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- PDB-9vy8: Structure of MIF binding with Samarium ions -

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Basic information

Entry
Database: PDB / ID: 9vy8
TitleStructure of MIF binding with Samarium ions
ComponentsPropeptide, PepSY amd peptidase M4
KeywordsMETAL BINDING PROTEIN / Rare earth / Metalloprotein
Function / homologyPepSY domain / Peptidase propeptide and YPEB domain / SAMARIUM (III) ION / Propeptide, PepSY amd peptidase M4
Function and homology information
Biological speciesMethylobacillus flagellatus KT (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.16 Å
AuthorsDu, Y.X. / Li, Z.Q. / 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)17,8967
Polymers16,9941
Non-polymers9026
Water30617
1
A: Propeptide, PepSY amd peptidase M4
hetero molecules

A: Propeptide, PepSY amd peptidase M4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,79214
Polymers33,9882
Non-polymers1,80412
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation15_554y,x,-z-11
Buried area4450 Å2
ΔGint-137 kcal/mol
Surface area14120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.052, 119.052, 79.209
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122
Space group name HallI4bw2bw
Symmetry operation#1: x,y,z
#2: -y+1/2,x,z+3/4
#3: y+1/2,-x,z+3/4
#4: x+1/2,-y,-z+3/4
#5: -x+1/2,y,-z+3/4
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z
#9: x+1/2,y+1/2,z+1/2
#10: -y+1,x+1/2,z+5/4
#11: y+1,-x+1/2,z+5/4
#12: x+1,-y+1/2,-z+5/4
#13: -x+1,y+1/2,-z+5/4
#14: -x+1/2,-y+1/2,z+1/2
#15: y+1/2,x+1/2,-z+1/2
#16: -y+1/2,-x+1/2,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-309-

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-SM / SAMARIUM (III) ION


Mass: 150.360 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Sm / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / 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: 4.13 Å3/Da / Density % sol: 70.21 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.1 M BIS-TRIS pH 6.1, 29.4% w/v polyethylene glycol 3,350, 0.5% w/v n-octyl-beta-D-glucoside

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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: Nov 28, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979176 Å / Relative weight: 1
ReflectionResolution: 2.15→84.18 Å / Num. obs: 15877 / % possible obs: 99.5 % / Redundancy: 14.1 % / Biso Wilson estimate: 34.95 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.12 / Rpim(I) all: 0.032 / Rrim(I) all: 0.124 / Net I/σ(I): 16.8
Reflection shell
Resolution (Å)Num. unique obsRpim(I) allDiffraction-ID
2.15-2.2725270.6671
2.27-2.4323740.3831
2.43-2.6322030.2041
2.63-2.8720400.1071
2.87-3.2118750.0541
3.21-3.6716590.0341
3.67-4.4714110.0271
4.47-6.0511170.0231
6.05-84.186710.0221

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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: 2.16→37.65 Å / SU ML: 0.2466 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 38.5356
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2334 746 4.82 %
Rwork0.2283 14743 -
obs0.2286 15489 99.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 62.58 Å2
Refinement stepCycle: LAST / Resolution: 2.16→37.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1168 0 6 17 1191
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01411188
X-RAY DIFFRACTIONf_angle_d1.55761603
X-RAY DIFFRACTIONf_chiral_restr0.0648177
X-RAY DIFFRACTIONf_plane_restr0.0083211
X-RAY DIFFRACTIONf_dihedral_angle_d6.6708155
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.16-2.330.38621300.37422896X-RAY DIFFRACTION99.12
2.33-2.560.31071630.32262883X-RAY DIFFRACTION99.28
2.56-2.930.29861370.25692922X-RAY DIFFRACTION99.51
2.93-3.690.22121560.22252951X-RAY DIFFRACTION99.78
3.69-37.650.1831600.17893091X-RAY DIFFRACTION99.88
Refinement TLS params.Method: refined / Origin x: 0.853407669983 Å / Origin y: 16.803939295 Å / Origin z: -30.8499608 Å
111213212223313233
T0.442723660633 Å20.0210069481391 Å20.0920878204989 Å2-0.320999022116 Å20.0105657496197 Å2--0.505501550295 Å2
L3.54477363135 °2-0.134622417824 °20.233444287129 °2-4.23846060754 °20.577684744059 °2--2.20506968043 °2
S-0.00443920876156 Å °-0.159495141911 Å °0.179976933316 Å °0.645980099215 Å °0.0443640205974 Å °0.523366210713 Å °-0.0781576026122 Å °-0.226917001475 Å °-0.0300387801654 Å °
Refinement TLS groupSelection details: all

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