PDB-5t8k: 1.95 Angstrom Crystal Structure of S-adenosylhomocysteinase from ...

ID or keywords:

Entry

Database: PDB / ID: 5t8k

Title

1.95 Angstrom Crystal Structure of S-adenosylhomocysteinase from Cryptosporidium parvum in Complex with Adenine and NAD

Components

(Adenosylhomocysteinase) x 2

Keywords

HYDROLASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID

Function / homology

Function and homology information

adenosylhomocysteinase / adenosylhomocysteinase activity / S-adenosylmethionine cycle / one-carbon metabolic process / nucleotide binding / cytosol
Similarity search - Function

Biological species

Cryptosporidium parvum (eukaryote)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.95 Å

Authors

Minasov, G. / Shuvalova, L. / Kiryukhina, O. / Dubrovska, I. / Bishop, B. / Kwon, K. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)

Citation

Journal: To Be Published
Title: 1.95 Angstrom Crystal Structure of S-adenosylhomocysteinase from Cryptosporidium parvum in Complex with Adenine and NAD.
Authors: Minasov, G. / Shuvalova, L. / Kiryukhina, O. / Dubrovska, I. / Bishop, B. / Kwon, K. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)

History

Deposition	Sep 7, 2016	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 28, 2016	Provider: repository / Type: Initial release
Revision 1.1	Oct 4, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_prerelease_seq / pdbx_struct_oper_list / struct_conn / struct_conn_type Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5t8k.cif.gz	843.9 KB	Display	PDBx/mmCIF format
PDB format	pdb5t8k.ent.gz	700.3 KB	Display	PDB format
PDBx/mmJSON format	5t8k.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5t8k_validation.pdf.gz	2.3 MB	Display	wwPDB validaton report
Full document	5t8k_full_validation.pdf.gz	2.4 MB	Display
Data in XML	5t8k_validation.xml.gz	91 KB	Display
Data in CIF	5t8k_validation.cif.gz	136.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/t8/5t8k ftp://data.pdbj.org/pub/pdb/validation_reports/t8/5t8k	HTTPS FTP

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Related structure data

Related structure data	5hm8S 5jpi 5jxw S: Starting model for refinement
Similar structure data	5tls-d 5tj9-d 5utu-1 5jxw-d 5hm8-2 5jpi-d 5hm8-1 5utu-2 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	TargetTrack: CSGID-IDP95479

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#210 - Jun 2017 Adenine Riboswitch in Action similarity (1) #130 - Oct 2010 Riboswitches similarity (1) #156 - Dec 2012 ABO Blood Type Glycosyltransferases similarity (1)

Deposited unit

A: Adenosylhomocysteinase

B: Adenosylhomocysteinase

C: Adenosylhomocysteinase

D: Adenosylhomocysteinase

hetero molecules

230 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	67.686, 182.785, 96.250
Angle α, β, γ (deg.)	90.00, 100.58, 90.00
Int Tables number	4
Space group name H-M	P12₁1

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Protein , 2 types, 4 molecules ABDC

#1: Protein	Adenosylhomocysteinase Mass: 56200.676 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Cryptosporidium parvum (strain Iowa II) (eukaryote) Strain: Iowa II / Gene: cgd3_80 / Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) MAGIC / References: UniProt: Q5CPH1, adenosylhomocysteinase
#2: Protein	Adenosylhomocysteinase Mass: 56276.793 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Cryptosporidium parvum (strain Iowa II) (eukaryote) Strain: Iowa II / Gene: cgd3_80 / Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) MAGIC / References: UniProt: Q5CPH1, adenosylhomocysteinase

#1: Protein

Adenosylhomocysteinase

Mass: 56200.676 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Cryptosporidium parvum (strain Iowa II) (eukaryote)
Strain: Iowa II / Gene: cgd3_80 / Plasmid: pMCSG53 / Production host:

Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) MAGIC / References: UniProt: Q5CPH1, adenosylhomocysteinase

#2: Protein

Adenosylhomocysteinase

Mass: 56276.793 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Cryptosporidium parvum (strain Iowa II) (eukaryote)
Strain: Iowa II / Gene: cgd3_80 / Plasmid: pMCSG53 / Production host:

Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) MAGIC / References: UniProt: Q5CPH1, adenosylhomocysteinase

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Non-polymers , 9 types, 1950 molecules

#3: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#4: Chemical	ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂₁H₂₇N₇O₁₄P₂ / Comment: NAD*YM
#5: Chemical	ChemComp-ADE / ADENINE Mass: 135.127 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₅H₅N₅
#6: Chemical	ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400 Mass: 282.331 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₁₂H₂₆O₇ / Comment: precipitant*YM
#7: Chemical	ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₄H₁₂NO₃ / Comment: pH buffer*YM
#8: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃H₈O₃
#9: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#10: Chemical	ChemComp-PGE / TRIETHYLENE GLYCOL Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₆H₁₄O₄
#11: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1925 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.6 Å³/Da / Density % sol: 52.7 %
Crystal grow	Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: Protein: 9.3 mg/ml, 0.1M Tris HCl (pH 8.3), 1mM Adenine, 1mM NAD, 1mM Homocysteine, Screen: Classics II (D9), 0.1M Bis-Tris-HCL (pH 8.5), 25% (w/v) PEG 3350

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
Detector	Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 16, 2016 / Details: C(111)
Radiation	Monochromator: beryllium lenses / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97856 Å / Relative weight: 1
Reflection	Resolution: 1.95→30 Å / Num. obs: 166729 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / B_iso Wilson estimate: 26 Å² / R_merge(I) obs: 0.076 / R_sym value: 0.076 / Net I/σ(I): 20.8
Reflection shell	Resolution: 1.95→1.98 Å / Redundancy: 3.7 % / R_merge(I) obs: 0.722 / Mean I/σ(I) obs: 2 / CC_1/2: 0.65 / % possible all: 100

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0155	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB-5HM8

5hm8

Resolution: 1.95→29.92 Å / Cor.coef. F_o:F_c: 0.975 / Cor.coef. F_o:F_c free: 0.964 / SU B: 5.705 / SU ML: 0.086 / Cross valid method: THROUGHOUT / ESU R: 0.131 / ESU R Free: 0.117 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.17296	8283	5 %	RANDOM
R_work	0.14092	-	-	-
obs	0.1425	158251	99.93 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å

Displacement parameters

B_iso mean: 33.031 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.58 Å²	0 Å²	-0.47 Å²
2-	-	0.14 Å²	0 Å²
3-	-	-	0.58 Å²

Refinement step

Cycle: 1 / Resolution: 1.95→29.92 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	15562	0	364	1925	17851

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.009	0.019	16863
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	16366
X-RAY DIFFRACTION	r_angle_refined_deg	1.443	1.993	22828
X-RAY DIFFRACTION	r_angle_other_deg	0.896	3	37874
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	3.175	5	2113
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	33.292	25.233	709
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	10.082	15	3158
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	8.183	15	72
X-RAY DIFFRACTION	r_chiral_restr	0.091	0.2	2563
X-RAY DIFFRACTION	r_gen_planes_refined	0.023	0.02	18921
X-RAY DIFFRACTION	r_gen_planes_other	0.019	0.02	3635
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	1.273	2.097	8255
X-RAY DIFFRACTION	r_mcbond_other	1.273	2.097	8253
X-RAY DIFFRACTION	r_mcangle_it	2.158	3.134	10433
X-RAY DIFFRACTION	r_mcangle_other	2.157	3.134	10434
X-RAY DIFFRACTION	r_scbond_it	1.588	2.425	8608
X-RAY DIFFRACTION	r_scbond_other	1.588	2.425	8608
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	2.641	3.504	12396
X-RAY DIFFRACTION	r_long_range_B_refined	5.741	26.993	20262
X-RAY DIFFRACTION	r_long_range_B_other	5.473	25.882	19578
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 1.95→2 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.256	615	-
R_work	0.231	11653	-
obs	-	-	99.99 %

