PDB-9vy5: Structure of MIF binding with Terbium ions

ID or keywords:

Entry

Database: PDB / ID: 9vy5

Title

Structure of MIF binding with Terbium ions

Components

Propeptide, PepSY amd peptidase M4

Keywords

METAL BINDING PROTEIN / Rare earth / Metalloprotein

Function / homology

PepSY domain / Peptidase propeptide and YPEB domain / TERBIUM(III) ION / Propeptide, PepSY amd peptidase M4

Function and homology information

Biological species

Methylobacillus flagellatus KT (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.58 Å

Authors

Du, Y.X. / Li, Z.Q. / Liu, L.

Funding support

China, 1items

Citation

Journal: To Be Published
Title: Adjacent Rare Earth Separation by a protein atomic ruler
Authors: Du, Y.X. / Li, Z.Q. / Liu, L.

History

Deposition	Jul 20, 2025	Deposition site: PDBJ / Processing site: PDBC
Revision 1.0	Jul 22, 2026	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9vy5.cif.gz	218.4 KB	Display	PDBx/mmCIF format
PDB format	pdb9vy5.ent.gz	157.5 KB	Display	PDB format
PDBx/mmJSON format	9vy5.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/vy/9vy5 ftp://data.pdbj.org/pub/pdb/validation_reports/vy/9vy5	HTTPS FTP

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Related structure data

Related structure data	9vy3C 9vy4C 9vy6C 9vy7C 9vy8C 9vy9C 9vyaC C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search
Other databases	PDB-Dev: D_1300061689the same protein binding with different rare-earth ions

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Propeptide, PepSY amd peptidase M4

B: Propeptide, PepSY amd peptidase M4

hetero molecules

35.9 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Propeptide, PepSY amd peptidase M4

hetero molecules

A: Propeptide, PepSY amd peptidase M4

hetero molecules

defined by author&software
Evidence: gel filtration
35.9 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Propeptide, PepSY amd peptidase M4

hetero molecules

B: Propeptide, PepSY amd peptidase M4

hetero molecules

defined by author&software
36 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	71.598, 120.081, 36.251
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	18
Space group name H-M	P2₁2₁2
Space group name Hall	P22ab
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

Components on special symmetry positions

ID	Model	Components
1	1	A-562- HOH
2	1	B-534- HOH
3	1	B-553- HOH

#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-TB / TERBIUM(III) ION Mass: 158.925 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Tb / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 531 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
Has protein modification	Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.29 Å³/Da / Density % sol: 46.35 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 10% v/v 2-propanol, 0.1 M BICINE pH 8.5, 30% polyethylene glycol 3,350

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

SSRF

/ Beamline: BL02U1 / Wavelength: 0.979176 Å

Detector

Type: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Jan 19, 2025

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.979176 Å / Relative weight: 1

Reflection

Resolution: 1.55→36.28 Å / Num. obs: 46026 / % possible obs: 99 % / Redundancy: 11.2 % / B_iso Wilson estimate: 10.76 Å² / CC_1/2: 0.989 / R_merge(I) obs: 0.19 / R_pim(I) all: 0.083 / R_rim(I) all: 0.207 / Net I/σ(I): 7.3

Reflection shell

Resolution (Å)	R_merge(I) obs	Num. unique obs	Diffraction-ID
6.53-36.28	0.155	618	1
4.79-6.53	0.122	1037	1
3.97-4.79	0.116	1275	1
3.45-3.97	0.13	1516	1
3.09-3.45	0.147	1686	1
2.83-3.09	0.157	1862	1
2.61-2.83	0.169	2001	1
2.45-2.61	0.177	2141	1
2.31-2.45	0.196	2277	1
2.19-2.31	0.199	2406	1
2.08-2.19	0.219	2514	1
2-2.08	0.235	2609	1
1.92-2	0.261	2733	1
1.85-1.92	0.289	2859	1
1.79-1.85	0.349	2901	1
1.73-1.79	0.429	3022	1
1.68-1.73	0.481	3145	1
1.63-1.68	0.603	3209	1
1.59-1.63	0.803	3188	1
1.55-1.57	0.866	3027	1

