PDB-2phz: Crystal structure of Iron-uptake system-binding protein FeuA from...

ID or keywords:

Entry

Database: PDB / ID: 2phz

Title

Crystal structure of Iron-uptake system-binding protein FeuA from Bacillus subtilis. Northeast Structural Genomics target SR580.

Components

Iron-uptake system-binding protein

Keywords

TRANSPORT PROTEIN / SR580 / iron uptake / NESG / Structural Genomics / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium

Function / homology

Function and homology information

iron ion transport / membrane raft / plasma membrane / cytoplasm
Similarity search - Function

Biological species

Bacillus subtilis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MAD / Resolution: 2.15 Å

Authors

Benach, J. / Neely, H. / Seetharaman, J. / Chen, C.X. / Cunningham, K. / Ma, L.-C. / Janjua, H. / Xiao, R. / Baran, M. / Acton, T.B. ...

Citation

Journal: To be Published
Title: Crystal structure of Iron-uptake system-binding protein FeuA from Bacillus subtilis.
Authors: Benach, J. / Neely, H. / Seetharaman, J. / Chen, C.X. / Cunningham, K. / Ma, L.-C. / Janjua, H. / Xiao, R. / Baran, M. / Acton, T.B. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast ...

History

Deposition	Apr 12, 2007	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 24, 2007	Provider: repository / Type: Initial release
Revision 1.1	May 1, 2008	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Version format compliance
Revision 1.3	Oct 18, 2017	Group: Refinement description / Category: software Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4	Oct 25, 2017	Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.5	Jan 24, 2018	Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name

Remark 300

BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 ...

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	2phz.cif.gz	70.8 KB	Display	PDBx/mmCIF format
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Validation report

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

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Related structure data

Similar structure data	2wi8-d 5m62-d 1oxk-2 5khl-d 4eqa-2 4elq-1 3pu5-d 1qna-1 5yis-d 1sw5-4 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: SR580

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#261 - Sep 2021 DNA-Sequencing Nanopores similarity (1) #22 - Oct 2001 Photosystem I similarity (1) #262 - Oct 2021 Fifty Years of Open Access to PDB Structures similarity (1) #29 - May 2002 Penicillin-binding Proteins similarity (1) #95 - Nov 2007 Multidrug Resistance Transporters similarity (1)

Deposited unit

A: Iron-uptake system-binding protein

35.2 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author
Evidence: light scattering

Unit cell

Length a, b, c (Å)	55.461, 55.461, 177.551
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	92
Space group name H-M	P4₁2₁2

Details

the AU contains the biol. assembly. Static light scattering shows it's a monomer in solution.

#1: Protein	Iron-uptake system-binding protein Mass: 35170.641 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: 168 / Gene: feuA, BSU01630 / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+Magic / References: UniProt: P40409
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 146 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

Iron-uptake system-binding protein

Mass: 35170.641 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Bacillus subtilis (bacteria) / Strain: 168 / Gene: feuA, BSU01630 / Plasmid: pET21 / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+Magic / References: UniProt: P40409

#2: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 146 / 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: 1.94 Å³/Da / Density % sol: 36.6 % Description: THE STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 1 microliter protein solution plus 1 microliter reservoir solution, 50mM MgNO3, 50mM MES pH 6.5, 27.5% PEG400, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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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:

NSLS

/ Beamline: X4A / Wavelength: 0.97950, 0.97900, 0.95000

Detector

Type: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 5, 2007 / Details: mirrors

Radiation

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

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	0.9795	1
2	0.979	1
3	0.95	1

Reflection

D res high: 2 Å / D res low: 50 Å

Redundancy (%)	ID	Av σ(I) over netI	Number	R_merge(I) obs	Χ²	Num. obs	% possible obs
9.1	1	13.8	325732	0.092	1.58	35899	99.9
8.8	2	19.9	301755	0.084	1.91	34198	96.4
13.5	3	15.9	484427	0.088	1.76	35910	99.9

