PDB-3u24: The structure of a putative lipoprotein of unknown function from ...

ID or keywords:

Entry

Database: PDB / ID: 3u24

Title

The structure of a putative lipoprotein of unknown function from Shewanella oneidensis.

Components

putative Lipoprotein

Keywords

LIPID BINDING PROTEIN / COG4805 / DUF885 /

Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG /

putative lipoprotein

Function / homology

Protein of unknown function DUF885 /

Bacterial protein of unknown function (DUF885) /

metal ion binding /

ACETIC ACID /

IMIDAZOLE / DUF885 family lipoprotein

Function and homology information

Biological species

Shewanella oneidensis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.25 Å

Authors

Cuff, M.E. / Hatzos-Skintges, C. / Bearden, J. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)

Citation

Journal: TO BE PUBLISHED
Title: The structure of a putative lipoprotein of unknown function from Shewanella oneidensis.
Authors: Cuff, M.E. / Hatzos-Skintges, C. / Bearden, J. / Joachimiak, A.

History

Deposition	Sep 30, 2011	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 9, 2012	Provider: repository / Type: Initial release
Revision 1.1	Nov 8, 2017	Group: Refinement description / Category: software

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3u24.cif.gz	244.4 KB	Display	PDBx/mmCIF format
PDB format	pdb3u24.ent.gz	202.1 KB	Display	PDB format
PDBx/mmJSON format	3u24.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/u2/3u24 ftp://data.pdbj.org/pub/pdb/validation_reports/u2/3u24	HTTPS FTP

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Related structure data

Similar structure data	5txc-1 5jay-d 2bf4-1 1itw-4 5txe-1 6m31-d 1j1w-2 1j1w-4 1itw-2 1r1j-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
Other databases	TargetDB: apc102173

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#4 - Apr 2000 Collagen similarity (1) #116 - Aug 2009 Sulfotransferases similarity (1) #134 - Feb 2011 Integrin similarity (1) #172 - Apr 2014 RecA and Rad51 similarity (1) #194 - Feb 2016 Designer Insulins similarity (1) #234 - Jun 2019 MDM2 and Cancer similarity (1) #259 - Jul 2021 Designed Proteins and Citizen Science similarity (1)

Deposited unit

A: putative Lipoprotein

hetero molecules

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

1

Idetical with deposited unit
defined by software

Unit cell

Length a, b, c (Å)	96.427, 96.427, 133.947
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	152
Space group name H-M	P3₁21

Components on special symmetry positions

ID	Model	Components
1	1	A-975- HOH

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Protein , 1 types, 1 molecules A

#1: Protein	putative Lipoprotein / Mass: 66387.359 Da / Num. of mol.: 1 / Fragment: residues 21-591 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Shewanella oneidensis (bacteria) / Strain: MR-1 / Gene: SO_2570 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) magic / References: UniProt: Q8EE20

#1: Protein

putative Lipoprotein /

Mass: 66387.359 Da / Num. of mol.: 1 / Fragment: residues 21-591
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Shewanella oneidensis (bacteria) / Strain: MR-1 / Gene: SO_2570 / Plasmid: pMCSG7 / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) magic / References: UniProt: Q8EE20

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Non-polymers , 6 types, 405 molecules

#2: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Zn
#3: Chemical	ChemComp-ACY / ACETIC ACID / Acetic acid Mass: 60.052 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₂H₄O₂
#4: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂H₆O₂
#5: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#6: Chemical	ChemComp-IMD / IMIDAZOLE / Imidazole Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₅N₂
#7: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 380 / 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: 2.71 Å³/Da / Density % sol: 54.54 %
Crystal grow	Temperature: 297 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 0.2M zinc acetate, 0.1M imidazole pH 8, 20% PEG 3000, 10% PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 297K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 19-BM / Wavelength: 0.97918 Å

Detector

Type: ADSC QUANTUM 210r / Detector: CCD / Date: Jun 24, 2009

Radiation

Monochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.97918 Å / Relative weight: 1

