PDB-1syr: Initial Structural Analysis of Plasmodium falciparum thioredoxin

ID or keywords:

Entry

Database: PDB / ID: 1syr

Title

Initial Structural Analysis of Plasmodium falciparum thioredoxin

Components

thioredoxin

Keywords

STRUCTURAL GENOMICS / UNKNOWN FUNCTION / SGPP / PSI / Protein Structure Initiative / Structural Genomics of Pathogenic Protozoa Consortium

Function / homology

Function and homology information

The NLRP3 inflammasome / TP53 Regulates Metabolic Genes / Detoxification of Reactive Oxygen Species / Interconversion of nucleotide di- and triphosphates / protein-disulfide reductase activity / cytosol
Similarity search - Function

Biological species

Plasmodium falciparum (malaria parasite P. falciparum)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MAD / Resolution: 2.95 Å

Authors

Robien, M.A. / Hol, W.G.J. / Structural Genomics of Pathogenic Protozoa Consortium (SGPP)

Citation

Journal: To be Published
Title: Initial Structural Analysis of Plasmodium falciparum thioredoxin
Authors: Robien, M.A. / Hol, W.G.J. / Structural Genomics of Pathogenic Protozoa Consortium

History

Deposition	Apr 1, 2004	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 13, 2004	Provider: repository / Type: Initial release
Revision 1.1	Apr 30, 2008	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.3	Jan 31, 2018	Group: Database references / Category: citation_author / Item: _citation_author.name

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	1syr.cif.gz	235 KB	Display	PDBx/mmCIF format
PDB format	pdb1syr.ent.gz	202.9 KB	Display	PDB format
PDBx/mmJSON format	1syr.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	1syr_validation.pdf.gz	524.5 KB	Display	wwPDB validaton report
Full document	1syr_full_validation.pdf.gz	550.8 KB	Display
Data in XML	1syr_validation.xml.gz	38.6 KB	Display
Data in CIF	1syr_validation.cif.gz	56 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/sy/1syr ftp://data.pdbj.org/pub/pdb/validation_reports/sy/1syr	HTTPS FTP

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Related structure data

Similar structure data	1cid-d 4v2n-d 1eru-1 4cw9-d 1xwb-5 1oqq-d 6m14-1 4v2l-d 5g30-2 3d73-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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
Other databases	TargetDB: Pfal007201AAA

Similar structure data

Other databases

TargetDB: Pfal007201AAA

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#233 - May 2019 S-Nitrosylated Hemoglobin similarity (4) #91 - Jul 2007 Thymine Dimers similarity (4)

Deposited unit

A: thioredoxin

B: thioredoxin

C: thioredoxin

D: thioredoxin

E: thioredoxin

F: thioredoxin

G: thioredoxin

H: thioredoxin

I: thioredoxin

J: thioredoxin

K: thioredoxin

L: thioredoxin

153 kDa, 12 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: thioredoxin

B: thioredoxin

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

2

C: thioredoxin

D: thioredoxin

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

3

E: thioredoxin

F: thioredoxin

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

4

G: thioredoxin

H: thioredoxin

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

5

I: thioredoxin

J: thioredoxin

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

6

K: thioredoxin

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

7

L: thioredoxin

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

Unit cell

Length a, b, c (Å)	108.189, 201.308, 200.504
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	20
Space group name H-M	C222₁

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
3	1	C
4	1	D
5	1	E
6	1	F
7	1	G
8	1	H
9	1	I
10	1	J
11	1	K
12	1	L

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg label comp-ID: VAL / End label comp-ID: ALA / Refine code: 5 / Auth seq-ID: 13 - 111 / Label seq-ID: 13 - 111

Dom-ID	Auth asym-ID	Label asym-ID
1	A	A
2	B	B
3	C	C
4	D	D
5	E	E
6	F	F
7	G	G
8	H	H
9	I	I
10	J	J
11	K	K
12	L	L

#1: Protein	thioredoxin Mass: 12758.550 Da / Num. of mol.: 12 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum) Strain: 3D7 / Gene: PF14_0545 / Plasmid: PET14B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21STAR/DE3 / References: UniProt: Q7KQL8

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

Crystal	Density Matthews: 3.5 Å³/Da / Density % sol: 65 % Description: The SeMAD wavelengths used were: 0.9795, 0.9638, 0.9797; and the resolutions were 3.1, 3.3 and 3.4 angstroms, respectively.
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4 Details: Ammonium sulfate, sodium citrate, pH 4, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

Diffraction

ID	Mean temperature (K)	Crystal-ID
1	100	1
2		1
1,2		1

Diffraction source

Source	Site	Beamline	ID	Wavelength (Å)
SYNCHROTRON	ALS	5.0.2	1	1.0781
SYNCHROTRON	ALS	5.0.2	2	0.9795, 0.9638, 0.9797