Diffraction reflection shell

Highest resolution (Å)	Lowest resolution (Å)	% possible obs (%)	ID	R_merge(I) obs	Chi squared	Redundancy
4.31	50	99.3	1	0.055	1.134	8.8
3.42	4.31	99.6	1	0.066	1.259	8.3
2.99	3.42	100	1	0.085	1.47	8.9
2.71	2.99	100	1	0.119	1.75	9.2
2.52	2.71	100	1	0.157	1.761	9.3
2.37	2.52	100	1	0.198	1.755	9.3
2.25	2.37	100	1	0.256	1.662	9.3
2.15	2.25	100	1	0.313	1.611	9.3
2.07	2.15	100	1	0.444	1.511	9.4
2	2.07	100	1	0.607	1.53	8.9
4.31	50	92.2	2	0.056	1.409	9.8
3.42	4.31	94.5	2	0.068	1.479	8.8
2.99	3.42	95.8	2	0.081	1.968	8.7
2.71	2.99	96.4	2	0.1	2.148	8.8
2.52	2.71	96.8	2	0.119	2.135	8.8
2.37	2.52	97.1	2	0.137	2.075	8.8
2.25	2.37	97.5	2	0.161	1.994	8.7
2.15	2.25	97.6	2	0.187	2.009	8.7
2.07	2.15	97.9	2	0.233	1.777	8.7
2	2.07	98.1	2	0.299	1.805	8.4
4.31	50	99.1	3	0.058	1.284	13.4
3.42	4.31	99.6	3	0.069	1.391	12.5
2.99	3.42	100	3	0.085	1.793	13.2
2.71	2.99	100	3	0.11	1.981	13.6
2.52	2.71	100	3	0.136	1.976	13.7
2.37	2.52	100	3	0.161	1.939	13.7
2.25	2.37	100	3	0.199	1.867	13.7
2.15	2.25	100	3	0.245	1.94	13.6
2.07	2.15	100	3	0.316	1.621	13.7
2	2.07	100	3	0.408	1.561	13.6

Reflection

Resolution: 2→50 Å / Num. obs: 35899 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 9.1 % / R_merge(I) obs: 0.092 / Χ²: 1.58 / Net I/σ(I): 13.8

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique all	Χ²	% possible all
2-2.07	8.9	0.607	3599	1.53	100
2.07-2.15	9.4	0.444	3573	1.511	100
2.15-2.25	9.3	0.313	3599	1.611	100
2.25-2.37	9.3	0.256	3589	1.662	100
2.37-2.52	9.3	0.198	3605	1.755	100
2.52-2.71	9.3	0.157	3560	1.761	100
2.71-2.99	9.2	0.119	3587	1.75	100
2.99-3.42	8.9	0.085	3610	1.47	100
3.42-4.31	8.3	0.066	3580	1.259	99.6
4.31-50	8.8	0.055	3597	1.134	99.3

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Phasing

Phasing dm

FOM : 0.64 / FOM acentric: 0.64 / FOM centric: 0.64 / Reflection: 18301 / Reflection acentric: 15138 / Reflection centric: 3163

Phasing dm shell

Resolution (Å)	FOM	FOM acentric	FOM centric	Reflection	Reflection acentric	Reflection centric
5.7-19.622	0.95	0.97	0.93	931	559	372
3.6-5.7	0.94	0.95	0.9	2689	2031	658
2.9-3.6	0.86	0.88	0.79	3227	2635	592
2.5-2.9	0.7	0.72	0.57	3111	2638	473
2.1-2.5	0.49	0.5	0.39	5295	4594	701
2-2.1	0.27	0.27	0.21	3048	2681	367

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
RESOLVE	2.08	phasing
CNS	1.1	refinement
PDB_EXTRACT	2	data extraction
ADSC	QUANTUM	data collection
HKL-2000		data reduction
SnB		phasing

Refinement

Method to determine structure:

MAD / Resolution: 2.15→20 Å / FOM work R set: 0.842 / σ(F): 2 / Stereochemistry target values: Engh & Huber / Details: THE FRIEDEL PAIRS WERE USED FOR PHASING

	R_factor	Num. reflection	% reflection
R_free	0.234	2569	8.9 %
R_work	0.2	-	-
obs	0.2	26990	93.8 %

Solvent computation

B_sol: 51.071 Å²

Displacement parameters

B_iso mean: 38.91 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.548 Å²	0 Å²	0 Å²
2-	-	2.225 Å²	0 Å²
3-	-	-	-0.677 Å²

Refinement step

Cycle: LAST / Resolution: 2.15→20 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2184	0	0	146	2330

