PDB-7wl6: Crystal structure of I73L mutated human transthyretin

ID or keywords:

Entry

Database: PDB / ID: 7wl6

Title

Crystal structure of I73L mutated human transthyretin

Components

Transthyretin

Keywords

TRANSPORT PROTEIN / TTR / transthyretin / human

Function / homology

Function and homology information

Retinoid cycle disease events / The canonical retinoid cycle in rods (twilight vision) / thyroid hormone binding / purine nucleobase metabolic process / Non-integrin membrane-ECM interactions / Retinoid metabolism and transport / hormone activity / azurophil granule lumen / Amyloid fiber formation / Neutrophil degranulation ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.41800705321 Å

Authors

Nakagawa, M. / Obita, T. / Mizuguchi, M.

Funding support

1items

Citation

Journal: Biochem.J. / Year: 2022
Title: The hydrophobic residue Leu73 is crucial for the high stability and low aggregation properties of murine transthyretin.
Authors: Nakagawa, M. / Obita, T. / Mizuguchi, M.

History

Deposition	Jan 12, 2022	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Nov 23, 2022	Provider: repository / Type: Initial release
Revision 1.1	Nov 29, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	7wl6.cif.gz	130.5 KB	Display	PDBx/mmCIF format
PDB format	pdb7wl6.ent.gz	82.6 KB	Display	PDB format
PDBx/mmJSON format	7wl6.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	7wl6_validation.pdf.gz	436.8 KB	Display	wwPDB validaton report
Full document	7wl6_full_validation.pdf.gz	437.9 KB	Display
Data in XML	7wl6_validation.xml.gz	12.2 KB	Display
Data in CIF	7wl6_validation.cif.gz	16.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/wl/7wl6 ftp://data.pdbj.org/pub/pdb/validation_reports/wl/7wl6	HTTPS FTP

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Related structure data

Related structure data	4n85S S: Starting model for refinement
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#37 - Jan 2003 Serum Albumin similarity (14) #189 - Sep 2015 Amyloids similarity (9) #267 - Mar 2022 Vascular Endothelial Growth Factor (VegF similarity (1) #237 - Sep 2019 Nanodiscs and HDL similarity (1) #92 - Aug 2007 Anabolic Steroids similarity (1)

Deposited unit

A: Transthyretin

B: Transthyretin

hetero molecules

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

1

A: Transthyretin

B: Transthyretin

hetero molecules

A: Transthyretin

B: Transthyretin

hetero molecules

defined by author&software
Evidence: gel filtration
59.9 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	42.8398, 85.84, 64.16
Angle α, β, γ (deg.)	90.0, 90.0, 90.0
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-361- HOH
2	1	B-344- HOH

#1: Protein	Transthyretin / ATTR / Prealbumin / TBPA Mass: 14939.712 Da / Num. of mol.: 2 / Mutation: I73L Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TTR, PALB / Production host: Escherichia coli (E. coli) / References: UniProt: P02766
#2: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 162 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 1.97 Å³/Da / Density % sol: 37.69 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.2 Details: 24% PEG400, 0.2 M magnesium acetate, 5% glycerol, 0.1 M Tris-HCl

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å
Detector	Type: RAYONIX MX225HE / Detector: CCD / Date: Jun 21, 2017
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.418→35.7 Å / Num. obs: 45459 / % possible obs: 99.7 % / Redundancy: 7 % / B_iso Wilson estimate: 15.4395742663 Å² / CC_1/2: 0.996 / R_merge(I) obs: 0.085 / R_pim(I) all: 0.035 / R_rim(I) all: 0.092 / Net I/σ(I): 13.3
Reflection shell	Resolution: 1.418→1.49 Å / R_merge(I) obs: 0.471 / Mean I/σ(I) obs: 3.5 / Num. unique obs: 6529 / CC_1/2: 0.898 / R_pim(I) all: 0.197 / R_rim(I) all: 0.512

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Processing

Software

Name	Version	Classification
PHENIX	1.9_1692	refinement
MOSFLM		data reduction
SCALA		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4N85

4n85

Resolution: 1.41800705321→35.6739160745 Å / SU ML: 0.13808567928 / Cross valid method: FREE R-VALUE / σ(F): 1.343194049 / Phase error: 20.0661919681

