PDB-4nla: Structure of the central NEAT domain, N2, of the listerial Hbp2 p...

ID or keywords:

Entry

Database: PDB / ID: 4nla

Title

Structure of the central NEAT domain, N2, of the listerial Hbp2 protein, apo form

Components

Iron-regulated surface determinant protein A

Keywords

PROTEIN BINDING /

Heme / NEAT domain /

listeria /

hemoglobin / N2 / Hbp / Hbp2 / HEME-BINDING PROTEIN /

HEME BINDING

Function / homology

Function and homology information

cellular response to iron ion / iron ion transport /

cell surface / extracellular region /

membrane /

metal ion binding
Similarity search - Function

Biological species

Listeria monocytogenes (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MAD / Resolution: 2.7 Å

Authors

Malmirchegini, G.R. / Sawaya, M.R. / Clubb, R.T.

Citation

Journal: J.Biol.Chem. / Year: 2014
Title: Novel Mechanism of Hemin Capture by Hbp2, the Hemoglobin-binding Hemophore from Listeria monocytogenes.
Authors: Malmirchegini, G.R. / Sjodt, M. / Shnitkind, S. / Sawaya, M.R. / Rosinski, J. / Newton, S.M. / Klebba, P.E. / Clubb, R.T.

History

Deposition	Nov 14, 2013	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 22, 2014	Provider: repository / Type: Initial release
Revision 1.1	Dec 31, 2014	Group: Database references
Revision 1.2	Sep 20, 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 / 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 / _struct_ref_seq_dif.details / _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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PDBx/mmCIF format	4nla.cif.gz	65.5 KB	Display	PDBx/mmCIF format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/nl/4nla ftp://data.pdbj.org/pub/pdb/validation_reports/nl/4nla	HTTPS FTP

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Related structure data

Related structure data	4mypC 3sz6S C: citing same article (ref.) S: Starting model for refinement
Similar structure data	4g3u-2 4g3u-1 4ht9-1 6ob2-2 4e2p-d 3gib-1 4zxe-d 4x9c-d 4ht8-d 5new-1 Search similar-shape structures by Omokage search (details) 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	#41 - May 2003 Hemoglobin similarity (1)

Deposited unit

A: Iron-regulated surface determinant protein A

hetero molecules

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

1

A: Iron-regulated surface determinant protein A

hetero molecules

A: Iron-regulated surface determinant protein A

hetero molecules

A: Iron-regulated surface determinant protein A

hetero molecules

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

Unit cell

Length a, b, c (Å)	89.300, 89.300, 89.300
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	197
Space group name H-M	I23

Details

The authors state that the biological unit is not known

#1: Protein	Iron-regulated surface determinant protein A / P64 protein / Surface virulence-associated protein A Mass: 13545.126 Da / Num. of mol.: 1 / Fragment: unp residues 183-303 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Listeria monocytogenes (bacteria) / Strain: EGD-e / Gene: BN418_2635, lmo2185, M639_06195 / Plasmid: pHIS-SUMO / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9KGV9, UniProt: Q7AP54*PLUS
#2: Chemical	ChemComp-SO4 / SULFATE ION / Sulfate Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO₄
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 9 / 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: 2.19 Å³/Da / Density % sol: 43.85 %
Crystal grow	Temperature: 298 K / Method: evaporation / pH: 5.4 Details: 100 mM sodium citrate tribasic dihydrate, 200 mM potassium sodium tartrate tetrahydrate, 2.0 M ammonium sulfate, pH 5.4, vapor diffusion, temperature 298K, EVAPORATION

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 24-ID-C / Wavelength: 0.97950, 0.9686, 1.5418

Detector

Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 6, 2013
Details: MIRRORS. BENT CYLINDERS, STRIPES OF PT, RH AND CLEAR.