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target
X-RAY DIFFRACTION	c_bond_d	0.004329
X-RAY DIFFRACTION	c_bond_d_na
X-RAY DIFFRACTION	c_bond_d_prot
X-RAY DIFFRACTION	c_angle_d
X-RAY DIFFRACTION	c_angle_d_na
X-RAY DIFFRACTION	c_angle_d_prot
X-RAY DIFFRACTION	c_angle_deg	1.08738
X-RAY DIFFRACTION	c_angle_deg_na
X-RAY DIFFRACTION	c_angle_deg_prot
X-RAY DIFFRACTION	c_dihedral_angle_d
X-RAY DIFFRACTION	c_dihedral_angle_d_na
X-RAY DIFFRACTION	c_dihedral_angle_d_prot
X-RAY DIFFRACTION	c_improper_angle_d
X-RAY DIFFRACTION	c_improper_angle_d_na
X-RAY DIFFRACTION	c_improper_angle_d_prot
X-RAY DIFFRACTION	c_mcbond_it	2.517	1.5
X-RAY DIFFRACTION	c_mcangle_it	3.881	2
X-RAY DIFFRACTION	c_scbond_it	4.817	2
X-RAY DIFFRACTION	c_scangle_it	7.727	2.5

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 50

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection obs
2.15-2.16	0.221	51	0.225	444	495
2.16-2.18	0.251	58	0.218	470	528
2.18-2.19	0.249	48	0.217	455	503
2.19-2.21	0.228	42	0.187	468	510
2.21-2.23	0.232	48	0.191	434	482
2.23-2.24	0.264	58	0.204	454	512
2.24-2.26	0.241	39	0.223	441	480
2.26-2.28	0.276	46	0.216	468	514
2.28-2.3	0.315	44	0.231	486	530
2.3-2.32	0.235	32	0.208	462	494
2.32-2.34	0.229	46	0.203	481	527
2.34-2.36	0.366	39	0.22	461	500
2.36-2.38	0.223	52	0.199	480	532
2.38-2.4	0.325	40	0.21	464	504
2.4-2.42	0.248	50	0.212	445	495
2.42-2.44	0.246	57	0.225	459	516
2.44-2.47	0.379	42	0.238	471	513
2.47-2.49	0.446	30	0.223	503	533
2.49-2.52	0.305	54	0.215	518	572
2.52-2.55	0.305	51	0.201	419	470
2.55-2.58	0.233	37	0.22	499	536
2.58-2.61	0.257	45	0.209	504	549
2.61-2.64	0.248	31	0.217	511	542
2.64-2.67	0.241	49	0.238	485	534
2.67-2.71	0.275	56	0.204	489	545
2.71-2.74	0.293	50	0.235	495	545
2.74-2.78	0.218	54	0.224	506	560
2.78-2.83	0.213	45	0.192	483	528
2.83-2.87	0.324	53	0.225	502	555
2.87-2.92	0.247	49	0.221	516	565
2.92-2.97	0.259	64	0.238	473	537
2.97-3.02	0.302	68	0.224	496	564
3.02-3.08	0.24	52	0.216	524	576
3.08-3.14	0.273	59	0.201	480	539
3.14-3.21	0.291	36	0.193	514	550
3.21-3.28	0.246	56	0.218	531	587
3.28-3.36	0.271	67	0.203	479	546
3.36-3.46	0.206	71	0.201	509	580
3.46-3.56	0.253	59	0.176	507	566
3.56-3.67	0.189	62	0.178	518	580
3.67-3.8	0.198	36	0.188	514	550
3.8-3.95	0.236	71	0.179	522	593
3.95-4.13	0.165	74	0.164	486	560
4.13-4.35	0.178	69	0.185	490	559
4.35-4.61	0.218	61	0.157	529	590
4.61-4.97	0.144	48	0.154	519	567
4.97-5.46	0.2	53	0.192	510	563
5.46-6.23	0.256	39	0.216	539	578
6.23-7.77	0.342	60	0.247	514	574
7.77-20	0.185	68	0.189	494	562

Xplor file

Refine-ID	Serial no	Param file
X-RAY DIFFRACTION	1	protein_rep.par
X-RAY DIFFRACTION	2	water_rep.param

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