PDB-6wcy: N160D Deamidation Mutant of Human gammaD-Crystallin

ID or keywords:

Entry

Database: PDB / ID: 6wcy

Title

N160D Deamidation Mutant of Human gammaD-Crystallin

Components

Gamma-crystallin D

Keywords

STRUCTURAL PROTEIN / deamidation / lens / cataract / protein modification / aging

Function / homology

Function and homology information

lens fiber cell differentiation / structural constituent of eye lens / lens development in camera-type eye / visual perception / cellular response to reactive oxygen species / nucleus / cytoplasm
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.204 Å

Authors

Whitley, M.J. / Rathi, N. / Ambarian, M. / Gronenborn, A.M.

Funding support

United States, 1items

Citation

Journal: Structure / Year: 2021
Title: Assessing the Structures and Interactions of gamma D-Crystallin Deamidation Variants.
Authors: Guseman, A.J. / Whitley, M.J. / Gonzalez, J.J. / Rathi, N. / Ambarian, M. / Gronenborn, A.M.

History

Deposition	Mar 31, 2020	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jan 20, 2021	Provider: repository / Type: Initial release
Revision 1.1	Mar 17, 2021	Group: Database references / Category: citation Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2	Oct 18, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	6wcy.cif.gz	247.5 KB	Display	PDBx/mmCIF format
PDB format	pdb6wcy.ent.gz	180.6 KB	Display	PDB format
PDBx/mmJSON format	6wcy.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	6wcy_validation.pdf.gz	445.8 KB	Display	wwPDB validaton report
Full document	6wcy_full_validation.pdf.gz	446.3 KB	Display
Data in XML	6wcy_validation.xml.gz	17.9 KB	Display
Data in CIF	6wcy_validation.cif.gz	26.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/wc/6wcy ftp://data.pdbj.org/pub/pdb/validation_reports/wc/6wcy	HTTPS FTP

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Related structure data

Related structure data	6w5bC 1hk0S C: citing same article (ref.) S: Starting model for refinement
Similar structure data	4jgf-2 1hk0-d 1a7h-d 6w5b-d 4jgf-1 2kfb-d 4w9a-d 4zcv-1 4zcu-3 6eta-2 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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	#127 - Jul 2010 Crystallins similarity (5)

Deposited unit

A: Gamma-crystallin D

B: Gamma-crystallin D

hetero molecules

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

1

A: Gamma-crystallin D

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

2

B: Gamma-crystallin D

hetero molecules

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

Unit cell

Length a, b, c (Å)	50.811, 51.872, 113.991
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁
Space group name Hall	P2ac2ab
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

#1: Protein	Gamma-crystallin D / Gamma-D-crystallin / Gamma-crystallin 4 Mass: 20635.955 Da / Num. of mol.: 2 / Mutation: N161D Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CRYGD, CRYG4 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P07320
#2: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO₄
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 351 / 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: 1.82 Å³/Da / Density % sol: 32.41 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion, sitting drop / Details: 0.1 M succinic acid (pH 7.0), 15% w/v PEG 3350

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
Detector	Type: RAYONIX MX300-HS / Detector: CCD / Date: Dec 5, 2017
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.204→34.59 Å / Num. obs: 85435 / % possible obs: 90.94 % / Redundancy: 12.9 % / B_iso Wilson estimate: 17.25 Å² / CC_1/2: 0.999 / R_merge(I) obs: 0.053 / R_pim(I) all: 0.015 / R_rim(I) all: 0.055 / Net I/σ(I): 22.5
Reflection shell	Resolution: 1.204→1.247 Å / R_merge(I) obs: 1.185 / Mean I/σ(I) obs: 1 / Num. unique obs: 4861 / CC_1/2: 0.45 / % possible all: 52.45

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Processing

Software

Name	Version	Classification
PHENIX	1.17.1_3660	refinement
XDS		data reduction
XDS		data scaling
PHASER	2.8.3	phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1HK0

1hk0

Resolution: 1.204→34.59 Å / SU ML: 0.122 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.5691

	R_factor	Num. reflection	% reflection
R_free	0.1944	4272	5 %
R_work	0.1688	-	-
obs	0.1701	85433	90.95 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Displacement parameters

