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- PDB-9pi2: X-ray crystal structure of Ancylobacter lacus LanM bound to Nd(II... -

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Basic information

Entry
Database: PDB / ID: 9pi2
TitleX-ray crystal structure of Ancylobacter lacus LanM bound to Nd(III) and Ca(II)
ComponentsAncylobacter lacus lanthanum bound protein
KeywordsMETAL BINDING PROTEIN / lanthanide / lanmodulin / calcium / dimer
Function / homology:
Function and homology information
Biological speciesAncylobacter lacus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 0.99 Å
AuthorsJung, J.J. / 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: J.Am.Chem.Soc. / Year: 2026
Title: Near-Adjacent Heavy Lanthanide Separation and Sensing Using Dimerizing Lanmodulins.
Authors: Choi, W. / Zhou, X. / Dong, Z. / Song, F. / Jung, J.J. / Mattocks, J.A. / Chlebek, J.L. / Diep, P. / Johnson, A.C. / Crawford, S.E. / Jiao, Y. / Honaker, R. / Boal, A.K. / Park, D.M. / Cotruvo Jr., J.A.
History
DepositionJul 10, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 19, 2026Provider: repository / Type: Initial release
Revision 1.1Sep 9, 2026Group: 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.title / _citation.year
Revision 1.2Sep 16, 2026Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ancylobacter lacus lanthanum bound protein
B: Ancylobacter lacus lanthanum bound protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,69311
Polymers24,6522
Non-polymers1,0429
Water7,891438
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1470 Å2
ΔGint-38 kcal/mol
Surface area11520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.242, 76.377, 42.671
Angle α, β, γ (deg.)90.00, 113.35, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Ancylobacter lacus lanthanum bound protein


Mass: 12325.773 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ancylobacter lacus (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Chemical
ChemComp-ND / Neodymium Ion


Mass: 144.240 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Nd / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 438 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.44 Å3/Da / Density % sol: 49.64 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 200 mM ammonium sulfate, 30 % (w/v) PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.97934 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 24, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 0.99→38.19 Å / Num. obs: 1000252 / % possible obs: 76.9 % / Redundancy: 1.9 % / CC1/2: 0.993 / Net I/σ(I): 11.6
Reflection shellResolution: 0.99→1.03 Å / Num. unique obs: 1368 / CC1/2: 0.627

