PDB-3k1u: Beta-xylosidase, family 43 glycosyl hydrolase from Clostridium ac...

ID or keywords:

Entry

Database: PDB / ID: 3k1u

Title

Beta-xylosidase, family 43 glycosyl hydrolase from Clostridium acetobutylicum

Components

Beta-xylosidase, family 43 glycosyl hydrolase

Keywords

HYDROLASE / structural genomics / APC20493 / Beta-xylosidase / family 43 glycosyl hydrolase / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG

Function / homology

Function and homology information

hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate metabolic process
Similarity search - Function

Biological species

Clostridium acetobutylicum (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.55 Å

Authors

Osipiuk, J. / Wu, R. / Jedrzejczak, R. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)

Citation

Journal: To be Published
Title: X-ray crystal structure of beta-xylosidase, family 43 glycosyl hydrolase from Clostridium acetobutylicum at 1.55 A resolution
Authors: Osipiuk, J. / Wu, R. / Jedrzejczak, R. / Joachimiak, A.

History

Deposition	Sep 28, 2009	Deposition site: RCSB / Processing site: RCSB
Supersession	Oct 6, 2009	ID: 3CPN
Revision 1.0	Oct 6, 2009	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.2	Nov 1, 2017	Group: Refinement description / Category: software

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3k1u.cif.gz	90.9 KB	Display	PDBx/mmCIF format
PDB format	pdb3k1u.ent.gz	73.9 KB	Display	PDB format
PDBx/mmJSON format	3k1u.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	3k1u_validation.pdf.gz	459.7 KB	Display	wwPDB validaton report
Full document	3k1u_full_validation.pdf.gz	465.2 KB	Display
Data in XML	3k1u_validation.xml.gz	19.3 KB	Display
Data in CIF	3k1u_validation.cif.gz	29.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/k1/3k1u ftp://data.pdbj.org/pub/pdb/validation_reports/k1/3k1u	HTTPS FTP

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Related structure data

Similar structure data	1ett-d 6s5u-1 1ucy-2 1awh-2 6do3-1 3hk6-2 2pgb-d 1xmn-2 1iht-d 6do4-2 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: APC20493

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Beta-xylosidase, family 43 glycosyl hydrolase

hetero molecules

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	47.450, 59.658, 112.391
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

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Protein , 1 types, 1 molecules A

#1: Protein	Beta-xylosidase, family 43 glycosyl hydrolase Mass: 38694.867 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Clostridium acetobutylicum (bacteria) / Strain: ATCC 824 / Gene: CA_C1529 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q97IW1

#1: Protein

Beta-xylosidase, family 43 glycosyl hydrolase

Mass: 38694.867 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Clostridium acetobutylicum (bacteria) / Strain: ATCC 824 / Gene: CA_C1529 / Plasmid: pMCSG7 / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q97IW1

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Non-polymers , 5 types, 369 molecules

#2: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₂H₆O₂
#3: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Chemical	ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₄H₁₂NO₃ / Comment: pH buffer*YM
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 358 / Source method: isolated from a natural source / Formula: H₂O

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Details

Nonpolymer details	RESIDUE A801 REPRESENTS UNIDENTIFIED LIGAND, HAVING PARTIAL RESEMBLENCE TO TRIS MOLECULE.

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.06 Å³/Da / Density % sol: 40.16 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.2 M magnesium chloride, 0.1 M Hepes buffer, 25% PEG 3350, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792 Å
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 12, 2008
Radiation	Monochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9792 Å / Relative weight: 1
Reflection	Resolution: 1.55→37.2 Å / Num. all: 47116 / Num. obs: 47116 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.7 % / B_iso Wilson estimate: 24.9 Å² / R_merge(I) obs: 0.091 / Χ²: 2.313 / Net I/σ(I): 10.7
Reflection shell	Resolution: 1.55→1.58 Å / Redundancy: 4.2 % / R_merge(I) obs: 0.596 / Mean I/σ(I) obs: 2.17 / Num. unique all: 2299 / Χ²: 0.751 / % possible all: 99

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
REFMAC		refinement
PDB_EXTRACT	3.005	data extraction
SBC-Collect		data collection
HKL-3000		data reduction
HKL-3000		data scaling
SHELXD		phasing
MLPHARE		phasing
DM		phasing
SOLVE		phasing
RESOLVE		phasing
HKL-3000		phasing

Refinement

Method to determine structure:

