PDB-3h35: Structure of the uncharacterized protein ABO_0056 from the hydroc...

ID or keywords:

Entry

Database: PDB / ID: 3h35

Title

Structure of the uncharacterized protein ABO_0056 from the hydrocarbon-degrading marine bacterium Alcanivorax borkumensis SK2.

Components

uncharacterized protein ABO_0056

Keywords

structural genomics / unknown function / Alcanivorax borkumensis / ubiquitous hydrocarbon degrading bacterium / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG

Function / homology

Translation Initiation Factor IF3 - #190 / Abortive infection alpha / Abortive infection alpha / Translation Initiation Factor IF3 / 2-Layer Sandwich / Alpha Beta / S,R MESO-TARTARIC ACID / DUF4393 domain-containing protein

Function and homology information

Biological species

Alcanivorax borkumensis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MAD / Resolution: 2.15 Å

Authors

Cuff, M.E. / Evdokimova, E. / Kagan, O. / Edwards, A. / Savchenko, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)

Citation

Journal: TO BE PUBLISHED
Title: Structure of the uncharacterized protein ABO_0056 from the hydrocarbon-degrading marine bacterium Alcanivorax borkumensis SK2.
Authors: Cuff, M.E. / Evdokimova, E. / Kagan, O. / Edwards, A. / Savchenko, A. / Joachimiak, A.

History

Deposition	Apr 15, 2009	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 12, 2009	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Refinement description ...Advisory / Refinement description / Source and taxonomy / Version format compliance
Revision 1.2	Nov 1, 2017	Group: Refinement description / Category: software
Revision 1.3	Nov 27, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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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Download

PDBx/mmCIF format	3h35.cif.gz	106.3 KB	Display	PDBx/mmCIF format
PDB format	pdb3h35.ent.gz	80.1 KB	Display	PDB format
PDBx/mmJSON format	3h35.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/h3/3h35 ftp://data.pdbj.org/pub/pdb/validation_reports/h3/3h35	HTTPS FTP

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Related structure data

Similar structure data	2ynk-d 1k0a-d 2xuw-d 3ahr-d 5vog-1 3mmy-1 6wch-d 4ou9-2 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search
Other databases	TargetDB: apc40013

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: uncharacterized protein ABO_0056

B: uncharacterized protein ABO_0056

C: uncharacterized protein ABO_0056

hetero molecules

62.1 kDa, 3 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)	82.967, 82.967, 131.485
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	154
Space group name H-M	P3₂21

Details

Unknown but likely the trimer in asymmetric unit.

#1: Protein	uncharacterized protein ABO_0056 Mass: 20632.846 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Alcanivorax borkumensis (bacteria) / Strain: SK2 / Gene: ABO_0056 / Plasmid: modified p11 / Production host: Escherichia coli (E. coli) / Strain (production host): modified BL21 (DE3) / References: UniProt: Q0VTF8
#2: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₆O₂
#3: Chemical	ChemComp-SRT / S,R MESO-TARTARIC ACID Mass: 150.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₄H₆O₆
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 261 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	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: 2.11 Å³/Da / Density % sol: 41.72 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion / pH: 6 Details: 0.2M K/Na Tartrate*4H2O, 18% PEG3340, pH 6, VAPOR DIFFUSION, temperature 291K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 19-ID / Wavelength: 0.97940,0.97953

Detector

Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 6, 2009

Radiation

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

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	0.9794	1
2	0.97953	1

Reflection

Redundancy: 12 % / Av σ(I) over netI: 37.75 / Number: 351497 / R_merge(I) obs: 0.093 / Χ²: 1.34 / D res high: 2.15 Å / D res low: 50 Å / Num. obs: 29280 / % possible obs: 99.9

Diffraction reflection shell

Highest resolution (Å)	Lowest resolution (Å)	% possible obs (%)	ID	R_merge(I) obs	Chi squared	Redundancy
5.83	50	98.3	1	0.073	4.803	11
4.63	5.83	100	1	0.06	2.523	11.4
4.05	4.63	100	1	0.055	2.128	11.8
3.68	4.05	100	1	0.066	2.04	11.9
3.41	3.68	100	1	0.071	1.661	12
3.21	3.41	100	1	0.077	1.378	12.1
3.05	3.21	100	1	0.098	1.177	12.1
2.92	3.05	100	1	0.113	1.061	12.1
2.81	2.92	100	1	0.138	0.994	12.1
2.71	2.81	100	1	0.163	0.965	12.2
2.62	2.71	99.9	1	0.19	0.933	12.2
2.55	2.62	100	1	0.228	0.872	12.2
2.48	2.55	100	1	0.256	0.871	12.2
2.42	2.48	100	1	0.298	0.838	12.1
2.37	2.42	100	1	0.348	0.814	12.1
2.32	2.37	100	1	0.385	0.782	12.2
2.27	2.32	100	1	0.426	0.795	12.1
2.23	2.27	100	1	0.495	0.777	12.1
2.19	2.23	100	1	0.576	0.738	12.2
2.15	2.19	100	1	0.678	0.734	12.1

