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- PDB-9vya: Structure of MIF binding with Neodymium ions -

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Basic information

Entry
Database: PDB / ID: 9vya
TitleStructure of MIF binding with Neodymium ions
ComponentsPropeptide, PepSY amd peptidase M4
KeywordsMETAL BINDING PROTEIN / Rare earth / Metalloprotein
Function / homologyPepSY domain / Peptidase propeptide and YPEB domain / : / Propeptide, PepSY amd peptidase M4
Function and homology information
Biological speciesMethylobacillus flagellatus KT (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.41 Å
AuthorsDu, Y.X. / Liu, L.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)20241380001 China
CitationJournal: To Be Published
Title: Adjacent Rare Earth Separation by a protein atomic ruler
Authors: Du, Y.X. / Li, Z.Q. / Liu, L.
History
DepositionJul 20, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jul 22, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Propeptide, PepSY amd peptidase M4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,7156
Polymers16,9941
Non-polymers7215
Water3,351186
1
A: Propeptide, PepSY amd peptidase M4
hetero molecules

A: Propeptide, PepSY amd peptidase M4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,43012
Polymers33,9882
Non-polymers1,44210
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area1650 Å2
ΔGint-13 kcal/mol
Surface area13830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.540, 40.560, 56.020
Angle α, β, γ (deg.)90.000, 112.530, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11A-469-

HOH

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Components

#1: Protein Propeptide, PepSY amd peptidase M4


Mass: 16993.787 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methylobacillus flagellatus KT (bacteria)
Gene: Mfla_0908, Mfla_1052 / Plasmid: pET25b / Production host: Escherichia coli (E. coli) / References: UniProt: Q1H2G7
#2: Chemical
ChemComp-ND / Neodymium Ion


Mass: 144.240 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Nd / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 186 / 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: 2.21 Å3/Da / Density % sol: 44.31 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.1 M BIS-TRIS pH 5.5, 25% w/v polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.979176 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Sep 28, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979176 Å / Relative weight: 1
ReflectionResolution: 1.41→51.74 Å / Num. obs: 28608 / % possible obs: 99.5 % / Redundancy: 5.6 % / Biso Wilson estimate: 5.37 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.131 / Rpim(I) all: 0.059 / Rrim(I) all: 0.145 / Net I/σ(I): 14.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all
1.41-1.450.215.921010.6170.1710.272
1.45-1.490.2622029
1.49-1.530.3242025
1.53-1.570.3471935
1.57-1.630.3721902
1.63-1.690.4021828
1.69-1.750.3571728
1.75-1.810.2841689
1.81-1.90.2051609
1.9-20.151566
2-2.10.1161462
2.1-2.220.0961416
2.22-2.380.0871321
2.38-2.560.0651242
2.56-2.820.0571109
2.82-3.120.0471046
3.12-3.620.049909
3.62-4.360.046754
4.36-5.940.044602
5.94-51.740.043335

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
autoPROCdata reduction
Aimless0.7.4data scaling
PHENIX1.19.2_4158phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.41→31.84 Å / SU ML: 0.1135 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 13.8889
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1587 1360 4.76 %
Rwork0.1421 27239 -
obs0.1429 28599 99.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 13.68 Å2
Refinement stepCycle: LAST / Resolution: 1.41→31.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1168 0 5 186 1359
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01571188
X-RAY DIFFRACTIONf_angle_d1.3561603
X-RAY DIFFRACTIONf_chiral_restr0.0989177
X-RAY DIFFRACTIONf_plane_restr0.01211
X-RAY DIFFRACTIONf_dihedral_angle_d15.729443
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.41-1.460.22871580.24222679X-RAY DIFFRACTION99.33
1.46-1.520.19931290.1872723X-RAY DIFFRACTION99.72
1.52-1.590.20661430.16832715X-RAY DIFFRACTION99.79
1.59-1.670.14861340.12552702X-RAY DIFFRACTION99.93
1.67-1.780.17751380.12342712X-RAY DIFFRACTION99.23
1.78-1.910.15351280.11332712X-RAY DIFFRACTION99.06
1.91-2.110.13041340.11352708X-RAY DIFFRACTION99.2
2.11-2.410.13421290.11452758X-RAY DIFFRACTION99.52
2.41-3.040.12531280.1282749X-RAY DIFFRACTION99.76
3.04-31.840.15331390.14982781X-RAY DIFFRACTION98.32
Refinement TLS params.Method: refined / Origin x: 1.67035911774 Å / Origin y: 1.03608804988 Å / Origin z: 14.7137004019 Å
111213212223313233
T0.050309677936 Å20.0121005612578 Å2-0.00224497492903 Å2-0.0426358949679 Å20.00302836641852 Å2--0.0436500910464 Å2
L0.793062061933 °20.13132405485 °20.000470297296722 °2-0.786737473721 °20.155860730966 °2--0.9810032387 °2
S0.00854109126817 Å °0.025753811805 Å °-0.0557286530725 Å °0.049218890152 Å °0.00362607704614 Å °-0.0283888180301 Å °0.0755427636386 Å °0.0325155659188 Å °-0.0085983141118 Å °
Refinement TLS groupSelection details: all

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