PDB-8orr: Outer membrane protein assembly factor BamB from Klebsiella pneumoniae

ID or keywords:

Entry

Database: PDB / ID: 8orr

Title

Outer membrane protein assembly factor BamB from Klebsiella pneumoniae

Components

Outer membrane protein assembly factor BamB

Keywords

PROTEIN BINDING / Outer membrane protein assembly factor BamB

Function / homology

Function and homology information

Gram-negative-bacterium-type cell outer membrane assembly / protein insertion into membrane / cell outer membrane
Similarity search - Function

Biological species

Klebsiella pneumoniae (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.68 Å

Authors

Song, H. / Bolla, J.R.

Funding support

1items

Citation

Journal: To Be Published
Title: Outer membrane protein assembly factor BamB from Klebsiella pneumoniae
Authors: Song, H. / Bolla, J.R.

History

Deposition	Apr 17, 2023	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Apr 24, 2024	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8orr.cif.gz	148.2 KB	Display	PDBx/mmCIF format
PDB format	pdb8orr.ent.gz		Display	PDB format
PDBx/mmJSON format	8orr.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/or/8orr ftp://data.pdbj.org/pub/pdb/validation_reports/or/8orr	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	#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

AAA: Outer membrane protein assembly factor BamB

hetero molecules

39.5 kDa, 1 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)	50.095, 50.095, 259.774
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	96
Space group name H-M	P4₃2₁2

Components on special symmetry positions

ID	Model	Components
1	1	AAA-682- HOH

#1: Protein	Outer membrane protein assembly factor BamB Mass: 38829.234 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: yfgL / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0W8AU86
#2: Chemical	ChemComp-CD / CADMIUM ION Mass: 112.411 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cd / Feature type: SUBJECT OF INVESTIGATION
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 320 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.1 Å³/Da / Density % sol: 41.39 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 22% PEG 400, 0.1 M sodium acetate trihydrate (pH 4.6) and 0.08 M cadmium acetate trihydrate

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9282 Å
Detector	Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Feb 22, 2017
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9282 Å / Relative weight: 1
Reflection	Resolution: 1.57→29.285 Å / Num. obs: 48078 / % possible obs: 99.8 % / Redundancy: 24 % / CC_1/2: 1 / R_merge(I) obs: 0.073 / Net I/σ(I): 25.6
Reflection shell	Resolution: 1.57→1.61 Å / R_merge(I) obs: 0.665 / Mean I/σ(I) obs: 3.3 / Num. unique obs: 3386 / CC_1/2: 0.92 / % possible all: 97.7

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0267	refinement
XDS		data reduction
XDS		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.68→29.285 Å / Cor.coef. F_o:F_c: 0.964 / Cor.coef. F_o:F_c free: 0.942 / SU B: 3.544 / SU ML: 0.067 / Cross valid method: FREE R-VALUE / ESU R: 0.101 / ESU R Free: 0.102
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2098	1954	4.987 %
R_work	0.1711	37230	-
all	0.173	-	-
obs	-	39184	99.964 %

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: 22.911 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.191 Å²	-0 Å²	0 Å²
2-	-	0.191 Å²	0 Å²
3-	-	-	-0.382 Å²

Refinement step

Cycle: LAST / Resolution: 1.68→29.285 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2631	0	6	320	2957

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.006	0.013	2750
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.015	2594
X-RAY DIFFRACTION	r_angle_refined_deg	1.426	1.627	3761
X-RAY DIFFRACTION	r_angle_other_deg	1.271	1.581	5953
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.215	5	362
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	35.281	23.409	132
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.696	15	434
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	12.011	15	14
X-RAY DIFFRACTION	r_chiral_restr	0.058	0.2	360
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	3224
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	624
X-RAY DIFFRACTION	r_nbd_refined	0.188	0.2	409
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.17	0.2	2245
X-RAY DIFFRACTION	r_nbtor_refined	0.144	0.2	1261
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.07	0.2	1258
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.188	0.2	201
X-RAY DIFFRACTION	r_metal_ion_refined	0.176	0.2	6
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.274	0.2	13
X-RAY DIFFRACTION	r_nbd_other	0.163	0.2	31
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.137	0.2	19
X-RAY DIFFRACTION	r_mcbond_it	1.45	1.372	1433
X-RAY DIFFRACTION	r_mcbond_other	1.43	1.37	1432
X-RAY DIFFRACTION	r_mcangle_it	2.392	2.046	1800
X-RAY DIFFRACTION	r_mcangle_other	2.392	2.047	1801
X-RAY DIFFRACTION	r_scbond_it	1.856	1.621	1317
X-RAY DIFFRACTION	r_scbond_other	1.855	1.624	1318
X-RAY DIFFRACTION	r_scangle_it	2.952	2.331	1961
X-RAY DIFFRACTION	r_scangle_other	2.951	2.334	1962
X-RAY DIFFRACTION	r_lrange_it	5.745	17.665	2908
X-RAY DIFFRACTION	r_lrange_other	5.536	16.69	2818

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.68-1.724	0.247	143	0.198	2713	X-RAY DIFFRACTION	100
1.724-1.771	0.218	140	0.205	2595	X-RAY DIFFRACTION	100
1.771-1.822	0.249	144	0.191	2530	X-RAY DIFFRACTION	100
1.822-1.878	0.227	150	0.182	2459	X-RAY DIFFRACTION	100
1.878-1.94	0.201	94	0.182	2448	X-RAY DIFFRACTION	100
1.94-2.008	0.208	116	0.179	2357	X-RAY DIFFRACTION	100
2.008-2.083	0.235	132	0.169	2264	X-RAY DIFFRACTION	100
2.083-2.168	0.184	119	0.165	2138	X-RAY DIFFRACTION	100
2.168-2.265	0.208	106	0.166	2117	X-RAY DIFFRACTION	100
2.265-2.375	0.194	98	0.154	2023	X-RAY DIFFRACTION	100
2.375-2.503	0.237	85	0.178	1930	X-RAY DIFFRACTION	100
2.503-2.655	0.209	95	0.173	1822	X-RAY DIFFRACTION	100
2.655-2.838	0.223	89	0.17	1716	X-RAY DIFFRACTION	100
2.838-3.065	0.199	79	0.168	1614	X-RAY DIFFRACTION	100
3.065-3.357	0.207	97	0.172	1494	X-RAY DIFFRACTION	100
3.357-3.752	0.214	85	0.163	1349	X-RAY DIFFRACTION	100
3.752-4.33	0.199	56	0.157	1221	X-RAY DIFFRACTION	100
4.33-5.297	0.162	61	0.146	1059	X-RAY DIFFRACTION	100
5.297-7.466	0.186	40	0.187	860	X-RAY DIFFRACTION	100
7.466-29.285	0.323	25	0.205	521	X-RAY DIFFRACTION	97.5

Refinement TLS params.

Method: refined / Origin x: 4.6912 Å / Origin y: 19.3786 Å / Origin z: 277.8545 Å

	11	12	13	21	22	23	31	32	33
T	0.0241 Å²	0.0033 Å²	0.0078 Å²	-	0.0135 Å²	0.0015 Å²	-	-	0.0335 Å²
L	0.5947 °²	-0.0882 °²	0.2838 °²	-	2.3012 °²	0.4117 °²	-	-	0.7366 °²
S	-0.0007 Å °	0.0648 Å °	0.079 Å °	-0.1529 Å °	-0.0598 Å °	0.0811 Å °	-0.0699 Å °	-0.0254 Å °	0.0606 Å °

Refinement TLS group

Selection: ALL / Selection details: { AAA|31-392 }

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