PDB-2pij: Structure of the Cro protein from prophage Pfl 6 in Pseudomonas f...

ID or keywords:

Entry

Database: PDB / ID: 2pij

Title

Structure of the Cro protein from prophage Pfl 6 in Pseudomonas fluorescens Pf-5

Components

Prophage Pfl 6 Cro

Keywords

TRANSCRIPTION / transcription factor / helix-turn-helix / prophage / structural evolution

Function / homology

Function and homology information

regulation of DNA-templated transcription / DNA binding
Similarity search - Function

Biological species

Pseudomonas fluorescens (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MAD / Resolution: 1.7 Å

Authors

Roessler, C.G. / Roberts, S.A. / Montfort, W.R. / Cordes, M.H.J.

Citation

Journal: Proc.Natl.Acad.Sci.Usa / Year: 2008
Title: Transitive homology-guided structural studies lead to discovery of Cro proteins with 40% sequence identity but different folds.
Authors: Roessler, C.G. / Hall, B.M. / Anderson, W.J. / Ingram, W.M. / Roberts, S.A. / Montfort, W.R. / Cordes, M.H.

History

Deposition	Apr 13, 2007	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 4, 2008	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Source and taxonomy / Version format compliance
Revision 1.2	Oct 18, 2017	Group: Refinement description / Category: software / Item: _software.name
Revision 1.3	Nov 6, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	2pij.cif.gz	64.8 KB	Display	PDBx/mmCIF format
PDB format	pdb2pij.ent.gz	49 KB	Display	PDB format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/pi/2pij ftp://data.pdbj.org/pub/pdb/validation_reports/pi/2pij	HTTPS FTP

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Related structure data

Related structure data	3bd1C C: citing same article (ref.)
Similar structure data	3mkl-2 5xdp-d 3oio-d 1yiw-6 5x3m-d 4hob-2 5goh-d 1pmk-d 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	#244 - Apr 2020 Photosynthetic Supercomplexes similarity (1) #92 - Aug 2007 Anabolic Steroids similarity (1) #112 - Apr 2009 Oct and Sox Transcription Factors similarity (1) #39 - Mar 2003 lac Repressor similarity (1) #49 - Jan 2004 Carbonic Anhydrase similarity (1) #59 - Nov 2004 Photosystem II similarity (1) #127 - Jul 2010 Crystallins similarity (1) #174 - Jun 2014 GFP-like Proteins similarity (1) #89 - May 2007 Aconitase and Iron Regulatory Protein 1 similarity (1) #241 - Jan 2020 Twenty Years of Molecules similarity (1)

PDB pages

PDBj /

wwPDB /

NCBI

Related items in Molecule of the Month

#244 - Apr 2020
Photosynthetic Supercomplexes
similarity (1)
#92 - Aug 2007
Anabolic Steroids
similarity (1)
#112 - Apr 2009
Oct and Sox Transcription Factors
similarity (1)
#39 - Mar 2003
lac Repressor
similarity (1)
#49 - Jan 2004
Carbonic Anhydrase
similarity (1)
#59 - Nov 2004
Photosystem II
similarity (1)
#127 - Jul 2010
Crystallins
similarity (1)
#174 - Jun 2014
GFP-like Proteins
similarity (1)
#89 - May 2007
Aconitase and Iron Regulatory Protein 1
similarity (1)
#241 - Jan 2020
Twenty Years of Molecules
similarity (1)

Deposited unit

A: Prophage Pfl 6 Cro

B: Prophage Pfl 6 Cro

hetero molecules

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

1

Idetical with deposited unit
defined by author

Unit cell

Length a, b, c (Å)	40.940, 40.940, 123.500
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	152
Space group name H-M	P3₁21

#1: Protein	Prophage Pfl 6 Cro Mass: 7409.207 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas fluorescens (bacteria) / Strain: Pf-5 / Gene: Prophage Pfl 6 Cro / Plasmid: pet21b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Bl21(DE3) / References: UniProt: A6STU3, UniProt: J3IU59*PLUS
#2: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO₄
#3: Chemical	ChemComp-BCT / BICARBONATE ION Mass: 61.017 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CHO₃
#4: Chemical	ChemComp-DTT / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / 1,4-DITHIOTHREITOL Mass: 154.251 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₄H₁₀O₂S₂
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 61 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y
Sequence details	AUTHOR UPDATED THE FOLLOWING SEQUENCE DATABASE ENTRY THAT WAS NOT AVAILABLE AT THE TIME OF THE ...AUTHOR UPDATED THE FOLLOWING SEQUENCE DATABASE ENTRY THAT WAS NOT AVAILABLE AT THE TIME OF THE ORIGINAL DEPOSITION: REFSEQ YP_001312167.1; GB ABR57178.1; LOCUS TAG: PFL_3262