Reflection

Redundancy: 9.2 % / Av σ(I) over netI: 26.23 / Number: 320044 / R_merge(I) obs: 0.101 / Χ²: 1.41 / D res high: 2.25 Å / D res low: 50 Å / Num. obs: 34837 / % possible obs: 99.9

Diffraction reflection shell

Highest resolution (Å)	Lowest resolution (Å)	% possible obs (%)	ID	R_merge(I) obs	Chi squared	Redundancy
6.1	50	99.3	1	0.068	3.593	8.7
4.85	6.1	100	1	0.07	2.372	9.5
4.23	4.85	100	1	0.059	1.926	9.7
3.85	4.23	100	1	0.062	1.835	9.8
3.57	3.85	100	1	0.07	1.762	9.7
3.36	3.57	100	1	0.081	1.598	9.6
3.19	3.36	100	1	0.092	1.441	9.5
3.05	3.19	100	1	0.114	1.283	9.4
2.94	3.05	100	1	0.132	1.202	9.3
2.83	2.94	100	1	0.153	1.125	9.2
2.75	2.83	100	1	0.174	1.025	9.2
2.67	2.75	99.9	1	0.199	1.029	9.2
2.6	2.67	99.9	1	0.24	1.008	9.2
2.53	2.6	99.9	1	0.278	0.98	9.2
2.48	2.53	99.8	1	0.279	0.92	9.2
2.42	2.48	99.9	1	0.308	0.94	9.2
2.38	2.42	99.9	1	0.353	0.936	9.1
2.33	2.38	100	1	0.396	0.904	9.1
2.29	2.33	99.8	1	0.436	0.979	8.3
2.25	2.29	100	1	0.474	1.013	7.6

Reflection

Resolution: 2.25→50 Å / Num. all: 34837 / Num. obs: 34837 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 9.2 % / R_merge(I) obs: 0.101 / Net I/σ(I): 9.2

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Diffraction-ID	% possible all
2.25-2.29	7.6	0.474	1	100
2.29-2.33	8.3	0.436	1	99.8
2.33-2.38	9.1	0.396	1	100
2.38-2.42	9.1	0.353	1	99.9
2.42-2.48	9.2	0.308	1	99.9
2.48-2.53	9.2	0.279	1	99.8
2.53-2.6	9.2	0.278	1	99.9
2.6-2.67	9.2	0.24	1	99.9
2.67-2.75	9.2	0.199	1	99.9
2.75-2.83	9.2	0.174	1	100
2.83-2.94	9.2	0.153	1	100
2.94-3.05	9.3	0.132	1	100
3.05-3.19	9.4	0.114	1	100
3.19-3.36	9.5	0.092	1	100
3.36-3.57	9.6	0.081	1	100
3.57-3.85	9.7	0.07	1	100
3.85-4.23	9.8	0.062	1	100
4.23-4.85	9.7	0.059	1	100
4.85-6.1	9.5	0.07	1	100
6.1-50	8.7	0.068	1	99.3

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Phasing

Phasing

Method:

SAD

Phasing MAD

D res high: 2.25 Å / D res low: 50 Å / FOM : 0.264 / FOM acentric: 0.292 / FOM centric: 0 / Reflection: 34738 / Reflection acentric: 31329 / Reflection centric: 3409

Phasing MAD set

R cullis acentric: 1.99 / R cullis centric: 1 / Highest resolution: 2.25 Å / Lowest resolution: 50 Å / Loc acentric: 0.2 / Loc centric: 0.1 / Power acentric: 0 / Power centric: 0 / Reflection acentric: 31329 / Reflection centric: 3409