B_iso mean: 22.77 Å²

Refinement step

Cycle: LAST / Resolution: 1.204→34.59 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2877	0	5	351	3233

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0086	2998
X-RAY DIFFRACTION	f_angle_d	1.2083	4055
X-RAY DIFFRACTION	f_chiral_restr	0.1104	387
X-RAY DIFFRACTION	f_plane_restr	0.0077	541
X-RAY DIFFRACTION	f_dihedral_angle_d	19.9436	1138

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 (%)
1.2-1.22	0.3105	65	0.3118	1230	X-RAY DIFFRACTION	42.2
1.22-1.23	0.2926	85	0.2985	1614	X-RAY DIFFRACTION	54.51
1.23-1.25	0.2778	93	0.2863	1774	X-RAY DIFFRACTION	60.7
1.25-1.26	0.2697	100	0.2809	1903	X-RAY DIFFRACTION	64.91
1.26-1.28	0.2924	109	0.2489	2061	X-RAY DIFFRACTION	70.23
1.28-1.3	0.2815	118	0.2438	2256	X-RAY DIFFRACTION	75.82
1.3-1.32	0.2601	126	0.2327	2388	X-RAY DIFFRACTION	82.89
1.32-1.34	0.2528	139	0.2325	2649	X-RAY DIFFRACTION	89.13
1.34-1.36	0.2376	150	0.2204	2839	X-RAY DIFFRACTION	96.95
1.36-1.38	0.2343	152	0.2113	2893	X-RAY DIFFRACTION	97.94
1.38-1.4	0.2511	154	0.2136	2916	X-RAY DIFFRACTION	99.16
1.4-1.43	0.222	153	0.2024	2910	X-RAY DIFFRACTION	98.65
1.43-1.46	0.2523	153	0.1925	2921	X-RAY DIFFRACTION	98.49
1.46-1.48	0.1859	156	0.1942	2953	X-RAY DIFFRACTION	99.58
1.48-1.52	0.2034	153	0.19	2912	X-RAY DIFFRACTION	99.09
1.52-1.55	0.2108	153	0.1806	2905	X-RAY DIFFRACTION	99.06
1.55-1.59	0.2068	156	0.1773	2965	X-RAY DIFFRACTION	99.3
1.59-1.63	0.2199	155	0.1848	2943	X-RAY DIFFRACTION	99.87
1.63-1.68	0.1932	156	0.1693	2956	X-RAY DIFFRACTION	99.58
1.68-1.74	0.1817	156	0.1665	2972	X-RAY DIFFRACTION	99.62
1.74-1.8	0.1898	155	0.1712	2942	X-RAY DIFFRACTION	99.74
1.8-1.87	0.1878	157	0.1701	2979	X-RAY DIFFRACTION	99.75
1.87-1.96	0.1694	157	0.1603	2987	X-RAY DIFFRACTION	99.84
1.96-2.06	0.1781	157	0.1604	2978	X-RAY DIFFRACTION	100
2.06-2.19	0.1931	158	0.1543	3000	X-RAY DIFFRACTION	100
2.19-2.36	0.1857	158	0.1569	3013	X-RAY DIFFRACTION	100
2.36-2.59	0.1917	160	0.1651	3034	X-RAY DIFFRACTION	100
2.59-2.97	0.2074	159	0.1708	3018	X-RAY DIFFRACTION	99.97
2.97-3.74	0.1857	161	0.1574	3070	X-RAY DIFFRACTION	100
3.74-34.59	0.18	168	0.1548	3180	X-RAY DIFFRACTION	98.62

