PDB-9mrh: Fluorescence lifetime-readout citrate sensor

ID or keywords:

Entry

Database: PDB / ID: 9mrh

Title

Fluorescence lifetime-readout citrate sensor

Components

Fluorescence lifetime-readout citrate sensor

Keywords

FLUORESCENT PROTEIN / fluorescence lifetime / biosensor / citrate

Function / homology

CITRIC ACID

Function and homology information

Biological species

Aequorea (invertebrata)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 2.37 Å

Authors

Rosen, P.C. / Yellen, G. / Lim, D.C.

Funding support

United States, 1items

Citation

Journal: Proc.Natl.Acad.Sci.USA / Year: 2025
Title: Activity-dependent citrate dynamics in neurons.
Authors: Rosen, P.C. / Fu, P. / Ferran, B. / Kim, E. / Brooks, D.J. / Lim, D.C. / Diaz-Garcia, C.M. / Yellen, G.

History

Deposition	Jan 7, 2025	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 12, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9mrh.cif.gz	364.9 KB	Display	PDBx/mmCIF format
PDB format	pdb9mrh.ent.gz	248 KB	Display	PDB format
PDBx/mmJSON format	9mrh.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9mrh_validation.pdf.gz	1 MB	Display	wwPDB validaton report
Full document	9mrh_full_validation.pdf.gz	1 MB	Display
Data in XML	9mrh_validation.xml.gz	39.1 KB	Display
Data in CIF	9mrh_validation.cif.gz	50.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/mr/9mrh ftp://data.pdbj.org/pub/pdb/validation_reports/mr/9mrh	HTTPS FTP

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Related structure data

Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Fluorescence lifetime-readout citrate sensor

B: Fluorescence lifetime-readout citrate sensor

hetero molecules

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

1

A: Fluorescence lifetime-readout citrate sensor

hetero molecules

defined by author
43.4 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Fluorescence lifetime-readout citrate sensor

hetero molecules

defined by author
43.5 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	75.440, 96.190, 144.480
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	18
Space group name H-M	P22₁2₁
Space group name Hall	P22ab(z,x,y)
Symmetry operation	#1: x,y,z #2: x,-y,-z #3: -x,y+1/2,-z+1/2 #4: -x,-y+1/2,z+1/2

#1: Protein	Fluorescence lifetime-readout citrate sensor Mass: 42921.414 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: Residue SWG 74 is a chromophore generated from Ser-Trp-Gly in the translated sequence. Source: (gene. exp.) Aequorea (invertebrata) / Production host: Escherichia coli (E. coli)
#2: Chemical	ChemComp-CIT / CITRIC ACID Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₆H₈O₇ / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400 Mass: 238.278 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₀H₂₂O₆ / Comment: precipitant*YM
#4: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO₄
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 379 / 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: 3.05 Å³/Da / Density % sol: 59.73 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / Details: 0.1M Li2SO4, 0.1 M Bis-Tris pH 6.6, 16% PEG3350

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54 Å
Detector	Type: RIGAKU SATURN 944 / Detector: CCD / Date: Sep 19, 2023
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.54 Å / Relative weight: 1
Reflection	Resolution: 2.37→40.55 Å / Num. obs: 43193 / % possible obs: 99.39 % / Redundancy: 5.2 % / B_iso Wilson estimate: 33.02 Å² / CC_1/2: 0.987 / Net I/σ(I): 7.66
Reflection shell	Resolution: 2.37→2.455 Å / Num. unique obs: 4161 / CC_1/2: 0.747

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Processing

Software

Name	Version	Classification
PHENIX	1.20.1_4487	refinement
XDS		data reduction
XDS		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.37→40.55 Å / SU ML: 0.3208 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.9785
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2524	2000	4.6 %
R_work	0.2205	77058	-
obs	0.222	43186	99.4 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 37.71 Å²

Refinement step

Cycle: LAST / Resolution: 2.37→40.55 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5758	0	114	379	6251

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0017	5983
X-RAY DIFFRACTION	f_angle_d	0.4561	8075
X-RAY DIFFRACTION	f_chiral_restr	0.0426	886
X-RAY DIFFRACTION	f_plane_restr	0.0028	1048
X-RAY DIFFRACTION	f_dihedral_angle_d	14.2152	2221