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
PDB_EXTRACTdata extraction
autoPROCdata reduction
autoPROCdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 0.99→38.19 Å / SU ML: 0.06 / Cross valid method: NONE / σ(F): 1.34 / Phase error: 13.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1436 9877 5.13 %
Rwork0.1356 --
obs0.136 192594 74.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 0.99→38.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1732 0 13 438 2183
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041764
X-RAY DIFFRACTIONf_angle_d0.8062380
X-RAY DIFFRACTIONf_dihedral_angle_d13.2678
X-RAY DIFFRACTIONf_chiral_restr0.079272
X-RAY DIFFRACTIONf_plane_restr0.007312
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.99-10.3371100.3121147X-RAY DIFFRACTION2
1-1.020.347280.3147425X-RAY DIFFRACTION5
1.02-1.030.3384470.2858880X-RAY DIFFRACTION11
1.03-1.040.2553740.25521522X-RAY DIFFRACTION18
1.04-1.050.2263990.23622103X-RAY DIFFRACTION26
1.05-1.070.18641310.20512907X-RAY DIFFRACTION35
1.07-1.080.1961920.18413442X-RAY DIFFRACTION42
1.08-1.10.16552350.184058X-RAY DIFFRACTION50
1.1-1.120.17572440.16664777X-RAY DIFFRACTION58
1.12-1.140.1763100.15845634X-RAY DIFFRACTION69
1.14-1.160.15984090.14926911X-RAY DIFFRACTION85
1.16-1.180.15794230.1457319X-RAY DIFFRACTION91
1.18-1.20.14693960.13767637X-RAY DIFFRACTION93
1.2-1.220.13834360.13577693X-RAY DIFFRACTION95
1.22-1.250.13274060.13157808X-RAY DIFFRACTION95
1.25-1.280.134320.12957735X-RAY DIFFRACTION96
1.28-1.310.13954540.12797816X-RAY DIFFRACTION96
1.31-1.350.13923790.13167898X-RAY DIFFRACTION96
1.35-1.390.1274410.12737918X-RAY DIFFRACTION96
1.39-1.430.13315010.12497772X-RAY DIFFRACTION97
1.43-1.480.13794200.12027961X-RAY DIFFRACTION97
1.48-1.540.12914850.11787875X-RAY DIFFRACTION97
1.54-1.610.13284650.1187934X-RAY DIFFRACTION98
1.61-1.70.13274130.12237998X-RAY DIFFRACTION98
1.7-1.80.13224870.12577887X-RAY DIFFRACTION98
1.8-1.940.13933530.1298146X-RAY DIFFRACTION98
1.94-2.140.13243890.12548123X-RAY DIFFRACTION99
2.14-2.450.14254360.13268070X-RAY DIFFRACTION99
2.45-3.080.18173400.15218230X-RAY DIFFRACTION99
3.08-38.190.13664420.13818091X-RAY DIFFRACTION99
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)
10.0114-0.0428-0.12260.29060.79582.4387-0.02080.1085-0.0343-0.1542-0.04820.07180.1073-0.12960.05630.0616-0.0007-0.00550.0909-0.00690.0671-8.255914.5608-17.8024
21.1804-0.13290.0940.66660.27590.8117-0.0337-0.0345-0.15720.08280.02040.10230.0566-0.0720.020.0364-0.01020.00390.04430.00770.05442.903910.5896-10.5123
32.21720.5046-0.35551.7026-0.79692.38010.04120.5075-0.0199-0.14560.0554-0.0524-0.0747-0.2277-0.06720.08920.03290.01180.15-0.00830.062313.4168.3334-22.6789
42.0021-0.98310.43151.3811-0.22120.6257-0.00990.09060.0147-0.02980.0036-0.07520.00850.03410.00450.0366-0.01050.00180.0419-0.00130.029413.892413.5757-14.8344
53.01860.41-0.29273.42050.34472.0313-0.07360.09060.2895-0.13430.00540.0725-0.4074-0.02140.02550.12870.0006-0.03180.0550.01050.0956-1.379826.7044-17.8221
61.2848-1.11590.21742.4693-1.30362.5334-0.03270.3196-0.1287-0.2342-0.00890.06660.14340.08640.0170.0486-0.0203-0.00220.1026-0.01050.04341.619814.309-20.6926
70.0685-0.0252-0.12561.27351.62272.1983-0.0162-0.279-0.00680.2187-0.07350.04880.10.17670.02930.08240.01670.01180.12470.0290.07423.38830.11448.6861
80.9091-0.85850.12921.369-0.07130.5595-0.0514-0.09420.0240.10220.0359-0.0216-0.0311-0.01830.02170.0484-0.0058-0.00350.0582-0.00030.038914.139313.82561.422
91.3282-0.6811-0.01440.6667-0.14980.2476-0.0107-0.02660.0157-0.03630.0167-0.0054-0.01780.0433-0.00920.0484-0.0019-0.00060.0488-0.0070.04219.879914.1765-2.91
101.6278-0.04620.01411.4323-0.03391.6005-0.0072-0.1623-0.00340.05180.0137-0.0659-0.02510.20360.00510.0486-0.0015-0.00240.06780.00460.028628.1537.56162.7989
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 28 through 38 )
2X-RAY DIFFRACTION2chain 'A' and (resid 39 through 71 )
3X-RAY DIFFRACTION3chain 'A' and (resid 72 through 87 )
4X-RAY DIFFRACTION4chain 'A' and (resid 88 through 111 )
5X-RAY DIFFRACTION5chain 'A' and (resid 112 through 126 )
6X-RAY DIFFRACTION6chain 'A' and (resid 127 through 138 )
7X-RAY DIFFRACTION7chain 'B' and (resid 28 through 38 )
8X-RAY DIFFRACTION8chain 'B' and (resid 39 through 96 )
9X-RAY DIFFRACTION9chain 'B' and (resid 97 through 111 )
10X-RAY DIFFRACTION10chain 'B' and (resid 112 through 138 )

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