PDB-3u7v: The structure of a putative Beta-galactosidase from Caulobacter c...

ID or keywords:

Entry

Database: PDB / ID: 3u7v

Title

The structure of a putative Beta-galactosidase from Caulobacter crescentus CB15.

Components

Beta-galactosidase

Keywords

HYDROLASE /

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

TIM barrel / Glyco_hydro_42 / Carbohydrate transport and metabolism

Function / homology

Function and homology information

beta-galactosidase complex /

beta-galactosidase /

beta-galactosidase activity / carbohydrate metabolic process
Similarity search - Function

Biological species

Caulobacter crescentus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.8 Å

Authors

Cuff, M.E. / Tesar, C. / Clancy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)

Citation

Journal: TO BE PUBLISHED
Title: The structure of a putative Beta-galactosidase from Caulobacter crescentus CB15.
Authors: Cuff, M.E. / Tesar, C. / Clancy, S. / Joachimiak, A.

History

Deposition	Oct 14, 2011	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Dec 21, 2011	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	3u7v.cif.gz	213.3 KB	Display	PDBx/mmCIF format
PDB format	pdb3u7v.ent.gz	175.9 KB	Display	PDB format
PDBx/mmJSON format	3u7v.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/u7/3u7v ftp://data.pdbj.org/pub/pdb/validation_reports/u7/3u7v	HTTPS FTP

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Related structure data

Similar structure data	7ly3-d 4dy7-d 1v4j-2 1vg6-3 1v4i-2 6umx-d 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
Other databases	TargetDB: apc100071

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#198 - Jun 2016 Beta-galactosidase similarity (1) #39 - Mar 2003 lac Repressor similarity (1) #4 - Apr 2000 Collagen similarity (1) #116 - Aug 2009 Sulfotransferases similarity (1)

Deposited unit

A: Beta-galactosidase

hetero molecules

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

1

A: Beta-galactosidase

hetero molecules

A: Beta-galactosidase

hetero molecules

A: Beta-galactosidase

hetero molecules

A: Beta-galactosidase

hetero molecules

defined by software
245 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	148.306, 148.306, 53.792
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	79
Space group name H-M	I4

Details

likely the tetramer formed in the crystal x,y,z , y,-x,z , -y,x,z , -x,-y,z

#1: Protein	Beta-galactosidase / Mass: 61114.258 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Caulobacter crescentus (bacteria) / Strain: NA1000 / Gene: CCNA_00830, LacA / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) magic References: UniProt: B8H1H2, UniProt: A0A0H3C5N2*PLUS, beta-galactosidase
#2: Chemical	ChemComp-ACY / ACETIC ACID / Acetic acid Mass: 60.052 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂H₄O₂
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 427 / 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: 2.42 Å³/Da / Density % sol: 49.17 %
Crystal grow	Temperature: 297 K / Method: vapor diffusion, sitting drop / pH: 5.6 Details: 0.17 Amonium sulfate, 0.085 sodium citrate: HCl pH 5.6, 25.5% PEG 4K, 15% glycerol, 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-ID / Wavelength: 0.97912 Å

Detector

Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 11, 2010

Radiation

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

Radiation wavelength

Wavelength: 0.97912 Å / Relative weight: 1

Reflection

Redundancy: 7.8 % / Av σ(I) over netI: 21.84 / Number: 422096 / R_merge(I) obs: 0.116 / Χ²: 1.21 / D res high: 1.8 Å / D res low: 50 Å / Num. obs: 54354 / % possible obs: 100

Diffraction reflection shell

Highest resolution (Å)	Lowest resolution (Å)	% possible obs (%)	ID	R_merge(I) obs	Chi squared	Redundancy
4.88	50	99.5	1	0.09	2.503	7.2
3.88	4.88	100	1	0.084	2.074	7.3
3.39	3.88	100	1	0.092	2.222	7.5
3.08	3.39	99.9	1	0.102	2.178	7.7
2.86	3.08	100	1	0.109	1.841	7.8
2.69	2.86	100	1	0.114	1.6	7.8
2.55	2.69	100	1	0.118	1.427	7.9
2.44	2.55	100	1	0.125	1.255	7.9
2.35	2.44	100	1	0.137	1.165	7.9
2.27	2.35	100	1	0.144	1.078	7.9
2.2	2.27	100	1	0.152	0.944	7.9
2.13	2.2	100	1	0.162	0.909	7.9
2.08	2.13	100	1	0.176	0.842	7.9
2.03	2.08	100	1	0.189	0.757	7.9
1.98	2.03	100	1	0.212	0.688	7.9
1.94	1.98	100	1	0.24	0.624	7.9
1.9	1.94	100	1	0.284	0.576	7.9
1.86	1.9	100	1	0.305	0.555	7.8
1.83	1.86	100	1	0.357	0.533	7.9
1.8	1.83	100	1	0.398	0.51	7.8

