PDB-1vph: CRYSTAL STRUCTURE OF a YbjQ-like protein of unknown function (SSO...

ID or keywords:

Entry

Database: PDB / ID: 1vph

Title

CRYSTAL STRUCTURE OF a YbjQ-like protein of unknown function (SSO2532) FROM SULFOLOBUS SOLFATARICUS P2 AT 1.76 A RESOLUTION

Components

hypothetical protein SSO2532

Keywords

UNKNOWN FUNCTION / YBJQ-LIKE FOLD / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI

Function / homology

Function and homology information

YjbQ-like / Uncharacterised protein family UPF0047, YjbQ / YjbQ-like superfamily / Uncharacterised protein family UPF0047 / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology

Biological species

Sulfolobus solfataricus (archaea)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.764 Å

Authors

Joint Center for Structural Genomics (JCSG)

Citation

Journal: To be published
Title: Crystal structure of hypothetical protein (13815834) from Sulfolobus solfataricus at 1.76 A resolution
Authors: Joint Center for Structural Genomics (JCSG)

History

Deposition	Nov 3, 2004	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 16, 2004	Provider: repository / Type: Initial release
Revision 1.1	Apr 26, 2008	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.3	Oct 4, 2017	Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4	Jan 25, 2023	Group: Database references / Derived calculations Category: database_2 / pdbx_database_related ...database_2 / pdbx_database_related / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_related.db_name / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5	Sep 20, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	1vph.cif.gz	188.2 KB	Display	PDBx/mmCIF format
PDB format	pdb1vph.ent.gz	148.4 KB	Display	PDB format
PDBx/mmJSON format	1vph.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	1vph_validation.pdf.gz	503.5 KB	Display	wwPDB validaton report
Full document	1vph_full_validation.pdf.gz	511.7 KB	Display
Data in XML	1vph_validation.xml.gz	34.6 KB	Display
Data in CIF	1vph_validation.cif.gz	48.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/vp/1vph ftp://data.pdbj.org/pub/pdb/validation_reports/vp/1vph	HTTPS FTP

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Related structure data

Related structure data	1vmfS S: Starting model for refinement
Similar structure data	2o8a-1 2y3y-1 1h13-d 6kbc-d 2o8a-2 6xrk-1 5k71-1 2b4f-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) Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search
Other databases	TargetDB: 358101

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: hypothetical protein SSO2532

B: hypothetical protein SSO2532

C: hypothetical protein SSO2532

D: hypothetical protein SSO2532

E: hypothetical protein SSO2532

F: hypothetical protein SSO2532

hetero molecules

104 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: hypothetical protein SSO2532

B: hypothetical protein SSO2532

C: hypothetical protein SSO2532

hetero molecules

defined by author&software
51.8 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

D: hypothetical protein SSO2532

E: hypothetical protein SSO2532

F: hypothetical protein SSO2532

hetero molecules

defined by author&software
51.9 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	79.860, 92.180, 114.130
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Ens-ID: 1

Dom-ID	Component-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Refine code	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	LYS	LYS	ILE	ILE	2	A	A	2 - 82	14 - 94
2	1	LYS	LYS	ILE	ILE	2	B	B	2 - 82	14 - 94
3	1	LYS	LYS	ILE	ILE	2	C	C	2 - 82	14 - 94
4	1	LYS	LYS	ILE	ILE	2	D	D	2 - 82	14 - 94
5	1	LYS	LYS	ILE	ILE	2	E	E	2 - 82	14 - 94
6	1	LYS	LYS	ILE	ILE	2	F	F	2 - 82	14 - 94
7	2	ASP	ASP	ASP	ASP	6	A	A	83	95
8	2	ASP	ASP	ASP	ASP	6	B	B	83	95
9	2	ASP	ASP	ASP	ASP	6	C	C	83	95
10	2	ASP	ASP	ASP	ASP	6	D	D	83	95
11	2	ASP	ASP	ASP	ASP	6	E	E	83	95
12	2	ASP	ASP	ASP	ASP	6	F	F	83	95
13	3	ASP	ASP	PRO	PRO	2	A	A	84 - 124	96 - 136
14	3	ASP	ASP	PRO	PRO	2	B	B	84 - 124	96 - 136
15	3	ASP	ASP	PRO	PRO	2	C	C	84 - 124	96 - 136
16	3	ASP	ASP	PRO	PRO	2	D	D	84 - 124	96 - 136
17	3	ASP	ASP	PRO	PRO	2	E	E	84 - 124	96 - 136
18	3	ASP	ASP	PRO	PRO	2	F	F	84 - 124	96 - 136
19	4	ARG	ARG	ARG	ARG	3	A	A	125	137
20	4	ARG	ARG	ARG	ARG	3	B	B	125	137
21	4	ARG	ARG	ARG	ARG	3	C	C	125	137
22	4	ARG	ARG	ARG	ARG	3	D	D	125	137
23	4	ARG	ARG	ARG	ARG	3	E	E	125	137
24	4	ARG	ARG	ARG	ARG	3	F	F	125	137
25	5	SER	SER	GLY	GLY	2	A	A	126 - 136	138 - 148
26	5	SER	SER	GLY	GLY	2	B	B	126 - 136	138 - 148
27	5	SER	SER	GLY	GLY	2	C	C	126 - 136	138 - 148
28	5	SER	SER	GLY	GLY	2	D	D	126 - 136	138 - 148
29	5	SER	SER	GLY	GLY	2	E	E	126 - 136	138 - 148
30	5	SER	SER	GLY	GLY	2	F	F	126 - 136	138 - 148