Radiation

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

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	0.9795	1
2	0.9686	1
3	1.5418	1

Reflection

Number: 126252 / R_merge(I) obs: 0.057 / D res high: 2.69 Å / Num. obs: 6256 / % possible obs: 100

Diffraction reflection shell

Highest resolution (Å)	Lowest resolution (Å)	Num. obs	% possible obs (%)	ID	R_merge(I) obs
2.69	2.76	490	99.4	1	0.723
2.76	2.84	467	100	1	0.543
2.84	2.92	419	100	1	0.416
2.92	3.01	436	100	1	0.297
3.01	3.11	380	100	1	0.193
3.11	3.22	410	100	1	0.135
3.22	3.34	387	100	1	0.104
3.34	3.48	375	100	1	0.091
3.48	3.63	335	100	1	0.072
3.81	4.01	307	100	1	0.057
4.01	4.26	314	100	1	0.053
4.26	4.55	268	100	1	0.047
4.55	4.92	281	100	1	0.046
4.92	5.39	236	100	1	0.045
5.39	6.02	226	100	1	0.048
6.02	6.95	200	100	1	0.046
6.95	8.52	165	100	1	0.042
8.52	12.04	124	100	1	0.041

Reflection

Resolution: 2.7→63.14 Å / Num. obs: 3370 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 21.4 % / B_iso Wilson estimate: 109.36 Å² / R_merge(I) obs: 0.052 / Net I/σ(I): 35.3

Reflection shell

Resolution: 2.7→2.85 Å / Redundancy: 22.8 % / R_merge(I) obs: 0.471 / Mean I/σ(I) obs: 6.3 / % possible all: 100

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Phasing

Phasing

Method:

MAD

Phasing MAD

D res high: 2.6 Å / D res low: 19.85 Å / FOM : 0.432 / FOM acentric: 0.453 / FOM centric: 0.279 / Reflection: 3695 / Reflection acentric: 3245 / Reflection centric: 450

Phasing MAD set

Highest resolution: 2.6 Å / Lowest resolution: 19.85 Å

ID	R cullis acentric	R cullis centric	Loc acentric	Loc centric	Power acentric	Power centric	Reflection acentric	Reflection centric
1	0.97	0.92	15.3	13.4	0.44	0.57	2728	401
2	0.98	1	15.2	13.5	0.22	0.27	2912	418
3	2.04	1	0.3	0.2	0	0	3245	450
4	0.92	0.81	11.6	12.4	0.6	0.7	3045	420

