PDB-3b77: Crystal structure of a ph domain containing bacterial protein (ex...

ID or keywords:

Entry

Database: PDB / ID: 3b77

Title

Crystal structure of a ph domain containing bacterial protein (exig_2160) from exiguobacterium sibiricum 255-15 at 2.42 A resolution

Components

Uncharacterized protein

Keywords

UNKNOWN FUNCTION / Pleckstrin-homology domain / structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2

Function / homology

Function and homology information

Uncharacterised domain YvbH-like, oligomerisation domain / YvbH-like oligomerisation region / Bacterial Pleckstrin homology domain / Bacterial Pleckstrin homology domain / Bacterial Pleckstrin homology domain superfamily / Bacterial PH domain / Helix Hairpins - #210 / PH-domain like / Helix Hairpins / Roll ...
Similarity search - Domain/homology

Biological species

Exiguobacterium sibiricum (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MAD / Resolution: 2.42 Å

Authors

Joint Center for Structural Genomics (JCSG)

Citation

Journal: J.Mol.Biol. / Year: 2010
Title: Bacterial pleckstrin homology domains: a prokaryotic origin for the PH domain.
Authors: Xu, Q. / Bateman, A. / Finn, R.D. / Abdubek, P. / Astakhova, T. / Axelrod, H.L. / Bakolitsa, C. / Carlton, D. / Chen, C. / Chiu, H.J. / Chiu, M. / Clayton, T. / Das, D. / Deller, M.C. / ...

History

Deposition	Oct 30, 2007	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 13, 2007	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.2	Oct 25, 2017	Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3	Jul 24, 2019	Group: Data collection / Derived calculations / Refinement description Category: software / struct_conn Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4	Jan 25, 2023	Group: Database references / Category: database_2 / struct_ref_seq_dif Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5	Nov 20, 2024	Group: Data collection / Refinement description / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim Item: _pdbx_entry_details.has_protein_modification / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id

Remark 999

SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ...

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3b77.cif.gz	235 KB	Display	PDBx/mmCIF format
PDB format	pdb3b77.ent.gz	191 KB	Display	PDB format
PDBx/mmJSON format	3b77.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/b7/3b77 ftp://data.pdbj.org/pub/pdb/validation_reports/b7/3b77	HTTPS FTP

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Related structure data

Related structure data	3dcxC 3hsaC C: citing same article (ref.)
Similar structure data	4rqp-d 6mgq-d 3mdj-d 4rs5-d 4yvw-d 4rr3-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: 380276

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Uncharacterized protein

B: Uncharacterized protein

C: Uncharacterized protein

D: Uncharacterized protein

E: Uncharacterized protein

F: Uncharacterized protein

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

1

A: Uncharacterized protein

B: Uncharacterized protein

C: Uncharacterized protein

A: Uncharacterized protein

B: Uncharacterized protein

C: Uncharacterized protein

A: Uncharacterized protein

B: Uncharacterized protein

C: Uncharacterized protein

A: Uncharacterized protein

B: Uncharacterized protein

C: Uncharacterized protein

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

2

D: Uncharacterized protein

E: Uncharacterized protein

F: Uncharacterized protein

D: Uncharacterized protein

E: Uncharacterized protein

F: Uncharacterized protein

D: Uncharacterized protein

E: Uncharacterized protein

F: Uncharacterized protein

D: Uncharacterized protein

E: Uncharacterized protein

F: Uncharacterized protein

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

Unit cell

Length a, b, c (Å)	150.990, 150.990, 76.219
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	75
Space group name H-M	P4