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 (%)
2.37-2.4	0.3207	128	0.3225	2675	X-RAY DIFFRACTION	90.59
2.4-2.43	0.3636	143	0.3124	2895	X-RAY DIFFRACTION	99.54
2.43-2.47	0.3228	137	0.3041	2867	X-RAY DIFFRACTION	99.54
2.47-2.5	0.2922	145	0.2868	2924	X-RAY DIFFRACTION	99.35
2.5-2.54	0.3077	137	0.2874	2862	X-RAY DIFFRACTION	99.4
2.54-2.58	0.3241	138	0.2723	2889	X-RAY DIFFRACTION	99.18
2.58-2.62	0.3047	139	0.2552	2905	X-RAY DIFFRACTION	99.31
2.62-2.66	0.3411	141	0.2648	2897	X-RAY DIFFRACTION	99.15
2.66-2.71	0.3176	145	0.2584	2925	X-RAY DIFFRACTION	99.51
2.71-2.77	0.2737	136	0.258	2844	X-RAY DIFFRACTION	99.1
2.77-2.82	0.2664	143	0.2514	2868	X-RAY DIFFRACTION	98.88
2.82-2.88	0.3231	142	0.2589	2886	X-RAY DIFFRACTION	98.92
2.88-2.95	0.3097	130	0.2644	2872	X-RAY DIFFRACTION	98.65
2.95-3.02	0.3132	141	0.2561	2882	X-RAY DIFFRACTION	98.4
3.02-3.11	0.2766	143	0.2435	2863	X-RAY DIFFRACTION	97.95
3.11-3.2	0.2384	137	0.2261	2837	X-RAY DIFFRACTION	97.76
3.2-3.3	0.3211	133	0.2303	2844	X-RAY DIFFRACTION	96.97
3.3-3.42	0.2669	140	0.2236	2779	X-RAY DIFFRACTION	96.62
3.42-3.55	0.2335	139	0.2111	2807	X-RAY DIFFRACTION	96.24
3.56-3.72	0.272	133	0.2027	2820	X-RAY DIFFRACTION	96.13
3.72-3.91	0.2096	128	0.1949	2799	X-RAY DIFFRACTION	96.79
3.91-4.16	0.2026	135	0.1775	2800	X-RAY DIFFRACTION	96.74
4.16-4.48	0.1651	141	0.1702	2831	X-RAY DIFFRACTION	96.52
4.48-4.93	0.1918	140	0.1638	2860	X-RAY DIFFRACTION	98.04
4.93-5.64	0.2298	137	0.1841	2870	X-RAY DIFFRACTION	98.75
5.64-7.1	0.198	138	0.2126	2888	X-RAY DIFFRACTION	99.05
7.1-40.55	0.2203	137	0.1929	2869	X-RAY DIFFRACTION	98.2

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	0.959259511628	0.212007907744	0.186608289717	1.14212269218	0.360838312049	0.721602157736	-0.0362131246206	0.0699542163227	-0.189796625221	-0.0367671300681	0.0665879666146	-0.211138877155	0.0309786228546	0.0722787628105	-8.97235503625	0.242335169597	0.0361799995594	-0.00344905787182	0.235553582565	-0.0450614688454	0.259433346779	84.516	63.254	11.677
2	0.678098905045	-0.27624756877	-0.0576153209581	1.28058039386	-0.391314480528	0.2753247657	-0.0959376876999	0.000349987635777	-0.08814820535	0.112191247163	0.106351016236	-0.0698402751116	0.0739175241272	0.0372659349594	-0.0212206970284	0.3485381508	-0.00691630812985	0.00617859350463	0.312006175201	-0.0789094183202	0.269074846979	77.515	63.478	16.355
3	0.746981295973	-0.0341186825864	-0.172853105967	1.40861280108	0.178111133187	0.552215541439	-0.0214532073257	0.0363518645895	-0.096231317819	0.0113374117244	0.0228856751963	0.202520448438	0.0707438741558	-0.0413625846919	0.00286428718475	0.215323764737	-0.00451869432415	-0.00788702522877	0.190901438174	-0.00440411053008	0.178272089894	66.274	80.726	17.685
4	0.960786643469	0.319047529051	0.0725512422744	1.46228139355	-0.193014033245	0.49608966527	0.0665254287865	-0.0455495196317	-0.191744496516	0.095222266106	0.00151526818465	-0.00988116967792	0.0875245107746	0.0677285252486	-0.049660105957	0.224178227815	0.0564107580044	-0.0155812431415	0.228829025277	-0.0620862020651	0.230155804107	81.156	64.413	18.42
5	1.8342444464	0.329996861006	-0.667886139493	1.73739909677	0.198227332995	1.18202429002	0.0068496404253	-0.0575126843204	0.14635051653	0.205932825158	0.089667852444	0.103631086574	-0.055639287513	0.023643881845	-0.0745521508968	0.212864072604	-0.0140258978248	-0.00525168834298	0.256472895027	0.00199672863766	0.213686933458	64.003	61.753	50.953
6	1.31456473997	0.338763540141	-0.051064620772	0.791358834945	-0.195401529671	0.295460537188	0.0212589519602	0.121949206648	-0.0151633451528	-0.0379464374675	0.0449590406165	0.139087027247	-0.06887866197	-0.111051851226	-0.0563017694765	0.247129007945	0.00801983431168	-0.0255822109497	0.296817735817	0.0155807654275	0.299963713454	48.558	46.75	48.441
7	1.09733920957	-0.297896149979	-0.0955110765148	1.54182808492	0.354461716601	1.27366852551	-0.00926522876018	0.0355874783284	0.151867322171	0.069108004008	0.077944677084	0.0214175161952	-0.0145470325316	-0.0621704260049	-0.058008229155	0.224744580608	-0.0495746381145	-0.0205869050596	0.219176431197	0.0314333232347	0.22375972247	64.104	58.194	42.834

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	( CHAIN A AND RESID 8:111 )	A	8 - 111
2	X-RAY DIFFRACTION	2	( CHAIN A AND RESID 112:180 )	A	112 - 180
3	X-RAY DIFFRACTION	3	( CHAIN A AND RESID 181:315 )	A	181 - 315
4	X-RAY DIFFRACTION	4	( CHAIN A AND RESID 316:379 )	A	316 - 379
5	X-RAY DIFFRACTION	5	( CHAIN B AND RESID 9:111 )	B	9 - 111
6	X-RAY DIFFRACTION	6	( CHAIN B AND RESID 112:290 )	B	112 - 290
7	X-RAY DIFFRACTION	7	( CHAIN B AND RESID 291:379 )	B	291 - 379

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