Phasing MAD set shell

ID: 1 / R cullis centric: 1 / Power acentric: 0 / Power centric: 0

Resolution (Å)	R cullis acentric	Loc acentric	Loc centric	Reflection acentric	Reflection centric
13.69-50	1.48	0.5	0.3	95	77
7.93-13.69	1.17	0.5	0.3	519	177
5.58-7.93	2.04	0.5	0.2	1278	278
4.31-5.58	1.37	0.4	0.2	2363	386
3.51-4.31	1.38	0.3	0.2	3789	472
2.96-3.51	1.93	0.2	0.1	5559	585
2.56-2.96	2.95	0.2	0.1	7657	665
2.25-2.56	3.37	0.1	0	10069	769

Phasing MAD set site

Atom type symbol: Se / Occupancy iso: 0

ID	B iso	Fract x	Fract y	Fract z	Occupancy
1	34.9179	0.464	0.016	0.07	3.793
2	30.5304	0.311	-0.03	-0.027	3.194
3	27.6052	0.502	-0.088	0.28	3.125
4	30.7357	0.487	-0.263	0.093	2.909
5	30.5601	0.329	-0.013	0.005	2.78
6	25.3649	0.104	-0.197	0.046	3.013
7	36.4372	0.123	-0.348	0.115	3.211
8	24.7069	0.185	-0.112	-0.032	2.878
9	71.6938	0.105	-0.204	-0.02	3.195
10	34.5144	0.413	-0.101	0.037	2.805
11	55.8156	0.033	-0.385	0.039	2.922
12	28.635	0.14	-0.308	0.065	2.409
13	30.5814	0.304	-0.146	0.139	2.648
14	33.4021	0.144	-0.251	0.14	2.154
15	25.9077	0.303	-0.187	-0.001	1.782
16	43.9658	0.052	-0.285	-0.105	1.467
17	36.127	0.565	0.014	0.129	1.324
18	35.3084	0.531	-0.078	0.15	1.346
19	52.5159	0.282	-0.236	0.269	1.363
20	99.7199	0.661	0.147	0.096	1.633
21	30.634	0.153	-0.104	-0.08	0.731
22	48.928	0.327	-0.049	-0.018	0.505

Phasing MAD shell

Resolution (Å)	FOM	FOM acentric	Reflection	Reflection acentric	Reflection centric
13.69-50	0.243	0.439	172	95	77
7.93-13.69	0.401	0.538	696	519	177
5.58-7.93	0.441	0.536	1556	1278	278
4.31-5.58	0.429	0.5	2749	2363	386
3.51-4.31	0.405	0.456	4261	3789	472
2.96-3.51	0.329	0.364	6144	5559	585
2.56-2.96	0.221	0.24	8322	7657	665
2.25-2.56	0.128	0.137	10838	10069	769

Phasing dm

Method: Solvent flattening and Histogram matching / Reflection: 34738

Phasing dm shell

Resolution (Å)	Delta phi final	FOM	Reflection
9.5-100	68	0.547	518
7.5-9.5	65.3	0.872	505
6.39-7.5	60.6	0.848	606
5.66-6.39	64.5	0.873	695
5.13-5.66	59.8	0.896	774
4.73-5.13	60	0.914	830
4.41-4.73	60.8	0.92	895
4.15-4.41	61.5	0.922	950
3.93-4.15	60.5	0.92	993
3.74-3.93	60.6	0.927	1047
3.57-3.74	60	0.913	1107
3.43-3.57	60.7	0.916	1127
3.3-3.43	65.2	0.905	1182
3.19-3.3	63	0.909	1238
3.08-3.19	65.5	0.901	1287
2.99-3.08	64.6	0.895	1313
2.9-2.99	65.2	0.896	1326
2.82-2.9	67.4	0.9	1368
2.75-2.82	70.9	0.911	1436
2.68-2.75	70.6	0.909	1449
2.62-2.68	72.7	0.903	1498
2.56-2.62	72.1	0.901	1554
2.51-2.56	74	0.911	1539
2.46-2.51	76	0.916	1593
2.41-2.46	76	0.91	1588
2.36-2.41	77.2	0.909	1647
2.32-2.36	79.4	0.904	1674
2.25-2.32	80.2	0.87	2999