Phasing MAD set shell

ID	Resolution (Å)	R cullis acentric	R cullis centric	Loc acentric	Loc centric	Power acentric	Power centric	Reflection acentric	Reflection centric
1	10.85-19.85	0.8	0.84	18.7	41	1.27	0.49	33	18
1	7.47-10.85	0.58	0.56	8.9	10.2	2.13	1.49	84	30
1	5.69-7.47	0.89	0.74	17.3	9.7	0.81	1.34	166	39
1	4.6-5.69	1	1.14	36.6	14.5	0.3	0.71	267	54
1	3.86-4.6	1.01	0.95	14	11.4	0.58	0.64	403	59
1	3.32-3.86	1.01	1.02	17.1	13.8	0.34	0.4	571	72
1	2.92-3.32	0.99	0.99	10.4	12.8	0.39	0.24	748	85
1	2.6-2.92	0.97	0.96	10.1	9.8	0.29	0.31	456	44
2	10.85-19.85	1.1	0.95	16.2	42.5	0.63	0.21	33	18
2	7.47-10.85	0.92	1.05	9.3	12.1	0.88	0.55	84	30
2	5.69-7.47	1.03	1.08	22.4	10.4	0.28	0.56	166	39
2	4.6-5.69	0.97	1.01	42.7	21.5	0.11	0.22	267	54
2	3.86-4.6	1.01	0.98	11.1	12	0.34	0.27	403	59
2	3.32-3.86	0.97	1.01	16.7	11.5	0.17	0.23	571	72
2	2.92-3.32	0.98	0.97	9.3	9.8	0.26	0.2	748	85
2	2.6-2.92	0.98	0.99	10.7	9.8	0.17	0.2	640	61
3	10.85-19.85	0.83	1	0.7	0.6	0	0	33	18
3	7.47-10.85	0.94	1	0.5	0.6	0	0	84	30
3	5.69-7.47	1.33	1	0.5	0.3	0	0	166	39
3	4.6-5.69	4.39	1	1.4	0.3	0	0	267	54
3	3.86-4.6	1.14	1	0.3	0.3	0	0	403	59
3	3.32-3.86	2.39	1	0.4	0.1	0	0	571	72
3	2.92-3.32	1.69	1	0.1	0.1	0	0	748	85
3	2.6-2.92	2.62	1	0.1	0	0	0	973	93
4	10.85-19.85	0.61	0.73	24.2	23.1	1.43	1.17	31	16
4	7.47-10.85	0.54	0.52	13.1	16.1	2.08	1.49	79	26
4	5.69-7.47	0.58	0.47	10	12.1	1.98	1.48	166	37
4	4.6-5.69	0.99	0.98	35.1	19.9	0.4	0.67	263	51
4	3.86-4.6	0.9	0.83	9.5	13.6	0.98	0.6	396	58
4	3.32-3.86	1.01	1.03	15.2	12.5	0.38	0.43	570	72
4	2.92-3.32	0.99	0.95	6	7.3	0.56	0.38	748	85
4	2.6-2.92	0.99	0.98	7	8.9	0.26	0.21	792	75

Phasing MAD set site

ID	Atom type symbol	B iso	Fract x	Fract y	Fract z	Occupancy	Occupancy iso
1	Sz	36.947	-0.834	-0.689	-0.097	0.557	0.06
2	Sz	65.116	-0.716	-0.74	-0.062	0.491	0.072
3	Sz	69.089	-0.941	-0.604	-0.046	0.573	0.06
4	Sz	162.98	-0.918	-0.587	-0.025	0.674	0.051
5	Sy	23.191	-0.836	-0.688	-0.098	0.401	0.025
6	Sy	116.2	-0.717	-0.743	-0.064	0.591	0.043
7	Sy	32.036	-0.942	-0.602	-0.048	0.35	0.022
8	Sy	40.402	-0.919	-0.585	-0.021	0.347	0.02
9	Sy	74.752	-0.836	-0.689	-0.097	0.54	0
10	Sy	86.527	-0.718	-0.742	-0.062	0.389	0
11	Sy	81.423	-0.942	-0.601	-0.048	0.421	0
12	Sy	92.034	-0.919	-0.584	-0.023	0.366	0
13	Se	78.099	-0.836	-0.688	-0.097	0.722	0.11
14	Se	100.519	-0.719	-0.742	-0.062	0.63	0.109
15	Se	86.901	-0.942	-0.603	-0.047	0.586	0.077
16	Se	83.902	-0.919	-0.584	-0.022	0.473	0.049

Phasing MAD shell

Resolution (Å)	FOM	FOM acentric	FOM centric	Reflection	Reflection acentric	Reflection centric
10.85-19.85	0.703	0.832	0.466	51	33	18
7.47-10.85	0.846	0.886	0.734	114	84	30
5.69-7.47	0.809	0.833	0.705	205	166	39
4.6-5.69	0.457	0.53	0.097	321	267	54
3.86-4.6	0.624	0.648	0.46	462	403	59
3.32-3.86	0.409	0.449	0.099	643	571	72
2.92-3.32	0.421	0.446	0.201	833	748	85
2.6-2.92	0.233	0.244	0.12	1066	973	93

