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- PDB-9vy4: Structure of MIF binding with Ytterbium ions -

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Basic information

Entry
Database: PDB / ID: 9vy4
TitleStructure of MIF binding with Ytterbium ions
ComponentsPropeptide, PepSY amd peptidase M4
KeywordsMETAL BINDING PROTEIN / Rare earth / Metalloprotein
Function / homologyPepSY domain / Peptidase propeptide and YPEB domain / YTTERBIUM (III) ION / Propeptide, PepSY amd peptidase M4
Function and homology information
Biological speciesMethylobacillus flagellatus KT (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.21 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)35,78715
Polymers33,9882
Non-polymers1,79913
Water8,773487
1
A: Propeptide, PepSY amd peptidase M4
hetero molecules

A: Propeptide, PepSY amd peptidase M4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,76414
Polymers33,9882
Non-polymers1,77612
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area4150 Å2
ΔGint-131 kcal/mol
Surface area13850 Å2
MethodPISA
2
B: Propeptide, PepSY amd peptidase M4
hetero molecules

B: Propeptide, PepSY amd peptidase M4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,81016
Polymers33,9882
Non-polymers1,82214
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Buried area4040 Å2
ΔGint-159 kcal/mol
Surface area14170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.222, 120.294, 36.011
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z

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Components

#1: Protein Propeptide, PepSY amd peptidase M4


Mass: 16993.787 Da / Num. of mol.: 2
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-YB / YTTERBIUM (III) ION


Mass: 173.040 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Yb / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 487 / 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: 2.3 Å3/Da / Density % sol: 46.55 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.1 M MES pH 6.5, 25% w/v Polyethylene glycol 4,000, 0.7% v/v 1-butanol

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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 30, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979176 Å / Relative weight: 1
ReflectionResolution: 1.21→61.92 Å / Num. obs: 73230 / % possible obs: 76.8 % / Redundancy: 9.2 % / Rmerge(I) obs: 0.097 / Rpim(I) all: 0.03 / Rrim(I) all: 0.102 / Net I/σ(I): 21.9
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsDiffraction-ID
1.21-1.280.55227511
1.28-1.360.37162381
1.36-1.440.24784601
1.44-1.570.15109921
1.57-1.710.101104941
1.71-1.910.06895281
1.91-2.190.05384841
2.19-2.670.04872611
2.67-3.610.04557051
3.61-61.920.04733171

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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: 1.21→35.06 Å / SU ML: 0.0651 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 13.1763
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1379 3585 4.9 %
Rwork0.1242 69549 -
obs0.1249 73134 76.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 17.03 Å2
Refinement stepCycle: LAST / Resolution: 1.21→35.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2336 0 13 487 2836
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01912376
X-RAY DIFFRACTIONf_angle_d1.53483206
X-RAY DIFFRACTIONf_chiral_restr0.1047354
X-RAY DIFFRACTIONf_plane_restr0.0114422
X-RAY DIFFRACTIONf_dihedral_angle_d15.403886
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.21-1.230.330490.282230X-RAY DIFFRACTION6.6
1.23-1.250.291340.2649559X-RAY DIFFRACTION16.41
1.25-1.270.3138440.2364863X-RAY DIFFRACTION25.16
1.27-1.280.2632690.21331210X-RAY DIFFRACTION34.92
1.28-1.30.1833810.1921438X-RAY DIFFRACTION42.05
1.3-1.330.1643830.17191631X-RAY DIFFRACTION47.32
1.33-1.350.15161020.15351804X-RAY DIFFRACTION52.7
1.35-1.370.17851130.14292001X-RAY DIFFRACTION58.22
1.37-1.40.14771360.1342194X-RAY DIFFRACTION64.13
1.4-1.430.1255970.12512496X-RAY DIFFRACTION71.47
1.43-1.460.13571590.12162783X-RAY DIFFRACTION80.62
1.46-1.490.13691530.11923247X-RAY DIFFRACTION92.64
1.49-1.530.13141620.10683383X-RAY DIFFRACTION98.47
1.53-1.570.12871710.10653456X-RAY DIFFRACTION98.45
1.57-1.620.12911670.10573438X-RAY DIFFRACTION99.12
1.62-1.670.10671690.10483445X-RAY DIFFRACTION99.12
1.67-1.730.1171840.10313459X-RAY DIFFRACTION99.02
1.73-1.80.12321830.10033476X-RAY DIFFRACTION99.51
1.8-1.880.12031760.1043476X-RAY DIFFRACTION99.48
1.88-1.980.10781920.10933455X-RAY DIFFRACTION99.64
1.98-2.10.11891890.11363492X-RAY DIFFRACTION99.78
2.1-2.270.13131740.11743541X-RAY DIFFRACTION99.87
2.27-2.50.14491610.12123537X-RAY DIFFRACTION99.97
2.5-2.860.13231740.13053581X-RAY DIFFRACTION100
2.86-3.60.14792190.14053584X-RAY DIFFRACTION100
3.6-35.060.15951840.13923770X-RAY DIFFRACTION99.82
Refinement TLS params.Method: refined / Origin x: -1.48929591529 Å / Origin y: 30.043161182 Å / Origin z: -13.3077185263 Å
111213212223313233
T0.0827911610526 Å2-0.00478649512344 Å20.0104602741908 Å2-0.101434862595 Å20.00317581726261 Å2--0.0922155883505 Å2
L0.0150127149834 °2-0.00289504897422 °20.0488839909707 °2-0.423771379062 °20.149925254504 °2--0.204420726488 °2
S0.0082885419628 Å °0.000698321437902 Å °-0.00684677520224 Å °0.0128967337333 Å °-0.0285816170618 Å °-0.0214614259219 Å °-0.00671546434668 Å °-0.0403252875414 Å °0.0165071425302 Å °
Refinement TLS groupSelection details: all

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