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Processing

Software

Name	Version	Classification
PHENIX	1.19.2_4158	refinement
xia2		data reduction
Aimless	0.7.4	data scaling
PHENIX	1.19.2_4158	phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.58→34.94 Å / SU ML: 0.1422 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.7492
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2034	2150	4.94 %
R_work	0.1792	41338	-
obs	0.1804	43488	99.32 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 22.41 Å²

Refinement step

Cycle: LAST / Resolution: 1.58→34.94 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2336	0	13	531	2880

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0076	2376
X-RAY DIFFRACTION	f_angle_d	0.8869	3206
X-RAY DIFFRACTION	f_chiral_restr	0.0551	354
X-RAY DIFFRACTION	f_plane_restr	0.0067	422
X-RAY DIFFRACTION	f_dihedral_angle_d	17.3371	886

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.58-1.62	0.2948	144	0.2535	2531	X-RAY DIFFRACTION	94.39
1.62-1.66	0.2156	127	0.2332	2741	X-RAY DIFFRACTION	98.93
1.66-1.7	0.2481	162	0.2082	2696	X-RAY DIFFRACTION	99.41
1.7-1.75	0.2588	151	0.2037	2692	X-RAY DIFFRACTION	99.41
1.75-1.81	0.2063	153	0.1855	2723	X-RAY DIFFRACTION	99.31
1.81-1.87	0.1816	128	0.1742	2740	X-RAY DIFFRACTION	99.62
1.87-1.95	0.2149	129	0.1725	2753	X-RAY DIFFRACTION	99.76
1.95-2.04	0.194	125	0.1731	2776	X-RAY DIFFRACTION	99.83
2.04-2.14	0.207	157	0.1724	2735	X-RAY DIFFRACTION	99.93
2.14-2.28	0.1936	151	0.1814	2759	X-RAY DIFFRACTION	99.79
2.28-2.45	0.203	136	0.1794	2772	X-RAY DIFFRACTION	99.9
2.45-2.7	0.1846	143	0.1823	2763	X-RAY DIFFRACTION	99.66
2.7-3.09	0.1898	153	0.1789	2820	X-RAY DIFFRACTION	99.93
3.09-3.89	0.2283	130	0.1583	2849	X-RAY DIFFRACTION	99.97
3.9-34.94	0.177	161	0.1694	2988	X-RAY DIFFRACTION	99.84