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	3.07563405939	-1.27368072536	-0.187451021812	3.20214699971	-0.0155288648105	3.03012554539	-0.0781430435015	0.0817076169751	-0.099425389823	0.112993651449	-0.0418612777238	-0.086249566862	-0.0125454895314	0.0836665486895	0.118906965647	0.0974118123617	-0.00396242603058	-0.0198163216931	0.109929656848	-0.00232562221646	0.132238906158	23.6364587774	-7.75976528549	23.9822667346
2	3.89719805326	0.774876067565	-0.391163951429	5.30831098247	-1.46279073558	2.06946954647	-0.0224097626155	0.0989030044034	-0.104019130434	0.0240230739739	-0.117408462699	0.0967648271047	-0.134689915145	-0.0357987235181	0.110350972942	0.120780576339	0.0190301251757	-0.0280598646465	0.121382732669	-0.0346574000558	0.112606365266	15.5460472482	-3.82976039857	21.4672592562
3	4.42694402173	-4.24030689917	-4.5059200082	4.06198166299	4.33096807417	4.85831810615	-0.201723426842	-0.18416239275	-0.071859698015	0.18494217098	0.138061049914	0.0442583259785	0.163330440402	0.167936782009	0.0464140634542	0.20005635963	-0.00493009998904	-0.0259327088228	0.145370487461	-0.00577926865244	0.169770608941	18.6130865575	5.39305775146	33.2000161384
4	2.4241775955	-0.293881761686	0.153963588795	2.38800723199	0.408551728329	0.884433786726	0.0912943155903	0.131758739787	0.117594380001	-0.0383891004078	-0.0617446506512	0.123046872993	-0.0273914055619	-0.0612453852551	-0.0274755889403	0.143853881445	0.00605608511119	-0.0174306629881	0.117552881515	0.00473156233572	0.144470504129	5.3940214187	14.5532309639	27.6688464324
5	4.42957319068	-0.980585835022	1.20734487551	2.14606240144	-1.9170693615	5.92065278373	0.214544147608	0.401873435429	-0.000787849765177	-0.145356687585	-0.0865209896689	0.140305443372	0.0125498934009	0.0915380996354	-0.0891039770967	0.177469699797	0.020755551116	-0.031427535245	0.0945600740746	-0.0488555345264	0.145531800559	9.26053727182	10.7081664419	24.4377803022
6	3.39757108848	0.542917786614	-0.526962419793	1.97769375157	-0.386151647116	2.97057646582	0.0111055638867	-0.118053754388	0.27236354029	0.0888021672968	0.0578501230135	-0.286709648241	-0.433450629631	0.186087689976	-0.0807004116497	0.236061659903	-0.0187979950962	-0.0282632453292	0.129159159767	-0.050489967584	0.205215576811	10.5473739153	10.8466700972	-3.90975557098
7	3.97680284958	0.106298305847	-0.0267664108614	4.1073924471	0.627761869507	3.43988243488	-0.00106772688865	-0.050599997002	-0.143914188886	-0.0794098381368	0.137746641859	-0.168486216002	-0.024814651618	0.0438597576937	-0.131808435004	0.120142877461	-0.00448508002269	-0.0026152919686	0.0937924034764	-0.0291786793019	0.119918292376	6.81357475267	2.43612929341	-6.60851912989
8	2.90248857038	2.38829929416	-1.92961008228	2.84655097817	-1.14100215686	1.50880310164	0.317118763947	-0.258612283499	0.0511841361932	0.415847709652	-0.252000035252	-0.00834867053292	-0.392910021262	-0.109124020939	-0.0771050186249	0.252261158171	0.0138654678041	-0.00496147871921	0.251674156652	-0.00957214672795	0.181013187606	-2.64226764061	5.90391641807	5.17774147089
9	2.78858731649	0.215575038875	-0.572532006334	1.43595407164	-0.0303855180158	1.09309103635	-0.0340681472302	0.0347649147938	-0.019359662972	0.00349794975268	0.0438635563948	0.0914203762029	0.0349371132551	-0.141278906484	-0.00625334503016	0.12432317404	-0.00542255021465	-0.00822504328791	0.168759544385	-0.0144080382844	0.117382184472	-11.3763348918	-7.89700182584	-0.612609176844
10	2.95862812362	-0.758345293219	-0.41917262765	4.54157747934	0.649540200392	4.96206940418	0.0709306421701	0.432479210721	0.108266683722	-0.247929764433	-0.033554179574	0.0758762989254	-0.132668207956	0.0901154099824	0.000142137568548	0.0802292623662	-0.0269701441673	0.0182777314879	0.15544727568	0.0292331288702	0.115344243256	-8.77931086829	-3.87874709846	-4.4049485557

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 45 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 46 through 76 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 77 through 87 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 88 through 150 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 151 through 172 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 1 through 45 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 46 through 76 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 77 through 87 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 88 through 150 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 151 through 171 )

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