SAD / Resolution: 1.55→37.2 Å / Cor.coef. F_o:F_c: 0.976 / Cor.coef. F_o:F_c free: 0.971 / WR_factor R_free: 0.16 / WR_factor R_work: 0.134 / Occupancy max: 1 / Occupancy min: 0.24 / FOM work R set: 0.927 / SU B: 2.386 / SU ML: 0.04 / SU R Cruickshank DPI: 0.067 / SU R_free: 0.067 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.067 / ESU R Free: 0.067 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS, U VALUES RESIDUAL ONLY.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.161	2379	5.1 %	RANDOM
R_work	0.136	-	-	-
all	0.137	47035	-	-
obs	0.137	47035	99.81 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK

Displacement parameters

B_iso max: 42.94 Å² / B_iso mean: 11.268 Å² / B_iso min: 2 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.54 Å²	0 Å²	0 Å²
2-	-	0.12 Å²	0 Å²
3-	-	-	0.42 Å²

Refinement step

Cycle: LAST / Resolution: 1.55→37.2 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2583	0	36	358	2977

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.019	0.022	2867
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	1967
X-RAY DIFFRACTION	r_angle_refined_deg	1.819	1.933	3929
X-RAY DIFFRACTION	r_angle_other_deg	1.05	3	4824
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.53	5	369
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	37.215	24.901	151
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.838	15	495
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	11.424	15	13
X-RAY DIFFRACTION	r_chiral_restr	0.128	0.2	409
X-RAY DIFFRACTION	r_gen_planes_refined	0.01	0.021	3236
X-RAY DIFFRACTION	r_gen_planes_other	0.003	0.02	587
X-RAY DIFFRACTION	r_mcbond_it	0.963	1.5	1670
X-RAY DIFFRACTION	r_mcbond_other	0.329	1.5	662
X-RAY DIFFRACTION	r_mcangle_it	1.577	2	2750
X-RAY DIFFRACTION	r_scbond_it	2.619	3	1197
X-RAY DIFFRACTION	r_scangle_it	4.047	4.5	1154

LS refinement shell

Resolution: 1.55→1.59 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.223	162	-
R_work	0.233	3226	-
all	-	3388	-
obs	-	3390	98.69 %