Reflection

Resolution: 1.8→50 Å / Num. all: 54354 / Num. obs: 54354 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 7.8 % / B_iso Wilson estimate: 15.7 Å² / R_merge(I) obs: 0.116 / Χ²: 1.205 / Net I/σ(I): 7.8

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique all	Χ²	Diffraction-ID	% possible all
1.8-1.83	7.8	0.398	2725	0.51	1	100
1.83-1.86	7.9	0.357	2690	0.533	1	100
1.86-1.9	7.8	0.305	2686	0.555	1	100
1.9-1.94	7.9	0.284	2713	0.576	1	100
1.94-1.98	7.9	0.24	2694	0.624	1	100
1.98-2.03	7.9	0.212	2662	0.688	1	100
2.03-2.08	7.9	0.189	2743	0.757	1	100
2.08-2.13	7.9	0.176	2697	0.842	1	100
2.13-2.2	7.9	0.162	2685	0.909	1	100
2.2-2.27	7.9	0.152	2700	0.944	1	100
2.27-2.35	7.9	0.144	2736	1.078	1	100
2.35-2.44	7.9	0.137	2713	1.165	1	100
2.44-2.55	7.9	0.125	2702	1.255	1	100
2.55-2.69	7.9	0.118	2726	1.427	1	100
2.69-2.86	7.8	0.114	2710	1.6	1	100
2.86-3.08	7.8	0.109	2717	1.841	1	100
3.08-3.39	7.7	0.102	2736	2.178	1	99.9
3.39-3.88	7.5	0.092	2742	2.222	1	100
3.88-4.88	7.3	0.084	2764	2.074	1	100
4.88-50	7.2	0.09	2813	2.503	1	99.5

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Phasing

Phasing

Method:

SAD

Phasing MAD

D res high: 2 Å / D res low: 50 Å / FOM : 0.259 / FOM acentric: 0.274 / FOM centric: 0 / Reflection: 39779 / Reflection acentric: 37631 / Reflection centric: 2148

Phasing MAD set

R cullis acentric: 1.3 / R cullis centric: 1 / Highest resolution: 2 Å / Lowest resolution: 50 Å / Loc acentric: 0.2 / Loc centric: 0.2 / Power acentric: 0 / Power centric: 0 / Reflection acentric: 37631 / Reflection centric: 2148

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
12.5-50	1.24	0.4	0.3	127	46
7.14-12.5	1.22	0.4	0.3	631	112
5-7.14	1.3	0.3	0.3	1547	174
3.85-5	0.94	0.3	0.3	2839	242
3.13-3.85	1.05	0.3	0.3	4580	298
2.63-3.13	1.45	0.2	0.2	6654	363
2.27-2.63	1.52	0.2	0.1	9166	427
2-2.27	1.5	0.1	0.1	12087	486

Phasing MAD set site

Atom type symbol: Se / Occupancy iso: 0

ID	B iso	Fract x	Fract y	Fract z	Occupancy
1	15.5346	0.003	0.65	0.09	2.163
2	14.8544	0.881	0.655	0.286	2.302
3	19.1011	0.234	0.192	0.321	2.117
4	15.5111	0.667	0.012	0.004	1.989
5	8.575	0.29	0.55	0.495	1.779
6	15.8081	0.688	0.881	0.037	1.978
7	27.0516	0.044	0.704	0.131	2.027
8	15.0751	0.271	0.05	0.116	1.786
9	14.7617	0.809	0.862	0.131	1.795
10	8.6164	0.771	0.157	0.293	1.671
11	17.147	0.708	0.153	0.268	1.787
12	12.3481	0.542	0.162	0.445	1.783
13	15.1181	0.739	0.181	0.384	1.814
14	30.7869	0.981	0.245	0.505	1.759
15	30.7577	0.176	0.004	0.208	1.282
16	44.715	0.249	0.194	0.369	0.637
17	53.636	0.841	0.664	0.301	0.571
18	29.882	0.415	0.639	0.005	0.432
19	25.721	0.788	0.873	0.129	0.362
20	44.095	0.223	0.075	0.016	0.496
21	24.054	0.237	0.564	0.077	0.264
22	50.661	0.26	0.03	0.134	0.46
23	24.987	0.363	0.049	0.088	0.272