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.02 Å³/Da / Density % sol: 38.96 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 9.5 Details: primary precipitating solution: 2.2M ammonium sulfate, 0.1M tris additional chemicals in drop: 2mM dithiothreitol, 0.2mM EDTA, 0.01% sodium azide, pH 9.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction

ID	Mean temperature (K)	Crystal-ID
1	100	1
2		1
3		1

Diffraction source

Source:

SYNCHROTRON / Site:

SSRL

/ Beamline: BL9-2 / Wavelength: 0.97935,0.97921,0.91165

Detector

Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 21, 2005
Details: flat collimating mirror double crystal monochromator toroid focusing mirror

Radiation

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

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	0.97935	1
2	0.97921	1
3	0.91165	1

Reflection

R_merge(I) obs: 0.03 / D res low: 34.06 Å

Redundancy (%)	ID	Av σ(I) over netI	Number	Χ²	D res high (Å)	Num. obs	% possible obs
2.42	1	12.8	75867	0.88	1.35	29115	57.9
2.42	2	12	76405	0.83	1.35	29206	58.1
2.38	3	11	92520	0.83	1.26	35177	56.7

Diffraction reflection shell

Highest resolution (Å)	Lowest resolution (Å)	% possible obs (%)	ID	R_merge(I) obs	Chi squared	Redundancy	Rejects
2.92	34.06	99.1	1	0.02	0.78	2.88	93
2.32	2.92	95.9	1	0.044	0.78	2.8	107
2.02	2.32	95.1	1	0.087	0.88	2.73	291
1.84	2.02	93.2	1	0.181	1.01	2.61	915
1.71	1.84	90.3	1	0.289	1.02	2.34	1857
1.61	1.71	61.4	1	0.364	0.9	1.46	1184
1.53	1.61	29.3	1	0.35	0.73	1.09	522
1.46	1.53	12.3	1	0.411	1.02	1.03	293
2.92	34.06	99.2	2	0.02	0.72	2.89	84
2.32	2.92	96.6	2	0.046	0.74	2.79	116
2.02	2.32	95.6	2	0.092	0.82	2.72	369
1.84	2.02	93.6	2	0.199	0.97	2.58	1049
1.71	1.84	91.1	2	0.311	0.98	2.32	1949
1.61	1.71	60.7	2	0.366	0.83	1.47	1278
1.53	1.61	28.8	2	0.374	0.67	1.09	559
1.46	1.53	12.4	2	0.381	0.99	1.02	301
1.4	1.46	2.5	2	0.215	0.17	1.01	66
2.72	34.06	98.5	3	0.019	0.69	2.87	73
2.16	2.72	94.7	3	0.054	0.7	2.77	176
1.89	2.16	92.4	3	0.133	0.88	2.69	693
1.71	1.89	90.4	3	0.255	0.98	2.49	2010
1.59	1.71	87.5	3	0.368	1.06	2.24	3044
1.5	1.59	59.9	3	0.407	0.69	1.44	1733
1.42	1.5	27.2	3	0.395	0.69	1.09	755
1.36	1.42	12.9	3	0.467	0.96	1.03	348
1.31	1.36	2.8	3	0.404	0.77	1.01	66

Reflection

Resolution: 1.7→34.08 Å / Num. all: 13741 / Num. obs: 13741 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.84 % / B_iso Wilson estimate: 39.3 Å² / R_merge(I) obs: 0.055 / Χ²: 1 / Net I/σ(I): 13.5 / Scaling rejects: 503

Reflection shell

Resolution: 1.7→1.76 Å / Redundancy: 4.28 % / R_merge(I) obs: 0.434 / Mean I/σ(I) obs: 3 / Num. measured all: 5236 / Num. unique all: 1222 / Χ²: 0.83 / % possible all: 90.7

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Phasing

Phasing

Method:

MAD

Phasing set

ID
1
2
3

Phasing MAD

D res high: 1.77 Å / D res low: 30 Å / FOM : 0.53 / Reflection: 12231

Phasing MAD set

Clust-ID	Expt-ID	Set-ID	Wavelength (Å)	F double prime refined	F prime refined
1	3 wavelength	1	0.9792	4.78	-5.76
1	3 wavelength	2	0.9793	4.3	-8.12
1	3 wavelength	3	0.9117	2.61	-3.01

Phasing MAD set site

ID	Atom type symbol	B iso	Fract x	Fract y	Fract z	Occupancy
1	Se	32.817	0.73	0.074	0.007	0.783
2	Se	38.819	0.506	0.753	0.154	0.795
3	Se	40.345	0.161	0.866	0.094	0.79
4	Se	52.048	0.498	0.313	0.087	0.872

