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- PDB-9vy7: Structure of MIF binding with Lanthanum ions -

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Basic information

Entry
Database: PDB / ID: 9vy7
TitleStructure of MIF binding with Lanthanum ions
ComponentsPropeptide, PepSY amd peptidase M4
KeywordsMETAL BINDING PROTEIN / Rare earth / Metalloprotein
Function / homologyPepSY domain / Peptidase propeptide and YPEB domain / LANTHANUM (III) ION / Propeptide, PepSY amd peptidase M4
Function and homology information
Biological speciesMethylobacillus flagellatus KT (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 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)17,6886
Polymers16,9941
Non-polymers6955
Water4,270237
1
A: Propeptide, PepSY amd peptidase M4
hetero molecules

A: Propeptide, PepSY amd peptidase M4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,37712
Polymers33,9882
Non-polymers1,38910
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area4270 Å2
ΔGint-118 kcal/mol
Surface area13760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.896, 40.741, 56.416
Angle α, β, γ (deg.)90.000, 112.519, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Components on special symmetry positions
IDModelComponents
11A-515-

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-LA / LANTHANUM (III) ION


Mass: 138.905 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: La / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 237 / 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: 44.46 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.2 M ammonium acetate, 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: Mar 14, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979176 Å / Relative weight: 1
ReflectionResolution: 1.19→52.11 Å / Num. obs: 39396 / % possible obs: 82.4 % / Redundancy: 4.6 % / Biso Wilson estimate: 10.76 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.073 / Rpim(I) all: 0.035 / Rrim(I) all: 0.081 / Net I/σ(I): 16.6
Reflection shell
Resolution (Å)Num. unique obsRpim(I) allDiffraction-ID
1.19-1.2621350.311
1.26-1.3238470.1871
1.32-1.4253550.1141
1.42-1.5457490.0721
1.54-1.6852790.051
1.68-1.8847960.0381
1.88-2.1442600.031
2.14-2.6235860.0281
2.62-3.5228150.0281
3.52-52.1115740.0291

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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: 1.25→26.06 Å / SU ML: 0.0641 / Cross valid method: FREE R-VALUE / σ(F): 1.41 / Phase error: 11.3276
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1289 1885 5.03 %
Rwork0.1207 35609 -
obs0.1211 37494 90.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 15.14 Å2
Refinement stepCycle: LAST / Resolution: 1.25→26.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1178 0 5 237 1420
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01561199
X-RAY DIFFRACTIONf_angle_d1.38411618
X-RAY DIFFRACTIONf_chiral_restr0.0998178
X-RAY DIFFRACTIONf_plane_restr0.0118213
X-RAY DIFFRACTIONf_dihedral_angle_d15.1206446
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.25-1.280.1865820.17581516X-RAY DIFFRACTION50.31
1.28-1.320.1346930.14591837X-RAY DIFFRACTION61.88
1.32-1.360.15131350.12932277X-RAY DIFFRACTION75.78
1.36-1.410.11741380.12372760X-RAY DIFFRACTION92.03
1.41-1.470.11371570.11382998X-RAY DIFFRACTION100
1.47-1.540.12751620.11342995X-RAY DIFFRACTION99.97
1.54-1.620.1181380.10423028X-RAY DIFFRACTION100
1.62-1.720.13991350.10673027X-RAY DIFFRACTION99.97
1.72-1.850.11051790.10653004X-RAY DIFFRACTION100
1.85-2.040.10471610.10533012X-RAY DIFFRACTION100
2.04-2.330.10991410.10943033X-RAY DIFFRACTION100
2.33-2.940.14262040.12593015X-RAY DIFFRACTION100
2.94-26.060.14591600.13923107X-RAY DIFFRACTION99.97
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)
12.05898735517-0.04737600756690.3449852479912.20497685480.2520536934222.02117945599-0.04315865719150.0387356350879-0.2014096428080.0180319893338-0.02354316223560.0009094003826040.24069798518-0.03214390947440.04174599952520.084836456804-0.0002691596798180.02996046107590.0693747024501-0.002496758413020.0625029738489-1.03979704466-6.837030565996.83469253063
21.54220604563-0.613142573733-0.06590849308214.038501192931.006484953231.70371687559-0.01750440560110.0452106843766-0.1651206845250.137062792917-0.06321063161740.1700408897570.145676623466-0.2546998645010.03316661080050.0753958086223-0.01424943688790.01428521263790.0850423219111-0.003712989946730.0710787023011-6.73830215626-2.1328315361412.9775628498
33.025850226-0.125094688012-0.6840071337771.269110495590.280378799341.905529609910.0116415934232-0.08248839460580.1564644059110.0333596223411-0.0148651469349-0.155725441624-0.1001721047330.148134422956-0.01203115702880.0608470839997-0.01210085927-0.006651698370270.04218255385490.01641730687070.08119426657894.444543803199.9789059710721.3199772709
44.902262424540.478378115793-1.700697417971.926858342530.07848099208473.41983736251-0.0779167043209-0.0101889360639-0.135384142335-0.00104609356560.00962401012495-0.1446509733070.14161453430.09807462460160.05636538498140.057434330240.0115308188925-0.0213079988720.02599524005720.01083799094650.05242756302733.261346066343.5608034308719.3533295134
52.952871022610.162371683089-0.6949210586991.700477989330.1339589316172.19132949743-0.0117072210070.0449447206315-0.01448099427920.05472181482580.0194087219884-0.2468757534250.1836489885090.2037404571020.01527036519890.05969348963750.0243893209409-0.0227567889140.06377842535320.01128591193510.1056822856299.955545476171.7309235809819.7698945863
61.24019566675-0.2475211264450.353558563450.6915225164111.394119443283.464327518760.008436943886960.07980771773450.0353734687699-0.01756363988550.0240006651112-0.09044450917010.04280183267080.1762801983830.01541951637240.05675736809340.005778713054080.007690527481130.04274248069040.01077460010520.075282675626.59743084321-0.93374602307510.3961651104
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 3 through 46 )3 - 461 - 44
22chain 'A' and (resid 47 through 71 )47 - 7145 - 69
33chain 'A' and (resid 72 through 109 )72 - 10970 - 107
44chain 'A' and (resid 110 through 123 )110 - 123108 - 121
55chain 'A' and (resid 124 through 139 )124 - 139122 - 137
66chain 'A' and (resid 140 through 153 )140 - 153138 - 151

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