	R_factor	Num. reflection	% reflection
R_free	0.210395487158	2245	4.93851602543 %
R_work	0.184394332498	43214	-
obs	0.185636914987	45459	99.5728742279 %

Solvent computation

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

Displacement parameters

B_iso mean: 23.7283313261 Å²

Refinement step

Cycle: LAST / Resolution: 1.41800705321→35.6739160745 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1766	0	2	162	1930

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.00742798941176	1818
X-RAY DIFFRACTION	f_angle_d	1.04801539985	2480
X-RAY DIFFRACTION	f_chiral_restr	0.0405769339793	283
X-RAY DIFFRACTION	f_plane_restr	0.00702329798019	314
X-RAY DIFFRACTION	f_dihedral_angle_d	12.6400886742	638

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 (%)
1.41800705321-1.4488	0.25224924643	146	0.248870697788	2606	X-RAY DIFFRACTION	98.2155603141
1.4488-1.4825	0.267761922547	128	0.229200519829	2698	X-RAY DIFFRACTION	99.9292786421
1.4825-1.5196	0.255624292348	120	0.221111417077	2678	X-RAY DIFFRACTION	100
1.5196-1.5607	0.235945633282	157	0.20740053633	2660	X-RAY DIFFRACTION	100
1.5607-1.6066	0.20009236336	156	0.199151666992	2663	X-RAY DIFFRACTION	100
1.6066-1.6585	0.241172712108	139	0.19265493109	2675	X-RAY DIFFRACTION	99.9289772727
1.6585-1.7178	0.214549344188	130	0.193803805164	2701	X-RAY DIFFRACTION	100
1.7178-1.7865	0.199723940214	158	0.191030865776	2684	X-RAY DIFFRACTION	100
1.7865-1.8678	0.240220545739	144	0.19060643664	2670	X-RAY DIFFRACTION	100
1.8678-1.9663	0.195708749308	135	0.16893753272	2698	X-RAY DIFFRACTION	100
1.9663-2.0895	0.180964511255	124	0.17848779534	2734	X-RAY DIFFRACTION	100
2.0895-2.2508	0.219379888934	142	0.171968211405	2707	X-RAY DIFFRACTION	100
2.2508-2.4773	0.210978380753	121	0.180753832908	2743	X-RAY DIFFRACTION	100
2.4773-2.8356	0.198362666669	165	0.185467141708	2726	X-RAY DIFFRACTION	100
2.8356-3.572	0.209359056212	134	0.178276795011	2802	X-RAY DIFFRACTION	99.8979244641
3.572-35.6739160745	0.20503094748	146	0.17888777419	2769	X-RAY DIFFRACTION	95.4798558795

