[English] 日本語
Yorodumi
- PDB-9vy3: Structure of apo MIF (Lanpepsy) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9vy3
TitleStructure of apo MIF (Lanpepsy)
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: 2.08 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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


Theoretical massNumber of molelcules
Total (without water)67,9754
Polymers67,9754
Non-polymers00
Water6,539363
1
A: Propeptide, PepSY amd peptidase M4
C: Propeptide, PepSY amd peptidase M4


Theoretical massNumber of molelcules
Total (without water)33,9882
Polymers33,9882
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1470 Å2
ΔGint-11 kcal/mol
Surface area14270 Å2
MethodPISA
2
B: Propeptide, PepSY amd peptidase M4
D: Propeptide, PepSY amd peptidase M4


Theoretical massNumber of molelcules
Total (without water)33,9882
Polymers33,9882
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1920 Å2
ΔGint-11 kcal/mol
Surface area14430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.704, 70.843, 130.412
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

-
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 363 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.4 Å3/Da / Density % sol: 48.8 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Ammonium fluoride, 20% w/v Polyethylene glycol 3,350

-
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: 2.08→39.72 Å / Num. obs: 40085 / % possible obs: 99.71 % / Redundancy: 12.5 % / CC1/2: 0.958 / CC star: 0.989 / Rmerge(I) obs: 0.168 / Rpim(I) all: 0.05 / Rrim(I) all: 0.176 / Net I/σ(I): 9.88
Reflection shell
Resolution (Å)Num. unique obsRpim(I) allDiffraction-ID
7.88-39.727010.0331
5.82-7.8811760.0251
4.82-5.8215190.0281
4.16-4.8217260.0261
3.76-4.1619670.0371
3.42-3.7621640.0411
3.18-3.4223470.0421
2.96-3.1824670.0511
2.8-2.9626660.0551
2.65-2.828080.0721
2.53-2.6529100.0871
2.43-2.5330810.1131
2.33-2.4331710.1391
2.25-2.3333300.2231
2.17-2.2534140.2451
2.1-2.1735540.2711

-
Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
autoPROCdata reduction
Aimless0.7.4data scaling
PHENIX1.19.2_4158phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.08→37.05 Å / SU ML: 0.2045 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.3894
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.249 1988 4.97 %
Rwork0.2189 37997 -
obs0.2204 39985 99.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 35.77 Å2
Refinement stepCycle: LAST / Resolution: 2.08→37.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4697 0 0 363 5060
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00744780
X-RAY DIFFRACTIONf_angle_d0.72876453
X-RAY DIFFRACTIONf_chiral_restr0.0486711
X-RAY DIFFRACTIONf_plane_restr0.0053851
X-RAY DIFFRACTIONf_dihedral_angle_d18.59761776
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.08-2.130.29781580.29062658X-RAY DIFFRACTION99.75
2.13-2.190.28281350.25922660X-RAY DIFFRACTION99.96
2.19-2.250.37691510.34052632X-RAY DIFFRACTION97.82
2.25-2.330.26191270.28532673X-RAY DIFFRACTION99.29
2.33-2.410.28751340.24852671X-RAY DIFFRACTION99.96
2.41-2.510.29461550.24362670X-RAY DIFFRACTION99.96
2.51-2.620.31991290.25072733X-RAY DIFFRACTION99.93
2.62-2.760.24161440.24812688X-RAY DIFFRACTION99.86
2.76-2.930.28971920.22252673X-RAY DIFFRACTION100
2.93-3.160.26891250.22722732X-RAY DIFFRACTION100
3.16-3.480.28561440.21842709X-RAY DIFFRACTION99.93
3.48-3.980.27361160.19562785X-RAY DIFFRACTION100
3.98-5.010.16181410.15362793X-RAY DIFFRACTION99.97
5.01-37.050.18741370.20242920X-RAY DIFFRACTION99.87
Refinement TLS params.Method: refined / Origin x: 21.2848412791 Å / Origin y: 34.0099426042 Å / Origin z: 17.2687299807 Å
111213212223313233
T0.16670771223 Å2-0.0128837319932 Å2-0.0105175141998 Å2-0.191593902565 Å20.0194183550226 Å2--0.20113691003 Å2
L0.125182381428 °2-0.0782567651902 °2-0.240111871047 °2-0.0824659600287 °20.229538365967 °2--0.730434957214 °2
S0.011533366614 Å °-0.0561540336663 Å °-0.0072935326776 Å °-0.0463153119358 Å °-0.0173608999302 Å °-0.0189619386414 Å °-0.117839778095 Å °0.140611355854 Å °0.00323065783825 Å °
Refinement TLS groupSelection details: all

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more