Reflection

Resolution: 2.15→50 Å / Num. all: 29280 / Num. obs: 29280 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 12 % / B_iso Wilson estimate: 37.4 Å² / R_merge(I) obs: 0.093 / Χ²: 1.34 / Net I/σ(I): 37.75

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique all	Χ²	Diffraction-ID	% possible all
2.15-2.19	12.1	0.678	1476	0.734	1	100
2.19-2.23	12.2	0.576	1422	0.738	1	100
2.23-2.27	12.1	0.495	1435	0.777	1	100
2.27-2.32	12.1	0.426	1433	0.795	1	100
2.32-2.37	12.2	0.385	1460	0.782	1	100
2.37-2.42	12.1	0.348	1418	0.814	1	100
2.42-2.48	12.1	0.298	1451	0.838	1	100
2.48-2.55	12.2	0.256	1443	0.871	1	100
2.55-2.62	12.2	0.228	1447	0.872	1	100
2.62-2.71	12.2	0.19	1449	0.933	1	99.9
2.71-2.81	12.2	0.163	1447	0.965	1	100
2.81-2.92	12.1	0.138	1454	0.994	1	100
2.92-3.05	12.1	0.113	1478	1.061	1	100
3.05-3.21	12.1	0.098	1468	1.177	1	100
3.21-3.41	12.1	0.077	1465	1.378	1	100
3.41-3.68	12	0.071	1459	1.661	1	100
3.68-4.05	11.9	0.066	1467	2.04	1	100
4.05-4.63	11.8	0.055	1515	2.128	1	100
4.63-5.83	11.4	0.06	1502	2.523	1	100
5.83-50	11	0.073	1591	4.803	1	98.3

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Phasing

Phasing

Method:

MAD

Phasing MAD

D res high: 2.15 Å / D res low: 50 Å / FOM : 0.293 / FOM acentric: 0.307 / FOM centric: 0.178 / Reflection: 29087 / Reflection acentric: 25933 / Reflection centric: 3154

Phasing MAD set

Highest resolution: 2.15 Å / Lowest resolution: 50 Å

ID	R cullis acentric	R cullis centric	Loc acentric	Loc centric	Power acentric	Power centric	Reflection acentric	Reflection centric
1	2.25	1	0.1	0.1	0	0	25933	3154
2	0.98	0.94	12.9	19	0.3	0.27	25876	3148

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	13.22-50	1.08	1	0.3	0.2	0	0	75	69
1	7.62-13.22	1.47	1	0.4	0.3	0	0	411	161
1	5.35-7.62	2.48	1	0.4	0.1	0	0	1041	257
1	4.12-5.35	1.52	1	0.2	0.1	0	0	1945	352
1	3.35-4.12	1.46	1	0.1	0.1	0	0	3138	443
1	2.83-3.35	2.55	1	0.1	0	0	0	4596	528
1	2.44-2.83	6.23	1	0.1	0	0	0	6334	629
1	2.15-2.44	9.8	1	0	0	0	0	8393	715
2	13.22-50	0.94	0.72	22.6	21.3	0.77	0.84	74	69
2	7.62-13.22	0.9	0.87	21.2	26.1	0.76	0.56	411	161
2	5.35-7.62	0.9	0.81	14.7	19.2	0.82	0.57	1041	257
2	4.12-5.35	0.98	0.93	19.8	29	0.45	0.29	1943	352
2	3.35-4.12	0.98	0.95	18.4	24.9	0.33	0.23	3138	442
2	2.83-3.35	0.98	0.97	12.8	16.8	0.31	0.22	4591	526
2	2.44-2.83	1	0.99	10.4	14.1	0.23	0.16	6318	628
2	2.15-2.44	1	1	10.5	14.6	0.13	0.09	8360	713

Phasing MAD set site

ID	Atom type symbol	B iso	Fract x	Fract y	Fract z	Occupancy
1	Se	54.12022	-0.183	-0.899	-0.164	0
2	Se	50.29788	-0.239	-0.929	-0.088	0
3	Se	79.65856	-0.195	-0.838	-0.287	0
4	Se	65.36664	-0.391	-1.009	-0.279	0
5	Se	108.12793	-0.567	-1.136	-0.196	0
6	Se	61.1647	-0.414	-1.106	-0.119	0
7	Se	59.76162	-0.38	-1.106	-0.12	0
8	Se	66.61812	-0.378	-1.008	-0.251	0
9	Se	45.52682	-0.183	-0.899	-0.165	-0.124
10	Se	45.46485	-0.239	-0.929	-0.088	-0.136
11	Se	73.60983	-0.195	-0.838	-0.287	-0.102
12	Se	50.35888	-0.392	-1.01	-0.279	-0.065
13	Se	96.33768	-0.567	-1.136	-0.197	-0.091
14	Se	63.50778	-0.414	-1.106	-0.119	-0.065
15	Se	55.09575	-0.378	-1.106	-0.121	-0.067
16	Se	74.39122	-0.379	-1.009	-0.252	-0.039