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	1.6343006279	1.40260008201	1.04634668416	2.0511687576	1.48065040037	1.87684364847	-0.071066080999	-0.47595994887	0.052743052344	0.192695519373	-0.000847822047181	0.010327006165	0.19268478172	0.133879413902	0.236361034513	0.140751273611	0.0129381031831	0.0101193370992	0.119737882303	0.0147178096303	0.0900201384688	44.3441512643	7.50646604424	29.420063267
2	1.02429516717	-2.69237934367	-1.52310094255	9.81360865563	8.2588521713	8.97339771185	-0.0413450554678	-0.0312877038967	0.084518047347	0.0984493403473	0.163316999024	-0.512533013929	0.00568301859902	0.311533818557	-0.212972740415	0.128963446803	0.00519567861006	-0.0209771742756	0.161170530759	0.00236037979694	0.17607380145	54.7423028729	4.37375104726	26.1059434412
3	8.04830399183	-5.33917569271	-1.24146321565	6.59110795279	0.340043564104	2.86030882306	0.236777278494	0.39574607417	0.556395141176	-0.316152477372	-0.198400959078	0.111677157173	-0.3584386156	-0.227606901029	0.00728085114154	0.189890354747	0.00633517830243	-0.0121953142792	0.14646486318	0.00250254785291	0.239759075817	38.2919819321	24.641782529	24.1415929088
4	6.08628185673	-4.13206224125	4.96757668237	3.02998063276	-3.47466696446	4.12290624798	-0.309417108521	-0.186235325776	0.373672464957	0.268268456261	0.119408524668	-0.182643195966	-0.27575138245	-0.0135173638185	0.391655457513	0.131175455024	-0.0163903618437	0.00529241471452	0.128428861054	-0.0307876541886	0.176579565612	42.4818274788	22.611439776	28.4236213341
5	4.04069538336	-3.90091507656	-4.32325112068	4.92056576983	2.61273785524	6.97881551397	-0.316502478844	-0.44566453974	0.00627153434761	0.620543158509	0.183777569631	0.0533447869905	0.490235604888	0.253616035861	0.182617077215	0.178497215617	0.0192543783961	-0.0134772518286	0.163704337219	-0.0162416443593	0.144095356701	47.9278170028	9.61058779824	34.4768104868
6	3.34362136451	-4.18215510671	1.16112296889	6.47110377222	1.5644195003	8.20037550426	-0.145093510068	-0.520577994168	0.122188195603	0.292810399111	-0.0177598252748	0.056440548493	0.335338507779	-0.46746769578	0.120169595547	0.137369710487	-0.00926176870925	0.0299400697909	0.212405514936	-0.0527357916168	0.199548180911	32.5177801346	19.5747108556	35.8005068602
7	5.53511392311	-5.0658018549	-3.03505135571	4.72579455996	2.39242430977	2.68937053242	-0.0342043216686	0.248849272103	0.678033462605	0.0553892599494	0.0127795797633	-0.215386024076	-0.10109199711	-0.117716202011	-0.171735309861	0.113602983813	-0.0101217068629	0.00470619160604	0.104454163293	-0.00862949254427	0.130891743778	41.6185312817	17.9992521173	23.5769141111
8	4.29270095841	1.28555218716	2.36797732872	6.02043560432	-1.67131933738	5.39270182538	0.126443923772	0.115143386188	0.0450859744369	-0.183284923564	-0.49471290714	-0.373533415409	0.00322775838708	0.751946482088	0.264560052399	0.103530281134	0.0226210121735	0.0358634102846	0.212149674274	0.0369719077188	0.156861446697	55.7182233622	11.9661875017	17.3957047926
9	3.70978847221	-4.13503406719	-4.9123250334	4.61448810521	5.59749245903	6.96814941032	-0.179615787774	-0.167615992785	0.286222184696	0.0484263285274	0.225841664548	-0.167251612766	0.127300711284	0.282760236753	-0.0782050931659	0.139656514617	0.00777353304727	0.00290010678537	0.147642522385	-0.0138214245759	0.138923954115	36.7977529062	15.3893994341	21.7066428719
10	4.43273314222	-1.51268063941	-3.84605812036	3.00317565185	1.25740113161	5.57641468279	-0.0995474142512	0.00905942277062	0.089777850528	0.153776919372	0.00636718591953	0.250417608956	0.168892148504	-0.190936897945	0.10930212245	0.115428729676	-0.00430888702396	-0.0109637417774	0.107412347629	-0.0183225243924	0.103471695899	37.6641645779	8.14130253617	25.1896871449
11	2.19389736528	1.98151348983	-0.288067483749	3.30804806541	-0.24138591788	7.73088630933	-0.364527800537	0.556252858588	-0.0440641127445	-0.469575370811	0.246281507614	-0.144891407521	0.0933878518211	0.126132116034	0.304665323725	0.125529788905	0.0343312171346	0.0102273974937	0.152209366874	0.0307200291542	0.116899045622	40.5078983157	7.24906301528	2.72040984479
12	0.108024926263	-0.386114473625	0.206642494563	8.93462097726	-5.85184302579	3.85092500167	0.0618644895784	0.157354357361	-0.0214403862517	-0.23446940228	0.0194077367484	0.249676754036	0.0394587918327	-0.0803652029507	-0.136388683545	0.164385976784	0.00886824380034	-0.0248927223547	0.158092650445	-0.00632447627617	0.151261084322	30.504463677	2.51197227347	5.67946705591
