 92
8X-RAY DIFFRACTION8chain 'A' and (resid 93 through 116 )A93 - 116
9X-RAY DIFFRACTION9chain 'A' and (resid 117 through 133 )A117 - 133

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