Phasing MAD shell

Resolution (Å)	FOM	FOM acentric	Reflection	Reflection acentric	Reflection centric
12.5-50	0.25	0.34	173	127	46
7.14-12.5	0.277	0.326	743	631	112
5-7.14	0.337	0.375	1721	1547	174
3.85-5	0.285	0.31	3081	2839	242
3.13-3.85	0.27	0.287	4878	4580	298
2.63-3.13	0.312	0.329	7017	6654	363
2.27-2.63	0.273	0.286	9593	9166	427
2-2.27	0.196	0.204	12573	12087	486

Phasing dm

Method: Solvent flattening and Histogram matching / Reflection: 54349

Phasing dm shell

Resolution (Å)	Delta phi final	FOM	Reflection
8.68-100	66.9	0.756	524
6.48-8.68	64.6	0.906	708
5.4-6.48	62.1	0.918	865
4.72-5.4	63	0.937	1015
4.25-4.72	59.7	0.951	1141
3.9-4.25	63	0.941	1239
3.62-3.9	61	0.936	1352
3.39-3.62	64.3	0.942	1429
3.21-3.39	65.8	0.928	1545
3.05-3.21	61.9	0.928	1607
2.91-3.05	62.1	0.919	1682
2.79-2.91	62.8	0.923	1751
2.68-2.79	62.4	0.927	1849
2.58-2.68	65.1	0.929	1876
2.5-2.58	64.9	0.917	1994
2.42-2.5	64.5	0.925	2030
2.35-2.42	65.5	0.92	2077
2.28-2.35	64.6	0.915	2171
2.22-2.28	67.5	0.92	2208
2.17-2.22	69	0.918	2251
2.12-2.17	71	0.914	2365
2.07-2.12	71.3	0.913	2325
2.02-2.07	72.2	0.917	2468
1.98-2.02	79.9	0.903	2477
1.94-1.98	89.3	0.902	2536
1.9-1.94	90.8	0.87	2580
1.87-1.9	88.4	0.838	2620
1.84-1.87	90.5	0.764	2658
1.8-1.84	88.9	0.567	3006

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
MLPHARE		phasing
DM	6.1	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: 1.8→36.4 Å / Cor.coef. F_o:F_c: 0.93 / Cor.coef. F_o:F_c free: 0.923 / WR_factor R_free: 0.2147 / WR_factor R_work: 0.1823 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.9067 / SU B: 4.319 / SU ML: 0.072 / SU R Cruickshank DPI: 0.1226 / SU R_free: 0.1158 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.116
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2147	2764	5.1 %	RANDOM
R_work	0.1838	-	-	-
all	0.1854	54352	-	-
obs	0.1854	54352	99.89 %	-

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: 51.46 Å² / B_iso mean: 18.6393 Å² / B_iso min: 10.53 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.78 Å²	0 Å²	0 Å²
2-	-	-0.78 Å²	0 Å²
3-	-	-	1.56 Å²

Refinement step

Cycle: LAST / Resolution: 1.8→36.4 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4015	0	8	427	4450

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.014	0.02	4153
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.02	2811
X-RAY DIFFRACTION	r_angle_refined_deg	1.515	1.945	5654
X-RAY DIFFRACTION	r_angle_other_deg	0.899	3	6817
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.412	5	520
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	34.27	23.85	187
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.555	15	638
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	18.671	15	25
X-RAY DIFFRACTION	r_chiral_restr	0.097	0.2	589
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.021	4718
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	891

LS refinement shell

Resolution: 1.801→1.847 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.246	191	-
R_work	0.171	3628	-
all	-	3819	-
obs	-	-	99.25 %

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	0.4223	0.2119	-0.0173	0.4096	0.016	0.1268	0.0037	-0.0114	0.0431	0.0184	-0.0104	-0.0032	-0.0092	0.0074	0.0067	0.027	0.0039	-0.0089	0.0139	-0.0024	0.0094	-1.4351	41.9511	13.6766
2	0.7832	0.3888	0.0217	0.517	-0.0201	0.142	-0.0199	0.0077	0.055	0.026	0.008	0.1057	0.0382	-0.038	0.012	0.0391	-0.0062	0.0005	0.0302	-0.0081	0.0326	-29.068	24.0893	13.0444

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	33 - 460
2	X-RAY DIFFRACTION	2	A	461 - 549

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