PDB-8fuh: Rubrerythrin from B. pseudomallei: apo form

ID or keywords:

Entry

Database: PDB / ID: 8fuh

Title

Rubrerythrin from B. pseudomallei: apo form

Components

Rubrerythrin

Keywords

OXIDOREDUCTASE / metalloprotein / oxidative stress / non-heme

Function / homology

Function and homology information

oxidoreductase activity / metal ion binding
Similarity search - Function

Biological species

Burkholderia pseudomallei (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.852 Å

Authors

Monteiro, D.C.F. / Snell, M.E. / Budziszewski, G.R. / Bowman, S.E.J.

Funding support

United States, 2items

Citation

Journal: To Be Published
Title: Rubrerythrin from B. pseudomallei: apo form
Authors: Monteiro, D.C.F. / Snell, M.E. / Budziszewski, G.R. / Bowman, S.E.J.

History

Deposition	Jan 17, 2023	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jan 31, 2024	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8fuh.cif.gz	337.2 KB	Display	PDBx/mmCIF format
PDB format	pdb8fuh.ent.gz	265.9 KB	Display	PDB format
PDBx/mmJSON format	8fuh.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/fu/8fuh ftp://data.pdbj.org/pub/pdb/validation_reports/fu/8fuh	HTTPS FTP

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Related structure data

Similar structure data	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	#35 - Nov 2002 Ferritin and Transferrin similarity (3) #114 - Jun 2009 Vaults similarity (1) #57 - Sep 2004 Catalase similarity (1)

Deposited unit

A: Rubrerythrin

B: Rubrerythrin

M: Rubrerythrin

S: Rubrerythrin

Y: Rubrerythrin

5: Rubrerythrin

hetero molecules

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

1

A: Rubrerythrin

B: Rubrerythrin

hetero molecules

defined by author&software
Evidence: gel filtration
37.4 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

M: Rubrerythrin

S: Rubrerythrin

hetero molecules

defined by author&software
37.4 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

Y: Rubrerythrin

5: Rubrerythrin

defined by author&software
37.3 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	202.373, 202.373, 70.329
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	146
Space group name H-M	H3

#1: Protein	Rubrerythrin Mass: 18655.389 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Burkholderia pseudomallei (bacteria) / Gene: BURPS1710b_A0924 / Production host: Escherichia coli (E. coli) / References: UniProt: Q3JK21
#2: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 936 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.48 Å³/Da / Density % sol: 50.33 %
Crystal grow	Temperature: 296 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 0.5 M lithium sulfate, 0.1 M bis-tris propane, pH 7.0

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

NSLS-II

/ Beamline: 17-ID-2 / Wavelength: 0.9201 Å

Detector

Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 27, 2022

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.9201 Å / Relative weight: 1

Reflection

Resolution: 1.85→29.21 Å / Num. obs: 90867 / % possible obs: 99.4 % / Redundancy: 3.6 % / CC_1/2: 0.993 / R_merge(I) obs: 0.101 / R_pim(I) all: 0.093 / R_rim(I) all: 0.138 / Net I/σ(I): 6.5

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique obs	CC_1/2	R_pim(I) all	R_rim(I) all
10.14-29.21	3.4	0.046	533	0.995	0.043	0.063
1.85-1.88	3.3	0.676	4220	0.608	0.643	0.934

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0352	refinement
Aimless		data scaling
Coot		model building
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.852→28.748 Å / Cor.coef. F_o:F_c: 0.973 / Cor.coef. F_o:F_c free: 0.956 / SU B: 2.834 / SU ML: 0.081 / Cross valid method: FREE R-VALUE / ESU R: 0.103 / ESU R Free: 0.104
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.1875	4443	4.89 %
R_work	0.1497	86407	-
all	0.152	-	-
obs	-	90850	99.406 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 24.497 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.613 Å²	-0.307 Å²	0 Å²
2-	-	-0.613 Å²	0 Å²
3-	-	-	1.99 Å²