13	6.29626882883	5.10668193086	3.04629295756	4.16032220843	3.30708411144	7.13391914611	0.0470449443595	-0.346157342195	0.858260583299	-0.0345324948437	-0.179814216458	0.389560791697	-0.744223996526	0.265688378807	0.0840954942221	0.219360212057	-0.0108881731769	0.0246792140117	0.156176742985	-1.80126199949E-5	0.278381696612	43.5253979527	24.8367551977	8.0511248335
14	6.22376157634	1.97716112981	5.8364718486	5.21229371482	5.11646097607	8.74119203945	-0.21399265548	-0.223005117685	0.519645161818	-0.0583926563769	-0.0728727394226	0.178762498602	-0.195531569245	-0.0234074073643	0.354268184508	0.138738252067	0.024482425687	0.0196630464577	0.182275306841	0.0280629177006	0.176552985062	39.7935283881	22.3770064413	3.87984049014
15	4.88946398208	2.68767883157	-5.37949886686	3.15616521919	-3.6876122042	8.21546438163	-0.0202186111827	0.370438840915	-0.0409414576009	-0.647666503901	-0.148550411139	-0.0488857164147	0.42915056413	0.0137200398221	0.257180926599	0.204683516519	0.0261800796399	-0.0177010795829	0.217876477021	0.0187074361209	0.141116669789	36.5326810089	8.63600137534	-2.49028994038
16	4.25281247366	3.96367506098	4.71513233909	3.68175478088	4.38760972201	5.2924406141	-0.355357446497	0.762687125635	0.531882658762	-0.351797417935	0.209552212205	-0.00987806371833	-0.0580385561187	0.455434865801	0.0100213657514	0.205903093964	-0.0116827990149	0.0186441845962	0.276976837787	0.0875843064584	0.238704947598	50.5457178472	20.6081019671	-3.67315310041
17	2.68473023671	2.41891252534	-4.25648896465	2.64519947576	-3.90526700288	6.77935502018	0.1259210209	-0.0899954186586	0.494124305495	0.0439052347842	-0.0453070200386	0.28308192333	-0.151317452609	0.178376117215	-0.13925022068	0.152315035991	0.0108360301756	0.0256841856732	0.119492579651	0.000593276108918	0.183514662649	43.852594168	18.573246251	8.2548264874
18	4.50622031283	0.279210031688	2.60173511281	5.54190865633	1.07657910128	7.14747872651	0.0435375770428	-0.0273363419703	0.0647482181588	0.34239992106	-0.0606972179585	0.474713736616	-0.0295786746404	-0.342979988015	0.0424210338386	0.0977731479871	0.0134629445555	0.0527729883267	0.133695449601	0.000947495275161	0.176151600232	28.5670905876	10.0778701135	14.2809727334
19	4.06196755998	3.9527362324	-4.27283543171	3.82402416601	-4.181780226	4.51368067728	0.232192474161	-0.220191246856	0.441982290307	-0.0335074805575	-0.00384235690375	0.123554907249	0.0103307535758	-0.20016384494	-0.280638209632	0.13867411655	-0.00789564205739	0.0224277263758	0.194685094077	0.0300565467443	0.175978618786	46.6385565807	16.1129123699	10.3465722322
20	5.40383610088	-1.8831479344	-2.81365855703	4.03290007345	5.61845832745	7.8277963442	-1.40814483869	0.336736112953	-1.76630861315	-0.611432952794	0.275328317762	-1.34594865633	1.05876681207	0.6500110136	1.0939093413	0.471353938785	-0.0725309596241	0.174914431697	0.445304499981	0.0911930505287	0.746706188581	58.6633875409	13.994462635	0.0915026574429
21	7.73794782066	0.637995841983	-3.24192035335	2.73603815745	-0.693610489871	3.42479831189	-0.111827226772	0.202644539891	0.0316035707555	-0.254766877114	0.0195260141183	-0.167154963721	0.119035815554	0.140547730755	0.0740579530771	0.125011979055	0.0176236951335	-0.00617329861705	0.102923163938	0.000749891033248	0.0778496337116	43.6487906622	6.5622693493	8.42738628839

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 11 through 18 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 19 through 28 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 29 through 40 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 41 through 48 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 49 through 58 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 59 through 66 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 67 through 74 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 75 through 90 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 91 through 97 )
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 98 through 124 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 11 through 18 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 19 through 28 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 29 through 40 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 41 through 48 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 49 through 58 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 59 through 66 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 67 through 73 )
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 74 through 90 )
19	X-RAY DIFFRACTION	19	chain 'B' and (resid 91 through 97 )
20	X-RAY DIFFRACTION	20	chain 'B' and (resid 98 through 103 )
21	X-RAY DIFFRACTION	21	chain 'B' and (resid 104 through 124 )

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