Detector

Type: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 11, 2003

Radiation

ID	Monochromator	Protocol	Monochromatic (M) / Laue (L)	Scattering type	Wavelength-ID
1	Double crystal Si(111)	SINGLE WAVELENGTH	M	x-ray	1
2	Double crystal Si(111)	MAD	M	x-ray	2

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	1.0781	1
2	0.9795	1
3	0.9638	1
4	0.9797	1

Reflection

Resolution: 2.95→70 Å / Num. all: 46212 / Num. obs: 46209 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 13.6 % / B_iso Wilson estimate: 89.787 Å² / R_sym value: 0.115 / Net I/σ(I): 18.1

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Processing

Software

Name	Version	Classification
REFMAC	5.1.24	refinement
MOSFLM		data reduction
CCP4	(SCALA)	data scaling
SHARP		phasing

Refinement

Method to determine structure:

MAD / Resolution: 2.95→30 Å / Cor.coef. F_o:F_c: 0.945 / Cor.coef. F_o:F_c free: 0.924 / SU B: 15.534 / SU ML: 0.278 / TLS residual ADP flag: LIKELY RESIDUAL
Isotropic thermal model: ISOTROPIC with TLS (monomer = TLS group)
Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.817 / ESU R Free: 0.334 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: SeMAD used to solve lower resolution crystal. Rigid body fit of SeMAD model refined against native data.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.23616	2330	5.1 %	RANDOM
R_work	0.19677	-	-	-
all	0.1988	43723	-	-
obs	0.1988	43723	99.34 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK

Displacement parameters

B_iso mean: 42.271 Å²

	B_aniso -1	B_aniso -2
1-	-0.52 Å²	0 Å²
2-	-	0.52 Å²
3-	-	-

Refinement step

Cycle: LAST / Resolution: 2.95→30 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9662	0	0	0	9662

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.009	0.022	9841
X-RAY DIFFRACTION	r_angle_refined_deg	1.132	1.958	13311
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.175	5	1209
X-RAY DIFFRACTION	r_chiral_restr	0.089	0.2	1557
X-RAY DIFFRACTION	r_gen_planes_refined	0.003	0.02	7140
X-RAY DIFFRACTION	r_nbd_refined	0.212	0.2	4229
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.093	0.2	180
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.227	0.2	134
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.119	0.2	5
X-RAY DIFFRACTION	r_mcbond_it	1.26	4	6097
X-RAY DIFFRACTION	r_mcangle_it	2.46	6	9975
X-RAY DIFFRACTION	r_scbond_it	3.205	6	3744
X-RAY DIFFRACTION	r_scangle_it	5.247	10	3336

Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	A	376	medium positional	0.11	0.2
2	B	376	medium positional	0.12	0.2
3	C	376	medium positional	0.11	0.2
4	D	376	medium positional	0.12	0.2
5	E	376	medium positional	0.12	0.2
6	F	376	medium positional	0.1	0.2
7	G	376	medium positional	0.11	0.2
8	H	376	medium positional	0.18	0.2
9	I	376	medium positional	0.11	0.2
10	J	376	medium positional	0.1	0.2
11	K	376	medium positional	0.12	0.2
12	L	376	medium positional	0.14	0.2
1	A	367	loose positional	0.51	4
2	B	367	loose positional	0.5	4
3	C	367	loose positional	0.41	4
4	D	367	loose positional	0.61	4
5	E	367	loose positional	0.54	4
6	F	367	loose positional	0.41	4
7	G	367	loose positional	0.47	4
8	H	367	loose positional	0.63	4
9	I	367	loose positional	0.59	4
10	J	367	loose positional	0.47	4
11	K	367	loose positional	0.47	4
12	L	367	loose positional	0.56	4
1	A	376	medium thermal	0.48	2
2	B	376	medium thermal	0.45	2
3	C	376	medium thermal	0.46	2
4	D	376	medium thermal	0.48	2
5	E	376	medium thermal	0.46	2
6	F	376	medium thermal	0.51	2
7	G	376	medium thermal	0.56	2
8	H	376	medium thermal	0.52	2
9	I	376	medium thermal	0.43	2
10	J	376	medium thermal	0.47	2
11	K	376	medium thermal	0.59	2
12	L	376	medium thermal	0.49	2
1	A	367	loose thermal	2.71	10
2	B	367	loose thermal	2.4	10
3	C	367	loose thermal	2.43	10
4	D	367	loose thermal	2.34	10
5	E	367	loose thermal	2.55	10
6	F	367	loose thermal	2.46	10
7	G	367	loose thermal	2.73	10
8	H	367	loose thermal	2.82	10
9	I	367	loose thermal	2.18	10
10	J	367	loose thermal	2.45	10
11	K	367	loose thermal	2.35	10
12	L	367	loose thermal	2.21	10

LS refinement shell

Resolution: 2.95→3.108 Å / Total num. of bins used: 10

	R_factor	Num. reflection	% reflection
R_free	0.329	329	-
R_work	0.304	6007	-
obs	-	6298	0.954 %