Refinement step

Cycle: LAST / Resolution: 1.852→28.748 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6468	0	14	936	7418

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.012	6678
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.016	5737
X-RAY DIFFRACTION	r_angle_refined_deg	1.416	1.661	9023
X-RAY DIFFRACTION	r_angle_other_deg	0.524	1.57	13397
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	4.903	5	846
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	6.613	5	44
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.752	10	1067
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	15.94	10	362
X-RAY DIFFRACTION	r_chiral_restr	0.076	0.2	928
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.02	7948
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1396
X-RAY DIFFRACTION	r_nbd_refined	0.233	0.2	1605
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.173	0.2	5400
X-RAY DIFFRACTION	r_nbtor_refined	0.185	0.2	3382
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.07	0.2	3460
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.161	0.2	782
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.073	0.2	2
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.169	0.2	6
X-RAY DIFFRACTION	r_nbd_other	0.13	0.2	28
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.132	0.2	23
X-RAY DIFFRACTION	r_mcbond_it	2.209	2.575	3351
X-RAY DIFFRACTION	r_mcbond_other	2.207	2.575	3351
X-RAY DIFFRACTION	r_mcangle_it	3.109	3.846	4184
X-RAY DIFFRACTION	r_mcangle_other	3.111	3.847	4185
X-RAY DIFFRACTION	r_scbond_it	3.034	2.904	3327
X-RAY DIFFRACTION	r_scbond_other	3.031	2.903	3326
X-RAY DIFFRACTION	r_scangle_it	4.656	4.205	4831
X-RAY DIFFRACTION	r_scangle_other	4.655	4.205	4832
X-RAY DIFFRACTION	r_lrange_it	5.952	33.576	8373
X-RAY DIFFRACTION	r_lrange_other	5.686	31.889	8049

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
1.852-1.9	0.289	318	0.263	6175	0.264	6736	0.941	0.948	96.3925	0.268
1.9-1.952	0.279	318	0.241	6229	0.243	6557	0.946	0.957	99.8475	0.246
1.952-2.008	0.251	290	0.219	6084	0.22	6374	0.955	0.967	100	0.222
2.008-2.069	0.242	308	0.197	5854	0.199	6195	0.962	0.974	99.4673	0.196
2.069-2.137	0.181	334	0.163	5680	0.164	6017	0.978	0.983	99.9501	0.161
2.137-2.211	0.202	294	0.155	5533	0.157	5827	0.972	0.985	100	0.152
2.211-2.294	0.198	301	0.153	5291	0.156	5601	0.975	0.985	99.8393	0.149
2.294-2.387	0.184	265	0.144	5136	0.146	5401	0.978	0.987	100	0.141
2.387-2.493	0.201	241	0.15	4950	0.152	5193	0.973	0.987	99.9615	0.146
2.493-2.614	0.185	197	0.138	4760	0.14	4971	0.98	0.989	99.7184	0.134
2.614-2.754	0.163	191	0.132	4471	0.134	4701	0.986	0.99	99.1704	0.131
2.754-2.919	0.175	238	0.13	4222	0.132	4480	0.982	0.99	99.5536	0.13
2.919-3.118	0.186	226	0.148	3941	0.15	4189	0.978	0.987	99.4748	0.15
3.118-3.365	0.191	178	0.153	3659	0.154	3896	0.976	0.987	98.4856	0.157
3.365-3.681	0.198	169	0.152	3420	0.154	3618	0.976	0.988	99.1985	0.158
3.681-4.107	0.166	160	0.13	3074	0.132	3244	0.982	0.99	99.6917	0.14
4.107-4.726	0.163	132	0.117	2745	0.119	2881	0.986	0.993	99.8612	0.127
4.726-5.75	0.169	109	0.135	2334	0.137	2446	0.984	0.991	99.8773	0.144
5.75-7.974	0.154	119	0.118	1787	0.12	1908	0.987	0.992	99.8952	0.128
7.974-28.748	0.133	55	0.129	1061	0.129	1120	0.989	0.989	99.6429	0.139

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