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
MLPHARE		phasing
DM	6	phasing
REFMAC		refinement
PDB_EXTRACT	3.1	data extraction
SBC-Collect		data collection
HKL-3000		data reduction
HKL-3000		data scaling
HKL-3000		phasing
SHELXD		phasing
SHELXE		model building
SOLVE		phasing
RESOLVE		phasing
ARP/wARP		model building
CCP4		phasing
O		model building
Coot		model building

Refinement

Method to determine structure:

SAD / Resolution: 2.25→39.37 Å / Cor.coef. F_o:F_c: 0.961 / Cor.coef. F_o:F_c free: 0.936 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 9.287 / SU ML: 0.121 / SU R Cruickshank DPI: 0.2237 / Cross valid method: THROUGHOUT / ESU R: 0.224 / ESU R Free: 0.177
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.20045	1747	5 %	RANDOM
R_work	0.1621	-	-	-
obs	0.16409	33008	99.9 %	-
all	-	34755	-	-

Solvent computation

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

Displacement parameters

B_iso mean: 28.158 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.12 Å²	-0.06 Å²	0 Å²
2-	-	-0.12 Å²	0 Å²
3-	-	-	0.18 Å²

Refinement step

Cycle: LAST / Resolution: 2.25→39.37 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4412	0	59	380	4851

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.015	0.02	4593
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	3130
X-RAY DIFFRACTION	r_angle_refined_deg	1.494	1.952	6205
X-RAY DIFFRACTION	r_angle_other_deg	0.943	3	7611
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.271	5	552
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	32.723	24.558	226
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.744	15	797
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	14.413	15	24
X-RAY DIFFRACTION	r_chiral_restr	0.087	0.2	657
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.02	5120
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	962
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it
X-RAY DIFFRACTION	r_scbond_it
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2.25→2.308 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.264	103	-
R_work	0.192	2256	-
obs	-	-	100 %

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	0.5112	-0.1162	-0.0596	0.3762	-0.0558	0.3444	0.0581	-0.0181	-0.0162	0.0288	-0.0674	-0.0733	0.033	0.0305	0.0093	0.1272	-0.0654	-0.0236	0.0708	0.018	0.0928	7.2077	53.8551	6.5653
2	0.9097	0.1384	0.3939	0.6834	0.2198	1.5294	0.0096	-0.0433	0.0486	-0.1521	-0.0047	0.0833	0.0366	-0.3324	-0.0049	0.1055	-0.056	0.0001	0.1023	0.0129	0.1003	-28.0223	70.2795	-5.9462
3	4.038	-0.858	0.0034	0.2642	-0.2717	0.9258	-0.1104	0.678	-0.2972	0.0316	-0.1148	-0.0049	0.0117	-0.0082	0.2252	0.1309	-0.0428	0.0224	0.1721	-0.0835	0.1055	-3.4783	68.082	-13.1143
4	0.679	0.1628	0.5139	0.1353	0.1324	0.5934	-0.0299	0.0288	0.06	0.0008	0.0217	0.0241	-0.0159	-0.0479	0.0082	0.1516	-0.0707	0.0275	0.0595	0.0062	0.1261	-14.7242	71.8874	-2.4485
5	0.9293	0.1003	0.0655	1.4584	-0.3098	0.396	0.0919	-0.1382	0.1082	0.0002	-0.0763	0.069	-0.0414	-0.0499	-0.0156	0.1464	-0.0751	0.0159	0.0713	-0.0284	0.0873	-12.9614	69.2035	10.1803

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	39 - 294
2	X-RAY DIFFRACTION	2	A	295 - 359
3	X-RAY DIFFRACTION	3	A	360 - 404
4	X-RAY DIFFRACTION	4	A	405 - 486
5	X-RAY DIFFRACTION	5	A	487 - 591

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Protein , 1 types, 1 molecules A

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Non-polymers , 6 types, 405 molecules

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Experiment

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Sample preparation

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Data collection

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Phasing

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Protein , 1 types, 1 molecules A

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Non-polymers , 6 types, 405 molecules

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