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Protein , 1 types, 6 molecules ABCDEF

#1: Protein	hypothetical protein SSO2532 Mass: 17057.352 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Strain: P2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q97VS8

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Non-polymers , 5 types, 303 molecules

#2: Chemical	ChemComp-K / POTASSIUM ION Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#3: Chemical	ChemComp-PO4 / PHOSPHATE ION Mass: 94.971 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: PO₄
#4: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₆O₂
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 286 / 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: 2.13 Å³/Da / Density % sol: 41.76 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, sitting drop, nanodrop / pH: 7.5 Details: 10.0% iso-Propanol, 20.0% PEG-4000, 0.1M HEPES pH7.5, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.979245
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 18, 2004
Radiation	Monochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.979245 Å / Relative weight: 1
Reflection	Resolution: 1.764→28.68 Å / Num. obs: 75897 / % possible obs: 90.9 % / Redundancy: 3.9 % / B_iso Wilson estimate: 31.06 Å² / R_sym value: 0.062 / Net I/σ(I): 15.6
Reflection shell	Resolution: 1.764→1.86 Å / Redundancy: 1.9 % / Mean I/σ(I) obs: 3 / Num. unique all: 7634 / R_sym value: 0.312 / % possible all: 63.6

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Processing

Software

Name	Version	Classification
SOLVE		phasing
SCALA	5.0)	data scaling
MOLREP		phasing
REFMAC	5.2.0005	refinement
CCP4	(SCALA)	data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1VMF

1vmf

Resolution: 1.764→16.22 Å / Cor.coef. F_o:F_c: 0.957 / Cor.coef. F_o:F_c free: 0.944 / SU B: 5.534 / SU ML: 0.086 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.141 / ESU R Free: 0.129
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 2. FOUR POTASSIUM IONS MODELLED TO FIT THE DENSITY NEAR HIS79/HIS89/ASN85. HOWEVER, THERE ARE STILL SOME UNEXPLAINED DENSITIES NEARBY. ...

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.22173	3791	5 %	RANDOM
R_work	0.18914	-	-	-
obs	0.19082	72013	90.69 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK

Displacement parameters

B_iso mean: 22.167 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.58 Å²	0 Å²	0 Å²
2-	-	-2.01 Å²	0 Å²
3-	-	-	1.43 Å²

Refinement step

Cycle: LAST / Resolution: 1.764→16.22 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6658	0	64	286	7008

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.017	0.021	6888
X-RAY DIFFRACTION	r_bond_other_d	0.003	0.02	6238
X-RAY DIFFRACTION	r_angle_refined_deg	1.607	1.934	9353
X-RAY DIFFRACTION	r_angle_other_deg	0.961	3	14411
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.46	5	833
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	36.54	24.082	343
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.27	15	1161
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	11.353	15	43
X-RAY DIFFRACTION	r_chiral_restr	0.1	0.2	1066
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.02	7636
X-RAY DIFFRACTION	r_gen_planes_other	0.003	0.02	1407
X-RAY DIFFRACTION	r_nbd_refined	0.272	0.2	1305
X-RAY DIFFRACTION	r_nbd_other	0.202	0.2	6545
X-RAY DIFFRACTION	r_nbtor_other	0.09	0.2	4176
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.148	0.2	305
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.165	0.2	26
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.267	0.2	71
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.15	0.2	10
X-RAY DIFFRACTION	r_mcbond_it	1.599	3	4169
X-RAY DIFFRACTION	r_mcbond_other	0.371	3	1725
X-RAY DIFFRACTION	r_mcangle_it	2.714	5	6775
X-RAY DIFFRACTION	r_scbond_it	4.767	8	2731
X-RAY DIFFRACTION	r_scangle_it	6.712	11	2578
X-RAY DIFFRACTION	r_nbtor_refined	0.182	0.2	3261
X-RAY DIFFRACTION	r_xyhbond_nbd_other	0.128	0.2	1
X-RAY DIFFRACTION	r_metal_ion_refined	0.479	0.2	19