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	12.2628	-3.1989	1.2381	6.1346	-1.0174	9.7829	-0.6406	-0.5894	1.1259	0.8006	0.1287	-0.7249	-1.0239	0.8188	0.5119	0.3115	-0.1143	-0.0932	0.3383	0.0736	0.3787	35.8934	61.5739	91.9271
2	10.9137	-0.2531	-2.447	3.9213	0.9368	8.412	-0.3441	0.005	-1.378	-0.0203	-0.4064	0.3611	0.1283	-0.7653	0.7505	0.2273	-0.1148	-0.0983	0.4605	-0.046	0.4872	61.1334	46.289	95.4594
3	5.6888	1.1889	-0.4309	6.7673	-0.4088	6.9636	0.1317	-0.0675	-0.0612	0.741	-0.1929	-0.4025	-0.3364	0.5766	0.0612	0.4857	0.0589	0.0179	0.3994	0.0148	0.1179	32.4815	54.953	119.2177
4	3.495	-0.6729	-1.2957	5.2238	2.3647	9.2708	0.033	0.423	0.0539	-1.0453	-0.2651	0.3572	-0.0398	-0.007	0.2322	0.8273	-0.0407	0.0487	0.2548	0.0114	0.3314	22.1726	80.6843	130.0832
5	9.0031	2.3574	-5.8381	7.7386	-4.2981	10.0627	1.0849	-0.7513	0.18	1.5369	-0.4809	0.2266	-1.4414	0.5597	-0.604	0.7519	0.0187	0.0407	0.2739	0.0141	0.3003	27.5636	88.4864	63.7196
6	4.7089	-0.9078	-1.5431	10.1375	-1.556	6.6579	0.1334	0.2038	0.0262	-0.8901	0.1223	1.2564	-0.4249	-0.8263	-0.2557	0.3037	0.06	-0.1179	0.4082	0.1167	0.3313	14.9711	62.6021	71.4956
7	5.308	1.959	0.3696	6.797	1.3818	6.7591	0.2119	0.3637	-0.6625	0.7483	0.0761	-0.1255	0.5361	0.0785	-0.2879	0.2317	0.0434	0.0376	0.2482	-0.0129	0.3273	24.6449	36.8466	80.9806
8	6.4767	-0.903	-3.864	9.4303	3.822	12.3253	0.1319	0.4903	-0.0609	-0.9001	-0.7302	1.6382	-1.5418	-1.8551	0.5983	0.3427	0.1829	-0.3886	0.4927	-0.1536	0.6814	17.7304	28.0674	53.677
9	4.2992	-1.8051	0.0536	6.6872	-1.0075	7.5773	0.0269	-0.4546	-0.6772	-0.2714	0.1619	0.2756	0.9465	-0.364	-0.1888	0.6611	-0.0884	0.1353	0.2913	0.1551	0.3785	20.1074	29.3048	112.7448
10	3.7724	-0.9797	-1.6046	8.5956	-0.0353	13.4384	0.137	-0.0288	0.3847	-0.48	0.1637	-0.9504	-1.1003	1.4114	-0.3007	0.3634	-0.0421	0.0473	0.3749	0.0565	0.5098	34.5514	19.9711	137.0798
11	8.8535	3.9495	1.3337	12.2353	-1.3706	4.3872	-0.4432	1.0158	-0.3105	-0.4082	0.8654	0.5283	0.2966	-0.2266	-0.4221	0.0205	0.0313	-0.0804	0.4022	-0.0222	0.3434	13.4511	111.6298	44.0292
12	9.2887	1.5937	2.178	13.3388	1.7336	6.1601	-0.2335	1.2889	0.3487	-0.7036	0.6642	-1.6017	-0.3887	0.9931	-0.4307	0.1276	0.0601	0.1821	0.5902	-0.0737	0.6248	42.8056	97.9511	40.484

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	X-RAY DIFFRACTION	1	A	A	9 - 111	9 - 111
2	X-RAY DIFFRACTION	2	B	B	10 - 111	10 - 111
3	X-RAY DIFFRACTION	3	C	C	9 - 111	9 - 111
4	X-RAY DIFFRACTION	4	D	D	10 - 111	10 - 111
5	X-RAY DIFFRACTION	5	E	E	10 - 111	10 - 111
6	X-RAY DIFFRACTION	6	F	F	10 - 111	10 - 111
7	X-RAY DIFFRACTION	7	G	G	10 - 111	10 - 111
8	X-RAY DIFFRACTION	8	H	H	9 - 111	9 - 111
9	X-RAY DIFFRACTION	9	I	I	10 - 111	10 - 111
10	X-RAY DIFFRACTION	10	J	J	10 - 111	10 - 111
11	X-RAY DIFFRACTION	11	K	K	10 - 111	10 - 111
12	X-RAY DIFFRACTION	12	L	L	10 - 111	10 - 111

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