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- PDB-8dq2: X-ray crystal structure of Hansschlegelia quercus lanmodulin (Lan... -

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Basic information

Entry
Database: PDB / ID: 8dq2
TitleX-ray crystal structure of Hansschlegelia quercus lanmodulin (LanM) with lanthanum (III) bound at pH 7
ComponentsEF-hand domain-containing protein
KeywordsMETAL BINDING PROTEIN / methanol dehydrogenase
Function / homologyEF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / calcium ion binding / CITRIC ACID / LANTHANUM (III) ION / EF-hand domain-containing protein
Function and homology information
Biological speciesHansschlegelia quercus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 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
DepositionJul 18, 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
B: EF-hand domain-containing protein
C: EF-hand domain-containing protein
D: EF-hand domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,83622
Polymers47,6934
Non-polymers2,14318
Water4,738263
1
A: EF-hand domain-containing protein
C: EF-hand domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,72610
Polymers23,8472
Non-polymers8798
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2920 Å2
ΔGint-94 kcal/mol
Surface area11420 Å2
MethodPISA
2
B: EF-hand domain-containing protein
D: EF-hand domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,11012
Polymers23,8472
Non-polymers1,26410
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2890 Å2
ΔGint-95 kcal/mol
Surface area11400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.107, 108.658, 44.697
Angle α, β, γ (deg.)90.000, 90.020, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
EF-hand domain-containing protein


Mass: 11923.299 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hansschlegelia quercus (bacteria) / Gene: EYR15_14300 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: A0A4V2JDD3
#2: Chemical
ChemComp-LA / LANTHANUM (III) ION


Mass: 138.905 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: La / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 263 / 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: 2.04 Å3/Da / Density % sol: 39.77 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.01 M tri-sodium citrate, 27 % (w/v) PEG 6000

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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: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 29, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 41911 / % possible obs: 86.7 % / Redundancy: 6 % / Biso Wilson estimate: 17.53 Å2 / CC1/2: 0.995 / CC star: 0.999 / Rpim(I) all: 0.052 / Rrim(I) all: 0.133 / Net I/σ(I): 12.9
Reflection shellResolution: 1.8→1.865 Å / Redundancy: 4.2 % / Mean I/σ(I) obs: 1.39 / Num. unique obs: 1053 / CC1/2: 0.612 / CC star: 0.868 / Rpim(I) all: 0.531 / Rrim(I) all: 1.13 / % possible all: 15.2

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
HKL-2000data scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 1.8→40.11 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.43 / Phase error: 23.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2088 2106 5.03 %
Rwork0.1898 39790 -
obs0.1894 41896 59.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 81.42 Å2 / Biso mean: 26.0408 Å2 / Biso min: 8.23 Å2
Refinement stepCycle: final / Resolution: 1.8→40.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3336 0 42 263 3641
Biso mean--46.4 30.33 -
Num. residues----440
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8-1.840.3214330.331459863114
1.84-1.890.2515460.288386591120
1.89-1.940.2556660.27481107117325
1.94-20.2197810.24581383146431
2-2.060.2232900.2391613170337
2.06-2.130.2621150.22712067218246
2.13-2.220.2151170.21642343246053
2.22-2.320.22731360.21312716285262
2.32-2.440.23361600.2053101326170
2.44-2.60.21331940.21243584377880
2.6-2.80.22771910.2083825401686
2.8-3.080.22372100.20264056426692
3.08-3.520.22272120.19654134434693
3.52-4.440.19362240.15064124434893
4.44-40.110.15772310.1534274450597

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