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	GLY	GLY	ASP	ASP	1	A	A	16 - 63	5 - 52
2	1	GLY	GLY	ASP	ASP	1	B	B	16 - 63	5 - 52
3	1	GLY	GLY	ASP	ASP	1	C	C	16 - 63	5 - 52
4	1	GLY	GLY	ASP	ASP	1	D	D	16 - 63	5 - 52
5	1	GLY	GLY	ASP	ASP	1	E	E	16 - 63	5 - 52
6	1	GLY	GLY	ASP	ASP	1	F	F	16 - 63	5 - 52
7	2	GLY	GLY	LYS	LYS	6	A	A	64 - 71	53 - 60
8	2	GLY	GLY	LYS	LYS	6	B	B	64 - 71	53 - 60
9	2	GLY	GLY	LYS	LYS	6	C	C	64 - 71	53 - 60
10	2	GLY	GLY	LYS	LYS	6	D	D	64 - 71	53 - 60
11	2	GLY	GLY	LYS	LYS	6	E	E	64 - 71	53 - 60
12	2	GLY	GLY	LYS	LYS	6	F	F	64 - 71	53 - 60
13	3	ARG	ARG	LEU	LEU	1	A	A	72 - 157	61 - 146
14	3	ARG	ARG	LEU	LEU	1	B	B	72 - 157	61 - 146
15	3	ARG	ARG	LEU	LEU	1	C	C	72 - 157	61 - 146
16	3	ARG	ARG	LEU	LEU	1	D	D	72 - 157	61 - 146
17	3	ARG	ARG	LEU	LEU	1	E	E	72 - 157	61 - 146
18	3	ARG	ARG	LEU	LEU	1	F	F	72 - 157	61 - 146
19	4	GLY	GLY	ASP	ASP	6	A	A	158 - 164	147 - 153
20	4	GLY	GLY	ASP	ASP	6	B	B	158 - 164	147 - 153
21	4	GLY	GLY	GLN	GLN	6	C	C	158 - 162	147 - 151
22	4	GLY	GLY	ASP	ASP	6	D	D	158 - 164	147 - 153
23	4	GLY	GLY	GLY	GLY	6	E	E	158 - 163	147 - 152
24	4	GLY	GLY	ASP	ASP	6	F	F	158 - 164	147 - 153
25	5	MSE	MSE	ILE	ILE	1	A	A	165 - 202	154 - 191
26	5	MSE	MSE	ILE	ILE	1	B	B	165 - 202	154 - 191
27	5	MSE	MSE	ILE	ILE	1	C	C	165 - 202	154 - 191
28	5	MSE	MSE	ILE	ILE	1	D	D	165 - 202	154 - 191
29	5	MSE	MSE	ILE	ILE	1	E	E	165 - 202	154 - 191
30	5	MSE	MSE	ILE	ILE	1	F	F	165 - 202	154 - 191

#1: Protein	Uncharacterized protein Mass: 22475.662 Da / Num. of mol.: 6 / Fragment: Residues 13-204 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Exiguobacterium sibiricum (bacteria) / Strain: 255-15 / Gene: ZP_00539245.1, ExigDRAFT_1300 / Plasmid: speedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q41E03, UniProt: B1YJX4*PLUS
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 173 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y
Sequence details	REMARK 999 SEQUENCE: THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION REMARK 999 TAG ...REMARK 999 SEQUENCE: THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION REMARK 999 TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE REMARK 999 LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 3.07 Å³/Da / Density % sol: 59.98 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 9 Details: NANODROP, 10.0% PEG 6000, 0.1M Bicine pH 9.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

ALS

/ Beamline: 8.2.2 / Wavelength: 0.9799, 0.9795, 1.0000

Detector

Type: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 31, 2007

Radiation

Monochromator: Double crystal Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	0.9799	1
2	0.9795	1
3	1	1

Reflection

Resolution: 2.42→47.727 Å / Num. obs: 65515 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 3.71 % / B_iso Wilson estimate: 51.34 Å² / R_merge(I) obs: 0.081 / Net I/σ(I): 11.02

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. measured obs	Num. unique obs	% possible all
2.42-2.51	3.74	0.787	1.9	25290	6759	99.9
2.51-2.61		0.649	2.3	24322	6493	99.9
2.61-2.72		0.504	3	22650	6038	99.8
2.72-2.87		0.362	4	25467	6808	99.9
2.87-3.05		0.245	5.7	24464	6533	99.8
3.05-3.28		0.148	8.8	23867	6384	99.7
3.28-3.61		0.087	13.3	24552	6581	99.7
3.61-4.13		0.052	19.2	24303	6552	99.7
4.13-5.19		0.038	24.5	24020	6562	99.7
5.19-47.727		0.033	26.9	24076	6750	98.5

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Phasing

Phasing	Method: MAD

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Processing

Software

Name	Version	Classification
REFMAC	5.2.0019	refinement
PHENIX		refinement
SHELX		phasing
MolProbity	3beta29	model building
XSCALE		data scaling
PDB_EXTRACT	3	data extraction
ADSC	Quantum	data collection
XDS		data reduction
SHELXD		phasing
autoSHARP		phasing

Refinement

Method to determine structure:

MAD / Resolution: 2.42→47.727 Å / Cor.coef. F_o:F_c: 0.95 / Cor.coef. F_o:F_c free: 0.931 / SU B: 21.985 / SU ML: 0.231 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.316 / ESU R Free: 0.241
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN ...

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.254	3326	5.1 %	RANDOM
R_work	0.214	-	-	-
obs	0.216	65460	99.66 %	-

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: 54.869 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-3.16 Å²	0 Å²	0 Å²
2-	-	-3.16 Å²	0 Å²
3-	-	-	6.33 Å²

Refinement step

Cycle: LAST / Resolution: 2.42→47.727 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8975	0	0	173	9148