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°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)
1	0.827087888757	-1.13007996903	-0.959831683866	5.37652820195	-2.54206737145	5.67549996548	-0.118837650124	1.00481337589	-0.132048680063	-0.702300481527	0.0628685603734	0.678736404329	0.0713812518584	-0.930002778719	0.0322069052307	0.360385593091	-0.0151751641621	-0.090902391946	0.410832894773	-0.0588053842488	0.178999759572	-40.7537218524	5.81877272093	-25.7000714521
2	6.11405101606	5.26258372312	3.01401320219	6.431440849	1.14808101189	3.60018540814	0.0583255817505	0.119121546206	-0.580666408298	-0.0242967536403	0.194627499102	-0.590527788608	0.413439636919	0.394249951659	-0.137343591694	0.158988390158	0.0721357428695	0.0333317278641	0.25380887616	0.014875392954	0.125262899646	-25.8892538782	3.10862601531	-19.2723066997
3	3.32583653863	1.04013483806	-0.0210178654209	3.269256384	0.716991123486	2.90417911289	0.0823616809718	0.170383221059	-0.211295725995	0.0704378095395	-0.0156683862698	0.103875831647	0.0831537554598	-0.0297482543028	-0.0459791011764	0.0788228210338	0.000881746394039	6.67453704826E-5	0.0889628747129	-0.0152980890353	0.0510422341298	-32.4377424777	7.63291037096	-13.2648715741
4	3.25106209204	0.221078056782	0.240972097613	3.11726890883	0.990489620391	1.90416009742	-0.0145301399781	-0.0208041433387	0.100424730504	-0.122295701517	-0.0307544219137	-0.182455554148	0.0869072174807	0.211357248619	0.0672409824288	0.0622700945226	0.0052523447731	0.023685730509	0.129488611173	0.0067540140804	0.110136437429	-28.3829850172	10.9746889463	-13.8952879505
5	5.8749182392	-2.35938439114	0.278821463804	7.79029246622	0.677673173544	3.13756185014	-0.181711361552	-0.173109266677	0.127299453599	0.661076460974	0.161761037026	-0.553153193923	0.0444397647009	0.398467848415	0.010063206974	0.183329892481	-0.0302323620606	-0.0353529919262	0.21267869526	-0.0279337619251	0.140899062397	-27.949721142	22.3843099774	3.1628606977
6	4.36222828579	2.71066489372	-0.717124415557	3.45623575087	1.80890978946	2.99099938802	-0.0904428038503	-0.339397003852	0.605840827055	0.141102334024	-0.204425831425	0.501936558292	-0.730108867895	-0.599691191542	0.238333777736	0.213644509355	0.0465735351329	-0.0383982403588	0.161401048768	-0.0639289522164	0.207830193133	-43.2385287978	24.9400952898	-1.33904811284
7	5.04603724593	-1.60600929128	1.08277630324	2.55912762854	0.20221025602	3.39193665444	0.0507691271672	-0.303284737779	-0.357233813592	0.117860953257	-0.0444129993143	0.133760628455	0.233483676128	-0.155695245994	-0.0120477648872	0.134332179381	-0.01494933331	0.00936321811593	0.127817237359	0.00850443753518	0.112595241862	-39.9055252452	16.3061680344	-4.03818396739
8	4.49354387722	0.478149369162	0.645352418268	3.18217449663	0.306942814485	2.71513270899	-0.140593284884	0.119363267435	0.0950507729691	-0.0313504066984	0.045662276384	0.00495569579157	-0.340063160528	-0.114837592036	0.0886925741196	0.125206549035	0.0116781673666	-0.0107421883235	0.120917136258	-0.00196747203264	0.0652736558494	-38.3779682203	20.2710186164	-7.79956156873
9	2.4692839762	0.646536014641	0.0545438074823	4.39346953843	0.287449700742	1.80210565885	0.126664426923	-0.140342008866	0.101295946895	0.0774214462628	-0.144903505841	0.217821489999	-0.0424875877837	0.0399191754982	-0.019158130955	0.105071464794	-0.000501402410916	0.0210747081544	0.124909520754	-0.0116783554512	0.0585111661406	-39.6809786006	11.7980968242	-11.9975134045
10	2.89271798145	-0.709082354022	2.54614583459	1.68189275299	0.555884113755	3.47981967768	-0.461051789166	-0.353488710258	-0.333190356892	0.534239639302	0.163064553567	0.339401947848	-0.0110370118404	-0.878749366513	0.290194462337	0.336119751667	0.0391817375039	0.100409936332	0.290004832699	-0.0280494291155	0.1758301104	-38.6772890253	53.7017979915	-0.203915184461
11	0.898745616662	-0.724078838816	-1.68173359616	3.67890391589	0.595644468881	3.35936350416	-0.172229103333	-0.327999676752	0.212948932656	0.38036882255	0.191214187223	-0.573023902335	-0.320007257985	0.366120448875	0.00514238706819	0.172711994831	-0.0120063099303	-0.0797893513681	0.243354412227	0.0126783099517	0.150878593179	-26.0846799193	56.3763146659	-7.11251847343
12	2.54407994176	0.876590626443	-1.06271214588	2.58567601492	-1.65670103985	3.36997224139	-0.00495186399536	-0.150957612372	0.08759539265	-0.142834560701	-0.0132788307479	-0.0631037156101	0.0527739395	0.0885447090369	0.0215671050732	0.0793281528359	-0.0138944679312	-0.0163760259937	0.119395933246	-0.0177729952375	0.0849731677413	-32.9623625423	52.322722454	-13.1416355409
13	3.11748807637	-0.422962160138	0.184701351795	2.38525439393	0.798876445564	1.77403350486	-0.00234385425086	-0.114201175591	0.032854934916	0.0522495955776	0.0633550049565	-0.141502189985	0.0258396046813	0.213818278929	-0.0153397885423	0.0662904187933	-0.0219392320031	-0.00227945257727	0.0872644778943	-0.0011267776885	0.0878502959779	-29.1605221946	48.7798502185	-12.6268134097
14	5.66049888865	2.7603021857	-0.410575262867	6.39639665145	1.07273268528	3.44147182948	-0.292160322796	0.448422991432	-0.32587783532	-0.752174794799	0.278468584693	-0.316804687374	0.0846025525998	0.201958761349	0.0169027793335	0.18436322058	0.00143697424532	0.00924161427592	0.136138349704	-0.00360683582142	0.119785897222	-29.2851126092	37.1889743783	-29.5862659075
15	8.14729643889	0.489123710281	-5.92443099945	0.497769571001	0.20290628089	8.86842997157	-0.0972166815884	0.136575601831	-0.531811356664	-0.0971298350934	0.030982885808	0.541625630199	0.281112421195	-0.268851783608	0.079088921477	0.2177503135	-0.0980187779627	0.0255212059459	0.173642786684	0.0168223128594	0.236802649026	-44.407683547	35.6592535064	-24.8824092394
16	4.10573702144	-0.745417323032	-0.570108090144	2.13587680705	0.203212973418	1.81636709289	-0.0872767948566	-0.0803929671822	-0.00590535794476	-0.000426913097014	0.0626826862489	0.230387977884	0.242345814526	-0.243630721826	-0.00406530312492	0.106273007675	-0.0514567416359	-0.00900465015508	0.12559507661	-0.00756362471643	0.129598639175	-39.933424922	41.2252382018	-19.6970902093
17	1.54769044181	-0.879779704599	-1.27062254132	5.11083939674	1.17996785639	1.66262651843	-0.0800285294272	0.0583649918259	-0.0860151480456	-0.220371863401	0.104272607949	0.0838574111133	0.0274575529335	-0.0814346429651	-0.0164606947678	0.100111139486	-0.0307636408293	-0.00133978814705	0.166085351993	0.0167963235303	0.0928458673596	-40.4688405805	48.3526792498	-14.3188938652

Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

ID	Refine TLS-ID	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	chain 'A' and (resid 3 through 11 )	A	A	3 - 11	1 - 9
2	2	chain 'A' and (resid 12 through 22 )	A	A	12 - 22	10 - 20
3	3	chain 'A' and (resid 23 through 35 )	A	A	23 - 35	21 - 33
4	4	chain 'A' and (resid 36 through 71 )	A	A	36 - 71	34 - 69
5	5	chain 'A' and (resid 72 through 86 )	A	A	72 - 86	70 - 84
6	6	chain 'A' and (resid 87 through 97 )	A	A	87 - 97	85 - 95
7	7	chain 'A' and (resid 98 through 109 )	A	A	98 - 109	96 - 107
8	8	chain 'A' and (resid 110 through 139 )	A	A	110 - 139	108 - 137
9	9	chain 'A' and (resid 140 through 153 )	A	A	140 - 153	138 - 151
10	10	chain 'B' and (resid 5 through 11 )	B	I	5 - 11	1 - 7
11	11	chain 'B' and (resid 12 through 22 )	B	I	12 - 22	8 - 18
12	12	chain 'B' and (resid 23 through 35 )	B	I	23 - 35	19 - 31
13	13	chain 'B' and (resid 36 through 71 )	B	I	36 - 71	32 - 67
14	14	chain 'B' and (resid 72 through 86 )	B	I	72 - 86	68 - 82
15	15	chain 'B' and (resid 87 through 97 )	B	I	87 - 97	83 - 93
16	16	chain 'B' and (resid 98 through 139 )	B	I	98 - 139	94 - 135
17	17	chain 'B' and (resid 140 through 153 )	B	I	140 - 153	136 - 149

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