Phasing MAD shell

Resolution (Å)	FOM	Reflection
6.38-30	0.87	628
4.03-6.38	0.87	1051
3.15-4.03	0.78	1301
2.67-3.15	0.68	1520
2.36-2.67	0.55	1702
2.13-2.36	0.43	1861
1.96-2.13	0.33	2041
1.83-1.96	0.25	2127

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Processing

Software

Name	Version	Classification
d*TREK	9.2SSI	data scaling
SOLVE	2.09	phasing
RESOLVE	2.09	phasing
REFMAC		refinement
PDB_EXTRACT	2	data extraction
Blu-Ice		data collection
CrystalClear		data reduction
CrystalClear		data scaling

Refinement

Method to determine structure:

MAD / Resolution: 1.7→34.08 Å / Cor.coef. F_o:F_c: 0.954 / Cor.coef. F_o:F_c free: 0.942 / SU B: 6.573 / SU ML: 0.109 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.127 / ESU R Free: 0.131 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.271	677	4.9 %	RANDOM
R_work	0.218	-	-	-
all	0.221	13741	-	-
obs	0.221	13741	98.09 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 24.302 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.76 Å²	0.38 Å²	0 Å²
2-	-	0.76 Å²	0 Å²
3-	-	-	-1.15 Å²

Refine analyze

Luzzati coordinate error obs: 0.291 Å

Refinement step

Cycle: LAST / Resolution: 1.7→34.08 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	907	0	32	61	1000

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.021	0.022	949
X-RAY DIFFRACTION	r_angle_refined_deg	1.855	2.017	1280
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.084	5	119
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	36.48	24.211	38
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.701	15	174
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	23.688	15	8
X-RAY DIFFRACTION	r_chiral_restr	0.127	0.2	147
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.02	680
X-RAY DIFFRACTION	r_nbd_refined	0.224	0.2	409
X-RAY DIFFRACTION	r_nbtor_refined	0.306	0.2	630
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.157	0.2	57
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.193	0.2	61
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.185	0.2	18
X-RAY DIFFRACTION	r_mcbond_it	1.197	1.5	620
X-RAY DIFFRACTION	r_mcangle_it	1.586	2	954
X-RAY DIFFRACTION	r_scbond_it	2.517	3	366
X-RAY DIFFRACTION	r_scangle_it	3.522	4.5	325

LS refinement shell

Resolution: 1.695→1.739 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.304	50	-
R_work	0.275	819	-
obs	-	869	88.04 %