Phasing dm

Method: Solvent flattening and Histogram matching / Reflection: 3695

Phasing dm shell

Resolution (Å)	Delta phi final	FOM	Reflection
5.13-100	56.5	0.822	504
4.04-5.13	56.1	0.836	508
3.52-4.04	66.2	0.72	507
3.19-3.52	74.5	0.753	512
2.95-3.19	73.4	0.77	511
2.77-2.95	79.1	0.709	513
2.6-2.77	80.8	0.644	640

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Processing

Software

Name	Version	Classification
SCALEPACK		data scaling
MLPHARE		phasing
DM	6.2	phasing
BUSTER-TNT		refinement
PDB_EXTRACT	3.11	data extraction
XSCALE		data scaling
BUSTER	2.10.0	refinement

Refinement

Method to determine structure:

MAD
Starting model: PDB ENTRY 3SZ6

3sz6

Resolution: 2.7→63.14 Å / Cor.coef. F_o:F_c: 0.939 / Cor.coef. F_o:F_c free: 0.926 / Occupancy max: 1 / Occupancy min: 1 / SU R Cruickshank DPI: 0.457 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.293	337	10 %	RANDOM
R_work	0.254	-	-	-
obs	0.258	3370	100 %	-
all	-	5408	-	-

Displacement parameters

B_iso mean: 120.65 Å²

	B_aniso -1	B_aniso -2
1-	0 Å²	0 Å²
2-	-	0 Å²
3-	-	-

Refine analyze

Luzzati coordinate error obs: 0.968 Å

Refinement step

Cycle: LAST / Resolution: 2.7→63.14 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	947	0	5	9	961

Refine LS restraints

Refine-ID	Type	Dev ideal	Number	Restraint function	Weight
X-RAY DIFFRACTION	t_bond_d	0.008	968	HARMONIC	2
X-RAY DIFFRACTION	t_angle_deg	1.02	1315	HARMONIC	2
X-RAY DIFFRACTION	t_dihedral_angle_d		331	SINUSOIDAL	2
X-RAY DIFFRACTION	t_incorr_chiral_ct
X-RAY DIFFRACTION	t_pseud_angle
X-RAY DIFFRACTION	t_trig_c_planes		31	HARMONIC	2
X-RAY DIFFRACTION	t_gen_planes		136	HARMONIC	5
X-RAY DIFFRACTION	t_it		968	HARMONIC	20
X-RAY DIFFRACTION	t_nbd
X-RAY DIFFRACTION	t_omega_torsion	1.79
X-RAY DIFFRACTION	t_other_torsion	19.66
X-RAY DIFFRACTION	t_improper_torsion
X-RAY DIFFRACTION	t_chiral_improper_torsion		129	SEMIHARMONIC	5
X-RAY DIFFRACTION	t_sum_occupancies
X-RAY DIFFRACTION	t_utility_distance
X-RAY DIFFRACTION	t_utility_angle
X-RAY DIFFRACTION	t_utility_torsion
X-RAY DIFFRACTION	t_ideal_dist_contact		1000	SEMIHARMONIC	4

LS refinement shell

Resolution: 2.7→3.02 Å / Total num. of bins used: 5

	R_factor	Num. reflection	% reflection
R_free	0.4147	92	9.9 %
R_work	0.3553	837	-
all	0.3616	929	-
obs	-	-	100 %

Refinement TLS params.

Method: refined / Origin x: 16.3047 Å / Origin y: 37.9763 Å / Origin z: 28.8459 Å

	11	12	13	21	22	23	31	32	33
T	-0.2241 Å²	0.018 Å²	0.034 Å²	-	-0.233 Å²	-0.2749 Å²	-	-	0.079 Å²
L	10.7995 °²	4.8158 °²	2.107 °²	-	6.9195 °²	2.823 °²	-	-	5.455 °²
S	0.1176 Å °	-0.1677 Å °	1.0885 Å °	0.6502 Å °	-0.7062 Å °	1.02 Å °	0.0405 Å °	-0.7576 Å °	0.5886 Å °

Refinement TLS group

Selection details: { A|* }

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