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	0.7321	-0.1259	-0.6334	0.6801	0.3169	1.7495	0.0317	-0.2407	-0.0565	0.2076	-0.0391	-0.0205	0.0309	0.1418	0.0073	0.161	-0.0354	0.0011	0.2199	0.0215	0.0085	67.5148	36.7794	214.4989
2	0.5446	0.2686	0.0889	0.6089	0.0905	0.441	0.0455	-0.1466	-0.0243	0.1728	-0.0539	0.0897	0.0245	-0.0506	0.0084	0.1144	-0.0214	0.0613	0.1366	0.0026	0.0382	49.4278	32.6464	199.2099
3	0.4392	0.1375	0.0916	0.0786	0.182	2.1988	0.0319	-0.0235	0.1108	0.0377	-0.0347	0.0379	-0.2304	0.1448	0.0028	0.1254	-0.0459	0.0147	0.1184	-0.0135	0.0725	71.9058	49.7214	189.2108
4	1.6718	-0.0966	0.1821	1.1506	0.0019	0.7821	0.0301	0.3404	-0.0478	-0.3228	-0.0596	0.1486	0.0595	-0.0502	0.0296	0.1587	0.0257	-0.0423	0.1811	-0.0585	0.0374	38.858	19.1186	139.4652
5	0.4011	-0.1795	-0.0855	0.4943	0.0342	0.5142	0.0305	0.0725	-0.119	-0.0569	-0.0316	0.1302	0.0895	-0.0856	0.0012	0.0383	-0.0064	-0.0111	0.0793	-0.0403	0.1001	34.2888	18.9684	158.8145
6	0.8234	-0.3003	0.0055	0.3963	-0.0856	0.3224	0.0347	0.1168	-0.1033	-0.0655	-0.0544	0.0873	0.0747	-0.0474	0.0197	0.0319	-0.0076	-0.0011	0.0461	-0.0381	0.0378	40.4952	18.3512	157.8596
7	1.2184	0.1709	-0.427	0.9692	-0.0683	1.09	-0.0143	0.1859	0.1465	-0.1134	-0.0184	0.2079	-0.0969	-0.2059	0.0328	0.045	0.0459	-0.0321	0.0911	-0.0034	0.0732	40.2414	60.447	161.8714
8	1.6333	0.1564	-0.6542	2.615	-0.081	2.1285	0.0761	0.2036	0.3315	-0.2695	-0.0638	-0.2022	-0.423	0.1167	-0.0124	0.149	-0.0039	0.0152	0.0611	0.0639	0.111	60.6554	73.645	158.7041
9	0.4138	-0.0361	0.0264	0.4054	0.0685	0.3152	0.0001	0.0132	0.0657	-0.0109	-0.0307	0.0368	-0.0409	-0.0164	0.0305	0.0393	0.0055	0.0148	0.0543	-0.0036	0.0282	56.1728	48.1688	170.7298
10	1.8603	-0.4807	0.159	1.2334	0.0004	0.5357	-0.046	-0.2808	-0.1175	0.2568	0.0756	0.1306	0.0603	-0.063	-0.0296	0.1264	-0.0115	0.0525	0.0964	0.0638	0.0855	47.1078	-3.5412	198.4729
11	0.2712	-0.2948	0.3092	1.3483	-0.1302	0.4206	0.1184	0.0271	-0.0989	-0.0339	-0.0198	0.0783	0.1407	0.0641	-0.0986	0.1051	0.011	-0.001	0.0503	0.0208	0.1136	57.4181	-12.49	185.341
12	0.643	0.0927	0.0517	0.4925	-0.0574	0.2046	0.0361	-0.0331	-0.145	0.0681	-0.0405	-0.0137	0.0561	0.022	0.0044	0.0431	0.0014	0.0139	0.0241	0.0134	0.0574	55.8844	7.5956	180.0962

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	3 - 204
2	X-RAY DIFFRACTION	2	A	205 - 427
3	X-RAY DIFFRACTION	3	A	428 - 495
4	X-RAY DIFFRACTION	4	B	3 - 174
5	X-RAY DIFFRACTION	5	B	175 - 333
6	X-RAY DIFFRACTION	6	B	334 - 495
7	X-RAY DIFFRACTION	7	C	3 - 119
8	X-RAY DIFFRACTION	8	C	120 - 203
9	X-RAY DIFFRACTION	9	C	204 - 495
10	X-RAY DIFFRACTION	10	D	2 - 119
11	X-RAY DIFFRACTION	11	D	120 - 263
12	X-RAY DIFFRACTION	12	D	264 - 495

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