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- PDB-9vy9: Structure of MIF binding with Gadolinium ions -

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Basic information

Entry
Database: PDB / ID: 9vy9
TitleStructure of MIF binding with Gadolinium ions
ComponentsPropeptide, PepSY amd peptidase M4
KeywordsMETAL BINDING PROTEIN / Rare earth / Metalloprotein
Function / homologyPepSY domain / Peptidase propeptide and YPEB domain / BROMIDE ION / GADOLINIUM ATOM / 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. / 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
C: Propeptide, PepSY amd peptidase M4
D: Propeptide, PepSY amd peptidase M4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,46134
Polymers67,9754
Non-polymers4,48530
Water13,205733
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12020 Å2
ΔGint-302 kcal/mol
Surface area25950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.804, 101.146, 115.403
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein
Propeptide, PepSY amd peptidase M4


Mass: 16993.787 Da / Num. of mol.: 4
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-GD / GADOLINIUM ATOM


Mass: 157.250 Da / Num. of mol.: 27 / Source method: obtained synthetically / Formula: Gd / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Br
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 733 / 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: 2.48 Å3/Da / Density % sol: 50.43 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.15 M KBr, 30% w/v polyethylene glycol monomethyl ether 2,000, 10 mM sarcosine

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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: 1.41→76.07 Å / Num. obs: 129245 / % possible obs: 99.7 % / Redundancy: 9.3 % / Biso Wilson estimate: 13.42 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.177 / Rpim(I) all: 0.059 / Rrim(I) all: 0.187 / Net I/σ(I): 8.7
Reflection shell
Resolution (Å)Num. unique obsRpim(I) allDiffraction-IDRmerge(I) obs
1.41-1.49185650.8321
1.49-1.57176120.44811.256
1.57-1.69166530.25610.762
1.69-1.81155220.1510.434
1.81-2.01143470.08410.242
2.01-2.21130270.05910.16
2.21-2.57115370.04610.123
2.57-3.0998400.0410.092
3.09-4.2177140.03210.076
4.21-76.0744280.03110.08