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	788	tight positional	0.06	0.05
2	B	788	tight positional	0.07	0.05
3	C	788	tight positional	0.1	0.05
4	D	788	tight positional	0.08	0.05
5	E	788	tight positional	0.09	0.05
6	F	788	tight positional	0.09	0.05
1	A	1113	medium positional	0.38	0.5
2	B	1113	medium positional	0.35	0.5
3	C	1113	medium positional	0.52	0.5
4	D	1113	medium positional	0.44	0.5
5	E	1113	medium positional	0.43	0.5
6	F	1113	medium positional	0.58	0.5
1	A	30	loose positional	0.79	5
2	B	30	loose positional	0.6	5
3	C	30	loose positional	0.61	5
4	D	30	loose positional	0.4	5
5	E	30	loose positional	0.58	5
6	F	30	loose positional	0.38	5
1	A	788	tight thermal	0.27	0.5
2	B	788	tight thermal	0.29	0.5
3	C	788	tight thermal	0.28	0.5
4	D	788	tight thermal	0.29	0.5
5	E	788	tight thermal	0.27	0.5
6	F	788	tight thermal	0.29	0.5
1	A	1113	medium thermal	1.08	2
2	B	1113	medium thermal	1.11	2
3	C	1113	medium thermal	1.17	2
4	D	1113	medium thermal	1.16	2
5	E	1113	medium thermal	1.09	2
6	F	1113	medium thermal	1.19	2
1	A	30	loose thermal	3.44	10
2	B	30	loose thermal	4.42	10
3	C	30	loose thermal	2.13	10
4	D	30	loose thermal	2.86	10
5	E	30	loose thermal	3.95	10
6	F	30	loose thermal	2.53	10

LS refinement shell

Resolution: 1.764→1.81 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.312	156	4.42 %
R_work	0.239	3373	-
obs	-	-	57.56 %

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	0.8637	-0.051	0.2429	1.713	-0.1368	0.3767	0.0414	0.0662	-0.0395	-0.2143	-0.0014	0.1982	0.1345	-0.0181	-0.0399	-0.0515	-0.0035	-0.014	-0.0401	0.0036	-0.0612	-9.2394	69.0975	1.3757
2	0.4482	-0.3247	-0.0575	1.5868	-0.0798	0.4675	0.031	-0.0612	0.0131	0.1615	-0.0653	-0.1956	0.0235	0.0841	0.0344	-0.0424	-0.0031	-0.0097	-0.0372	0.0169	-0.044	6.0723	72.3525	12.872
3	0.3461	0.327	0.1016	0.5962	0.1294	0.6157	-0.003	-0.0629	0.0318	0.2575	-0.0119	0.1457	-0.0206	-0.0678	0.0149	-0.0053	0.0033	0.0458	-0.0182	0.0126	-0.0297	-11.4845	72.4853	20.1369
4	0.8377	-0.4524	-0.0095	2.4118	-0.0379	0.367	-0.0022	-0.0499	-0.0221	0.2122	-0.0659	0.2076	-0.0903	-0.0463	0.0681	-0.0839	-0.0025	0.0111	-0.0341	-0.0051	-0.0456	-8.7594	115.81	-1.0963
5	0.5292	0.0533	0.0271	1.5042	-0.0621	0.5312	0.0504	0.1216	0.0388	-0.2442	-0.092	-0.2494	-0.0548	0.0495	0.0416	-0.0487	0.0123	0.027	-0.0129	0.0342	-0.0235	6.4674	113.1095	-12.8219
6	0.465	-0.2675	-0.09	1.0628	0.1221	0.5179	0.0032	0.0968	-0.0588	-0.307	-0.0758	0.1754	-0.0092	-0.0443	0.0726	0.0005	-0.002	-0.052	0.0159	-0.0171	-0.018	-11.1045	113.7308	-19.9545

Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

ID	Refine TLS-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	A	A	0 - 137	12 - 149
2	2	B	B	1 - 137	13 - 149
3	3	C	C	-6 - 137	6 - 149
4	4	D	D	0 - 137	12 - 149
5	5	E	E	0 - 137	12 - 149
6	6	F	F	-5 - 137	7 - 149

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Yorodumi