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.015	0.022	9227
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.02	6096
X-RAY DIFFRACTION	r_angle_refined_deg	1.498	1.937	12462
X-RAY DIFFRACTION	r_angle_other_deg	0.901	3	14859
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	4.608	5	1095
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	36.51	25.021	484
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.383	15	1546
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	15.324	15	15
X-RAY DIFFRACTION	r_chiral_restr	0.084	0.2	1293
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	10320
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	1935
X-RAY DIFFRACTION	r_nbd_refined	0.229	0.2	1693
X-RAY DIFFRACTION	r_nbd_other	0.181	0.2	5690
X-RAY DIFFRACTION	r_nbtor_refined	0.191	0.2	4422
X-RAY DIFFRACTION	r_nbtor_other	0.087	0.2	4672
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.134	0.2	201
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.203	0.2	21
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.182	0.2	64
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.108	0.2	3
X-RAY DIFFRACTION	r_mcbond_it	1.684	3	5640
X-RAY DIFFRACTION	r_mcbond_other	0.46	3	2255
X-RAY DIFFRACTION	r_mcangle_it	2.631	3	8744
X-RAY DIFFRACTION	r_scbond_it	2.33	4	4201
X-RAY DIFFRACTION	r_scangle_it	3.324	4	3715

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	2319	TIGHT POSITIONAL	0.14	0.15
2	B	2319	TIGHT POSITIONAL	0.18	0.15
3	C	2319	TIGHT POSITIONAL	0.15	0.15
4	D	2319	TIGHT POSITIONAL	0.13	0.15
5	E	2319	TIGHT POSITIONAL	0.15	0.15
6	F	2319	TIGHT POSITIONAL	0.15	0.15
1	A	42	LOOSE POSITIONAL	0.47	5
2	B	42	LOOSE POSITIONAL	0.45	5
3	C	42	LOOSE POSITIONAL	0.44	5
4	D	42	LOOSE POSITIONAL	0.7	5
5	E	42	LOOSE POSITIONAL	0.47	5
6	F	42	LOOSE POSITIONAL	0.54	5
1	A	2319	TIGHT THERMAL	0.26	1
2	B	2319	TIGHT THERMAL	0.31	1
3	C	2319	TIGHT THERMAL	0.26	1
4	D	2319	TIGHT THERMAL	0.23	1
5	E	2319	TIGHT THERMAL	0.22	1
6	F	2319	TIGHT THERMAL	0.26	1
1	A	42	LOOSE THERMAL	4.31	10
2	B	42	LOOSE THERMAL	4.07	10
3	C	42	LOOSE THERMAL	1.91	10
4	D	42	LOOSE THERMAL	1.38	10
5	E	42	LOOSE THERMAL	2.06	10
6	F	42	LOOSE THERMAL	4.87	10

LS refinement shell

Resolution: 2.42→2.551 Å / Total num. of bins used: 10

	R_factor	Num. reflection	% reflection
R_free	0.359	452	-
R_work	0.319	9062	-
all	-	9514	-
obs	-	-	99.92 %

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	2.4811	0.4764	0.538	1.229	0.2974	0.1498	0.0931	-0.0091	0.0878	-0.126	0.0546	-0.4853	0.0089	-0.2834	-0.1477	-0.1355	-0.0004	0.0021	-0.0999	-0.0112	-0.0355	-25.7841	-77.5411	1.9274
2	0.8988	0.8283	0.686	1.342	0.7952	0.5695	0.0043	0.1369	0.2032	-0.1935	0.0892	-0.2005	0.1208	-0.1208	-0.0935	-0.1238	0.0023	-0.0262	-0.1035	-0.0621	-0.1668	-31.4451	-52.191	1.8115
3	1.2317	-0.0636	0.1811	1.057	0.5938	0.4704	-0.1145	0.0015	0.6626	-0.1704	0.0019	0.0338	0.0406	-0.0425	0.1127	-0.0965	0.0012	-0.0415	-0.097	-0.0337	0.045	-48.9912	-33.2592	1.8269
4	1.5469	1.0884	-0.535	1.4312	-1.0812	0.9314	0.1195	-0.2755	0.1897	-0.0304	0.1084	0.2942	-0.1162	-0.1487	-0.2279	-0.0172	-0.0715	0.1203	0.1657	-0.003	-0.0176	-45.4799	-20.2423	-35.9799
5	1.7002	0.4099	-0.8965	0.9682	-1.0114	1.5102	-0.2596	-0.1517	-0.9399	-0.2	0.0144	-0.0254	0.2707	-0.1729	0.2452	0.0747	-0.1101	0.1066	0.0558	0.1033	0.235	-29.3177	-40.1954	-36.4218
6	0.8792	0.3005	-0.0264	3.2762	-1.2219	1.1986	-0.0379	-0.0084	-0.7978	0.1672	-0.0067	0.0853	0.1856	-0.0448	0.0446	0.2049	-0.0213	0.1552	-0.0243	0.1024	0.1703	-5.2848	-49.0401	-36.4273

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	14 - 203	3 - 192
2	X-RAY DIFFRACTION	2	B	B	14 - 203	3 - 192
3	X-RAY DIFFRACTION	3	C	C	14 - 203	3 - 192
4	X-RAY DIFFRACTION	4	D	D	14 - 203	3 - 192
5	X-RAY DIFFRACTION	5	E	E	15 - 203	4 - 192
6	X-RAY DIFFRACTION	6	F	F	15 - 203	4 - 192

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