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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→51.68 Å / SU ML: 0.1212 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 15.4394
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1661 6479 5.02 %
Rwork0.1502 122595 -
obs0.151 129074 99.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.03 Å2
Refinement stepCycle: LAST / Resolution: 1.41→51.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4690 0 30 733 5453
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01544771
X-RAY DIFFRACTIONf_angle_d1.49486440
X-RAY DIFFRACTIONf_chiral_restr0.0978711
X-RAY DIFFRACTIONf_plane_restr0.0115849
X-RAY DIFFRACTIONf_dihedral_angle_d16.50111775
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.41-1.430.28722180.29343983X-RAY DIFFRACTION99.1
1.43-1.450.30612120.28553981X-RAY DIFFRACTION97.63
1.45-1.460.29942130.27784043X-RAY DIFFRACTION99.67
1.46-1.480.27151960.25644005X-RAY DIFFRACTION98.15
1.48-1.50.27121950.24714080X-RAY DIFFRACTION99.91
1.5-1.520.23152270.22733974X-RAY DIFFRACTION98.43
1.52-1.550.22082080.21384040X-RAY DIFFRACTION99.98
1.55-1.570.22682200.19984042X-RAY DIFFRACTION98.82
1.57-1.590.20712250.18754039X-RAY DIFFRACTION99.98
1.59-1.620.19391980.18214044X-RAY DIFFRACTION99.07
1.62-1.650.18962150.16024063X-RAY DIFFRACTION99.79
1.65-1.680.1872270.15784009X-RAY DIFFRACTION99.46
1.68-1.710.15062260.14894066X-RAY DIFFRACTION99.51
1.71-1.740.15442110.1394099X-RAY DIFFRACTION100
1.74-1.780.15962050.13464061X-RAY DIFFRACTION99.65
1.78-1.820.14252190.13354048X-RAY DIFFRACTION99.74
1.82-1.870.14042110.12044102X-RAY DIFFRACTION99.81
1.87-1.920.13181930.11644091X-RAY DIFFRACTION100
1.92-1.980.12122200.12124093X-RAY DIFFRACTION99.88
1.98-2.040.12852280.11414066X-RAY DIFFRACTION99.95
2.04-2.110.1282230.11844103X-RAY DIFFRACTION99.98
2.11-2.20.16112470.12244078X-RAY DIFFRACTION100
2.2-2.30.14262120.12674118X-RAY DIFFRACTION99.98
2.3-2.420.14932050.13054125X-RAY DIFFRACTION100
2.42-2.570.15092230.13154122X-RAY DIFFRACTION100
2.57-2.770.15872180.13714149X-RAY DIFFRACTION100
2.77-3.050.18172070.14254177X-RAY DIFFRACTION100
3.05-3.490.15612200.14914176X-RAY DIFFRACTION100
3.49-4.390.1592120.14334236X-RAY DIFFRACTION100
4.39-51.680.16682450.16164382X-RAY DIFFRACTION99.78
Refinement TLS params.Method: refined / Origin x: 18.448 Å / Origin y: 10.071 Å / Origin z: 13.086 Å
111213212223313233
T0.115622177513 Å20.00257915081701 Å20.0096037113406 Å2-0.113371402057 Å20.00874377081889 Å2--0.115313600762 Å2
L0.250848949762 °2-0.0139952667373 °20.0449069313324 °2-0.366190181378 °20.34631872269 °2--0.579284489709 °2
S0.023895407176 Å °0.0524980505161 Å °0.0287624429645 Å °-0.0113271832314 Å °0.00652548324149 Å °-0.047233292136 Å °0.0111264748108 Å °-0.0250304835918 Å °-0.0335060828148 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND ( RESID 2:153 OR RESID 201:207 OR RESID 301:479 ) ) OR ( CHAIN B AND ( RESID 4:153 OR RESID 201:207 OR RESID 301:469 ) ) OR ( CHAIN C AND ( RESID 4:153 OR RESID 201:209 OR RESID 301:487 ) ) OR ( CHAIN D AND ( RESID 392:469 OR RESID 3:153 OR RESID 201:207 ) )A2 - 153