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	12.9066	-13.5821	14.163	17.8803	-19.2327	20.7643	-0.3746	0.0261	0.9489	-0.7892	0.2088	-1.3041	-0.1425	-0.2549	0.1658	0.2231	-0.0518	-0.0232	0.4078	-0.0307	0.154	7.3576	26.8831	37.1636
2	13.2737	0.0727	-8.1562	20.3227	17.675	28.1966	-0.1633	-0.2622	-0.0662	0.0498	0.2426	0.1505	-0.1612	0.7258	-0.0793	-0.1033	-0.0084	-0.0168	0.1904	-0.0069	-0.0482	6.7982	21.7914	45.302
3	9.3726	7.245	1.3449	6.855	0.4793	12.933	0.0856	0.2685	0.0384	0.1954	0.2467	-0.4374	-0.7362	0.6953	-0.3323	-0.0229	-0.0051	0.0071	0.2022	-0.0614	0.0855	3.9467	23.1762	48.3324
4	4.7532	0.6105	2.3904	6.1099	-1.8386	8.1761	-0.0408	0.7642	-0.2689	0.0549	0.1725	-0.1138	-0.0394	-0.1484	-0.1317	-0.1169	-0.0231	0.0061	0.2711	-0.0097	-0.0138	-3.9808	16.9471	42.2335
5	16.5673	0.5664	0.055	2.214	-4.039	7.4406	-0.1473	0.1849	-0.4405	0.4881	-0.1451	-0.1384	-0.0714	-0.4815	0.2925	0.0923	-0.0243	-0.0192	0.123	-0.0565	0.1906	-0.7236	10.5206	45.0899
6	28.8005	8.0577	-1.9649	13.9404	-0.0483	0.1556	-0.0632	-0.5675	-1.4692	0.844	-1.0266	-1.2429	0.279	-0.1177	1.0898	0.0863	-0.0612	-0.0162	0.1898	0.1652	0.2933	7.3915	9.3172	45.3338
7	14.5873	-8.8213	2.6744	11.8728	0.9489	11.6354	0.2676	-0.4584	-0.4413	-0.4999	-0.1294	0.0052	0.3751	-0.5615	-0.1382	-0.0968	-0.0381	0.0109	0.2048	-0.0397	0.0342	8.3899	16.4463	38.3768
8	24.095	-13.0466	4.923	20.7329	-2.5137	6.1603	-0.7412	1.1667	1.3343	0.6058	0.1374	0.3117	-1.1787	0.769	0.6038	0.1121	-0.1013	0.0126	0.2056	0.0875	0.0241	-0.7452	28.8822	35.7965
9	18.4751	-13.7457	-2.1925	19.8453	1.0725	1.332	0.1218	0.1934	0.1337	-0.3209	0.282	0.0917	-0.184	0.0532	-0.4039	-0.0156	-0.0332	0.0102	0.1743	0.0728	-0.0242	1.0874	20.8352	35.0573
10	35.3731	-28.1814	-28.2285	33.79	26.7686	45.3598	-0.5634	-1.3423	-0.7284	0.0719	0.93	-0.1551	2.5907	1.5565	-0.3667	0.1516	0.0797	-0.0642	0.0746	0.0294	0.0905	15.6629	10.4009	30.6515
11	12.6156	5.4589	12.0255	8.7995	8.831	17.3913	-0.0959	0.5752	1.0024	-0.0915	-0.4061	0.2079	-1.2719	0.3139	0.5019	0.1633	0.0058	0.0587	0.0542	0.0906	0.0216	16.6456	22.5856	22.4078
12	33.9314	-12.6316	-6.4568	10.9103	-13.715	43.08	0.0461	1.1932	0.7989	0.6031	-0.0056	-0.6018	-0.9875	-0.6959	-0.0405	0.1042	0.0966	0.0282	0.0856	0.0913	0	16.0705	17.9436	14.267
13	15.6488	-16.9718	0.3337	44.9234	-17.5266	20.4758	-0.3129	0.1363	1.0223	0.6892	0.7302	-0.7914	-0.8909	-0.2203	-0.4173	0.0034	0.015	0.0086	0.0612	-0.0496	0.0097	20.8172	16.1449	13.0645
14	2.011	-1.3111	2.2386	15.2766	6.0445	17.4652	-0.1294	0.0436	0.4076	0.4855	0.2567	-0.9176	0.9304	0.2932	-0.1273	0.0349	0.0614	-0.0165	0.0363	-0.0588	-0.0118	24.4629	10.5523	20.948
15	19.7788	-10.7712	3.0966	9.6567	0.2806	2.2689	-0.2773	0.3909	0.1609	0.1468	-0.1397	0.1669	-0.6728	-0.0783	0.417	0.395	-0.0359	-0.03	-0.0976	-0.0159	-0.0675	19.0379	4.7905	17.8246
16	21.0896	-11.3942	-13.2774	28.0267	1.9378	9.6125	-0.5469	-0.2219	-0.839	-1.6589	-0.1461	1.5216	0.6392	-1.1315	0.693	0.3303	0.1041	-0.1468	-0.0794	-0.0604	-0.0006	10.9449	6.4254	17.6225
17	12.4803	5.1281	2.9704	9.3312	2.686	11.9168	0.2469	-0.1829	-0.3193	-0.6692	-0.1397	-0.1517	-0.0597	-0.6861	-0.1072	0.0459	0.0917	-0.0341	0.033	-0.0051	-0.0307	11.9388	14.1089	23.152
18	6.9396	2.6453	8.7196	15.8916	-0.6897	15.4734	-0.5122	0.9798	0.1417	-0.3947	0.3818	-1.4598	-1.1929	1.115	0.1303	0.2287	-0.0355	0.0805	0.1722	0.0056	0.2107	25.445	23.2812	25.761
19	40.4566	10.4188	-5.4086	8.943	-1.3573	7.9639	-0.2069	-0.3521	0.1249	-0.639	0.1078	-0.0408	-0.1076	0.4958	0.0992	0.0882	0.0144	0.0148	0.1133	-0.0231	0.0071	19.9279	15.946	27.4603
20	80.5526	8.7094	-29.0257	6.059	0.2414	13.8523	-0.6959	-0.2344	-1.9443	0.1628	-0.082	-0.3709	1.8233	-0.2013	0.7779	0.1087	-0.093	0.007	0.2323	-0.0029	0.0631	3.4196	12.9812	31.4917

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	1 - 5	1 - 5
2	2	A	A	6 - 10	6 - 10
3	3	A	A	11 - 16	11 - 16
4	4	A	A	17 - 25	17 - 25
5	5	A	A	26 - 31	26 - 31
6	6	A	A	32 - 37	32 - 37
7	7	A	A	38 - 42	38 - 42
8	8	A	A	43 - 47	43 - 47
9	9	A	A	48 - 54	48 - 54
10	10	A	A	55 - 59	55 - 59
11	11	B	B	1 - 6	1 - 6
12	12	B	B	7 - 11	7 - 11
13	13	B	B	12 - 17	12 - 17
14	14	B	B	18 - 25	18 - 25
15	15	B	B	26 - 31	26 - 31
16	16	B	B	32 - 36	32 - 36
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