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	4.8665	-0.7997	0.6975	3.2501	0.0592	-1.3195	0.1047	0.6227	-0.2895	-0.5159	-0.005	-0.2423	0.0685	0.1235	-0.0997	0.1259	-0.0128	0.0858	0.1116	-0.0748	0.1305	13.6806	-9.9434	3.5786
2	1.9765	1.4727	0.4678	4.2009	-0.9599	1.6166	-0.2054	0.2847	-0.0395	-0.4377	0.0951	-0.1588	0.0136	0.0742	0.1104	0.0822	-0.0173	0.0343	0.0802	-0.0125	0.0482	18.8969	3.8049	7.9929
3	0.4511	0.1607	-0.3334	0.4489	-0.2785	0.6465	-0.0598	0.0644	-0.1454	-0.0542	0.002	-0.1029	0.0697	-0.0026	0.0578	0.0551	-0.0038	0.0277	0.0726	-0.0172	0.098	20.1623	-4.1371	11.1995
4	1.9875	-0.1379	-1.9031	-0.0024	0.417	3.4303	-0.0489	-0.1054	-0.1124	0.0635	0.0162	-0.1024	0.1078	0.1643	0.0327	0.0566	0.0046	-0.0124	0.0665	0.019	0.1208	22.5679	-2.6825	25.9673
5	1.3011	0.254	-0.2642	0.2687	-0.0342	0.3308	-0.0173	-0.0466	-0.0197	0.0257	-0.0085	-0.055	0.0085	0.0616	0.0259	0.0575	-0.0001	0.0018	0.0557	-0.0009	0.0669	16.4233	4.714	24.1263
6	0.1654	0.2196	0.0901	0.7042	-0.0107	1.0206	-0.0087	-0.028	0.0063	-0.0007	-0.0153	-0.016	-0.0783	0.0171	0.024	0.0598	0.0035	0.0058	0.0649	-0.004	0.0695	2.983	10.3229	22.8139
7	4.9993	-1.3505	-0.4955	0.4762	0.2327	1.5174	-0.0424	-0.1239	0.1674	-0.0234	0.0593	-0.1106	-0.034	0.0556	-0.0169	0.0707	-0.0204	-0.0024	0.0413	-0.0096	0.0924	11.2429	19.0094	23.3978
8	0.2581	0.3525	1.1264	3.825	3.5067	3.4536	-0.001	-0.0769	-0.0574	0.1163	-0.0333	0.183	0.0206	-0.1194	0.0343	0.0691	0.0073	0.0089	0.0711	-0.0034	0.0773	-2.9322	13.4633	22.101
9	0.4254	-0.7858	0.7229	2.9907	0.1679	3.8991	-0.046	-0.0561	-0.1241	0.0047	-0.0581	0.1392	0.0759	-0.2223	0.1041	0.0379	-0.0134	0.0088	0.0856	-0.0156	0.0848	-10.7416	0.3963	17.3341
10	0.0587	-0.209	0.346	0.1201	0.472	0.6471	0.0222	0.0149	-0.0313	0.0255	-0.0327	0.0333	0.0875	-0.0163	0.0105	0.0638	-0.0038	0.007	0.0643	-0.0028	0.0711	-2.3749	0.6709	17.1203
11	0.3263	0.7349	-0.656	2.6523	-1.2665	1.556	0.0564	0.0796	-0.0427	-0.0399	-0.0795	0.0581	-0.0602	-0.0069	0.0231	0.0634	0.0017	0.0012	0.0805	-0.0048	0.0564	-0.2965	7.3025	8.697
12	0.4548	-0.1174	-0.2145	1.076	0.4109	0.7564	-0.0113	0.0357	-0.0092	-0.1032	-0.0121	0.0622	-0.0581	-0.0984	0.0233	0.0583	-0.0038	-0.0033	0.0724	-0.0088	0.0531	-4.3455	8.0215	11.4463
13	10.1505	-9.1776	-2.2131	6.9542	4.1072	7.4223	-0.0287	0.0136	-0.8426	0.1091	-0.1823	0.803	0.5031	-0.7683	0.211	0.1629	-0.0831	-0.0167	0.0937	-0.0901	0.1628	-2.5916	-13.4298	3.4129
14	0.4981	-0.0689	0.3432	-0.1071	0.0213	-0.0088	-0.0281	0.1034	-0.0456	-0.0554	0.0179	0.0014	-0.0002	0.0023	0.0101	0.0935	-0.0229	0.0231	0.0753	-0.0355	0.0684	7.5992	-3.5307	5.3053
15	0.4243	0.6724	-0.0213	1.7783	-1.3542	1.9804	0.0294	-0.025	-0.1392	-0.0579	-0.028	-0.1123	0.12	-0.0041	-0.0014	0.0651	-0.0064	0.0182	0.0437	-0.0103	0.0881	6.8234	-13.7893	15.5747
16	0.3105	-0.4288	0.0335	2.9162	-2.734	1.4321	-0.0682	0.1634	-0.0572	-0.1112	0.1801	0.1188	0.1285	-0.1522	-0.1119	0.1163	-0.0331	-0.0178	0.1181	-0.0136	0.0282	-0.9026	4.5552	-2.6023
17	10.7867	-12.2218	5.8773	33.4517	-0.6238	12.5667	0.5876	1.0072	-0.3121	-1.4405	-0.3476	-1.2806	0.7515	1.3359	-0.24	0.2128	0.0048	0.1085	0.2112	-0.113	0.1705	8.1624	-14.2011	0.6063

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	5 - 13
2	X-RAY DIFFRACTION	2	A	14 - 26
3	X-RAY DIFFRACTION	3	A	27 - 53
4	X-RAY DIFFRACTION	4	A	54 - 67
5	X-RAY DIFFRACTION	5	A	68 - 125
6	X-RAY DIFFRACTION	6	A	126 - 165
7	X-RAY DIFFRACTION	7	A	166 - 175
8	X-RAY DIFFRACTION	8	A	176 - 181
9	X-RAY DIFFRACTION	9	A	182 - 187
10	X-RAY DIFFRACTION	10	A	188 - 202
11	X-RAY DIFFRACTION	11	A	203 - 215
12	X-RAY DIFFRACTION	12	A	216 - 247
13	X-RAY DIFFRACTION	13	A	248 - 254
14	X-RAY DIFFRACTION	14	A	255 - 282
15	X-RAY DIFFRACTION	15	A	283 - 299
16	X-RAY DIFFRACTION	16	A	300 - 313
17	X-RAY DIFFRACTION	17	A	314 - 320

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