Phasing MAD shell

Resolution (Å)	FOM	FOM acentric	FOM centric	Reflection	Reflection acentric	Reflection centric
13.22-50	0.484	0.586	0.373	144	75	69
7.62-13.22	0.571	0.647	0.377	572	411	161
5.35-7.62	0.628	0.679	0.42	1298	1041	257
4.12-5.35	0.538	0.588	0.258	2297	1945	352
3.35-4.12	0.475	0.513	0.201	3581	3138	443
2.83-3.35	0.372	0.396	0.159	5124	4596	528
2.44-2.83	0.222	0.234	0.104	6963	6334	629
2.15-2.44	0.102	0.106	0.051	9108	8393	715

Phasing dm

Method: Solvent flattening and Histogram matching / Reflection: 29087

Phasing dm shell

Resolution (Å)	Delta phi final	FOM	Reflection
8.56-100	46.2	0.858	505
6.76-8.56	45.7	0.913	513
5.85-6.76	45.6	0.922	537
5.23-5.85	50.1	0.91	600
4.77-5.23	48.7	0.927	664
4.41-4.77	56.1	0.932	702
4.13-4.41	53.7	0.926	770
3.89-4.13	54.7	0.931	805
3.69-3.89	52.7	0.929	861
3.52-3.69	60.1	0.914	896
3.37-3.52	56.3	0.908	919
3.24-3.37	55.9	0.903	971
3.12-3.24	58.7	0.88	1017
3.01-3.12	62.8	0.893	1045
2.92-3.01	66.8	0.881	1077
2.83-2.92	68.1	0.882	1098
2.75-2.83	67.1	0.877	1126
2.68-2.75	69.6	0.881	1153
2.61-2.68	70.5	0.881	1219
2.54-2.61	75.2	0.876	1237
2.49-2.54	74.4	0.88	1255
2.43-2.49	76.9	0.883	1260
2.38-2.43	78.5	0.877	1324
2.33-2.38	78.7	0.899	1344
2.29-2.33	82.6	0.881	1348
2.24-2.29	82	0.907	1380
2.2-2.24	86.7	0.904	1444
2.15-2.2	84.6	0.854	2017

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
MLPHARE		phasing
DM	6	phasing
REFMAC		refinement
PDB_EXTRACT	3.005	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:

MAD / Resolution: 2.15→41.49 Å / Cor.coef. F_o:F_c: 0.962 / Cor.coef. F_o:F_c free: 0.947 / WR_factor R_free: 0.204 / WR_factor R_work: 0.169 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.89 / SU B: 9.367 / SU ML: 0.111 / SU R Cruickshank DPI: 0.206 / SU R_free: 0.169 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.203 / ESU R Free: 0.169
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.212	1476	5.1 %	RANDOM
R_work	0.174	-	-	-
all	0.176	29085	-	-
obs	0.176	29085	99.91 %	-

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 max: 66.22 Å² / B_iso mean: 33.449 Å² / B_iso min: 16.76 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.74 Å²	0.37 Å²	0 Å²
2-	-	0.74 Å²	0 Å²
3-	-	-	-1.11 Å²

Refinement step

Cycle: LAST / Resolution: 2.15→41.49 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3325	0	14	261	3600

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.016	0.021	3469
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	2374
X-RAY DIFFRACTION	r_angle_refined_deg	1.501	1.972	4696
X-RAY DIFFRACTION	r_angle_other_deg	0.88	3	5734
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.353	5	438
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	33.285	22.577	163
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.137	15	599
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.567	15	38
X-RAY DIFFRACTION	r_chiral_restr	0.083	0.2	534
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	3923
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	764
X-RAY DIFFRACTION	r_mcbond_it	0.797	1.5	2152
X-RAY DIFFRACTION	r_mcbond_other	0.2	1.5	881
X-RAY DIFFRACTION	r_mcangle_it	1.501	2	3436
X-RAY DIFFRACTION	r_scbond_it	2.583	3	1317
X-RAY DIFFRACTION	r_scangle_it	4.122	4.5	1260

LS refinement shell

Resolution: 2.15→2.206 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.223	107	-
R_work	0.191	1985	-
all	-	2092	-
obs	-	-	99.9 %

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	1.3832	-0.0451	-0.644	0.735	0.0189	2.3791	0.0123	0.0748	-0.1321	-0.0457	-0.0268	0.0633	0.0721	-0.0603	0.0145	0.0248	-0.0258	0.0076	0.0519	-0.0445	0.0593	-16.5946	36.681	13.0583
2	2.3178	0.6136	0.2975	1.7201	0.2928	1.6608	-0.0364	0.1526	0.0838	-0.1262	0.003	-0.0162	-0.2395	0.1152	0.0333	0.0941	-0.0069	0.0288	0.0221	0.0167	0.0278	-9.7685	57.4043	15.6148
3	1.6064	-0.2956	0.2351	1.6116	0.6544	1.8806	0.0482	-0.0565	-0.0892	0.1942	0.0562	-0.0685	0.0397	0.0979	-0.1044	0.0341	-0.0113	-0.0129	0.0483	-0.0053	0.0356	-8.7633	43.5264	32.2089

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	31 - 174
2	X-RAY DIFFRACTION	2	B	36 - 174
3	X-RAY DIFFRACTION	3	C	34 - 175

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