2X-RAY DIFFRACTION1( CHAIN A AND ( RESID 2:153 OR RESID 201:207 OR RESID 301:479 ) ) OR ( CHAIN B AND ( RESID 4:153 OR RESID 201:207 OR RESID 301:469 ) ) OR ( CHAIN C AND ( RESID 4:153 OR RESID 201:209 OR RESID 301:487 ) ) OR ( CHAIN D AND ( RESID 392:469 OR RESID 3:153 OR RESID 201:207 ) )A201 - 207
3X-RAY DIFFRACTION1( CHAIN A AND ( RESID 2:153 OR RESID 201:207 OR RESID 301:479 ) ) OR ( CHAIN B AND ( RESID 4:153 OR RESID 201:207 OR RESID 301:469 ) ) OR ( CHAIN C AND ( RESID 4:153 OR RESID 201:209 OR RESID 301:487 ) ) OR ( CHAIN D AND ( RESID 392:469 OR RESID 3:153 OR RESID 201:207 ) )A301 - 479
4X-RAY DIFFRACTION1( CHAIN A AND ( RESID 2:153 OR RESID 201:207 OR RESID 301:479 ) ) OR ( CHAIN B AND ( RESID 4:153 OR RESID 201:207 OR RESID 301:469 ) ) OR ( CHAIN C AND ( RESID 4:153 OR RESID 201:209 OR RESID 301:487 ) ) OR ( CHAIN D AND ( RESID 392:469 OR RESID 3:153 OR RESID 201:207 ) )B4 - 153
5X-RAY DIFFRACTION1( CHAIN A AND ( RESID 2:153 OR RESID 201:207 OR RESID 301:479 ) ) OR ( CHAIN B AND ( RESID 4:153 OR RESID 201:207 OR RESID 301:469 ) ) OR ( CHAIN C AND ( RESID 4:153 OR RESID 201:209 OR RESID 301:487 ) ) OR ( CHAIN D AND ( RESID 392:469 OR RESID 3:153 OR RESID 201:207 ) )B201 - 207
6X-RAY DIFFRACTION1( CHAIN A AND ( RESID 2:153 OR RESID 201:207 OR RESID 301:479 ) ) OR ( CHAIN B AND ( RESID 4:153 OR RESID 201:207 OR RESID 301:469 ) ) OR ( CHAIN C AND ( RESID 4:153 OR RESID 201:209 OR RESID 301:487 ) ) OR ( CHAIN D AND ( RESID 392:469 OR RESID 3:153 OR RESID 201:207 ) )B301 - 469
7X-RAY DIFFRACTION1( CHAIN A AND ( RESID 2:153 OR RESID 201:207 OR RESID 301:479 ) ) OR ( CHAIN B AND ( RESID 4:153 OR RESID 201:207 OR RESID 301:469 ) ) OR ( CHAIN C AND ( RESID 4:153 OR RESID 201:209 OR RESID 301:487 ) ) OR ( CHAIN D AND ( RESID 392:469 OR RESID 3:153 OR RESID 201:207 ) )C4 - 153
8X-RAY DIFFRACTION1( CHAIN A AND ( RESID 2:153 OR RESID 201:207 OR RESID 301:479 ) ) OR ( CHAIN B AND ( RESID 4:153 OR RESID 201:207 OR RESID 301:469 ) ) OR ( CHAIN C AND ( RESID 4:153 OR RESID 201:209 OR RESID 301:487 ) ) OR ( CHAIN D AND ( RESID 392:469 OR RESID 3:153 OR RESID 201:207 ) )C201 - 209
9X-RAY DIFFRACTION1( CHAIN A AND ( RESID 2:153 OR RESID 201:207 OR RESID 301:479 ) ) OR ( CHAIN B AND ( RESID 4:153 OR RESID 201:207 OR RESID 301:469 ) ) OR ( CHAIN C AND ( RESID 4:153 OR RESID 201:209 OR RESID 301:487 ) ) OR ( CHAIN D AND ( RESID 392:469 OR RESID 3:153 OR RESID 201:207 ) )C301 - 487
10X-RAY DIFFRACTION1( CHAIN A AND ( RESID 2:153 OR RESID 201:207 OR RESID 301:479 ) ) OR ( CHAIN B AND ( RESID 4:153 OR RESID 201:207 OR RESID 301:469 ) ) OR ( CHAIN C AND ( RESID 4:153 OR RESID 201:209 OR RESID 301:487 ) ) OR ( CHAIN D AND ( RESID 392:469 OR RESID 3:153 OR RESID 201:207 ) )D392 - 469
11X-RAY DIFFRACTION1( CHAIN A AND ( RESID 2:153 OR RESID 201:207 OR RESID 301:479 ) ) OR ( CHAIN B AND ( RESID 4:153 OR RESID 201:207 OR RESID 301:469 ) ) OR ( CHAIN C AND ( RESID 4:153 OR RESID 201:209 OR RESID 301:487 ) ) OR ( CHAIN D AND ( RESID 392:469 OR RESID 3:153 OR RESID 201:207 ) )D3 - 153
12X-RAY DIFFRACTION1( CHAIN A AND ( RESID 2:153 OR RESID 201:207 OR RESID 301:479 ) ) OR ( CHAIN B AND ( RESID 4:153 OR RESID 201:207 OR RESID 301:469 ) ) OR ( CHAIN C AND ( RESID 4:153 OR RESID 201:209 OR RESID 301:487 ) ) OR ( CHAIN D AND ( RESID 392:469 OR RESID 3:153 OR RESID 201:207 ) )D201 - 207

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