PDB-4wu0: Structural Analysis of C. acetobutylicum ATCC 824 Glycoside Hydro...

ID or keywords:

Entry

Database: PDB / ID: 4wu0

Title

Structural Analysis of C. acetobutylicum ATCC 824 Glycoside Hydrolase From Family 105

Components

Similar to yteR (Bacilus subtilis)

Keywords

HYDROLASE / Pectin / Rhamnogalacturonan / unsaturated rhamnogalacturonan hydrolase / glycoside hydrolase / YteR

Function / homology

Function and homology information

catalytic activity
Similarity search - Function

Biological species

Clostridium acetobutylicum (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.6 Å

Authors

Germane, K.L. / Servinsky, M.D. / Gerlach, E.S. / Sund, C.J. / Hurley, M.M.

Citation

Journal: Acta Crystallogr.,Sect.F / Year: 2015
Title: Structural analysis of Clostridium acetobutylicum ATCC 824 glycoside hydrolase from CAZy family GH105.
Authors: Germane, K.L. / Servinsky, M.D. / Gerlach, E.S. / Sund, C.J. / Hurley, M.M.

History

Deposition	Oct 30, 2014	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jul 8, 2015	Provider: repository / Type: Initial release
Revision 1.1	Aug 12, 2015	Group: Database references
Revision 1.2	Aug 26, 2015	Group: Database references / Other
Revision 1.3	Sep 27, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	4wu0.cif.gz	434.4 KB	Display	PDBx/mmCIF format
PDB format	pdb4wu0.ent.gz	365.4 KB	Display	PDB format
PDBx/mmJSON format	4wu0.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	4wu0_validation.pdf.gz	422.4 KB	Display	wwPDB validaton report
Full document	4wu0_full_validation.pdf.gz	425.1 KB	Display
Data in XML	4wu0_validation.xml.gz	33.8 KB	Display
Data in CIF	4wu0_validation.cif.gz	53.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/wu/4wu0 ftp://data.pdbj.org/pub/pdb/validation_reports/wu/4wu0	HTTPS FTP

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Related structure data

Related structure data	1nc5S S: Starting model for refinement
Similar structure data	4ax6-1 3ewf-3 3h7k-d 4b7n-d 2htr-d 2ahf-2 1qk2-2 3rqd-1 3h7c-d 2htu-d Search similar-shape structures by Omokage search (details) 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

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#74 - Feb 2006 alpha-Amylase similarity (2)

Deposited unit

A: Similar to yteR (Bacilus subtilis)

B: Similar to yteR (Bacilus subtilis)

83.4 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Similar to yteR (Bacilus subtilis)

defined by author&software
41.7 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Similar to yteR (Bacilus subtilis)

defined by author&software
41.7 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	53.291, 93.601, 156.717
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Similar to yteR (Bacilus subtilis) Mass: 41706.527 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Clostridium acetobutylicum (bacteria) Strain: ATCC 824 / DSM 792 / JCM 1419 / LMG 5710 / VKM B-1787 Gene: CA_C0359 / Plasmid: pTXB1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q97M41
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 835 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

Similar to yteR (Bacilus subtilis)

Mass: 41706.527 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Clostridium acetobutylicum (bacteria)
Strain: ATCC 824 / DSM 792 / JCM 1419 / LMG 5710 / VKM B-1787
Gene: CA_C0359 / Plasmid: pTXB1 / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q97M41

#2: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 835 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION

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Sample preparation

Crystal	Density Matthews: 2.34 Å³/Da / Density % sol: 47.5 %
Crystal grow	Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.75 / Details: 0.1 M TRIS, 16% w/v polyethylene glycol 4,000

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 12, 2013
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.075 Å / Relative weight: 1
Reflection	Resolution: 1.6→19.9 Å / Num. obs: 103657 / % possible obs: 99.82 % / Redundancy: 5.7 % / R_merge(I) obs: 0.086 / Net I/av σ(I): 12.7 / Net I/σ(I): 29.345
Reflection shell	Redundancy: 3.2 % / R_merge(I) obs: 0.611 / Mean I/σ(I) obs: 4.511 / Num. measured all: 10151

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Processing

Software

Name: PHENIX / Version: (phenix.refine: 1.8.2_1309) / Classification: refinement

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB entry 1NC5

1nc5

Resolution: 1.6→19.9 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 13.81 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1628	5177	4.99 %
R_work	0.1365	-	-
obs	0.1378	103657	99.82 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 1.6→19.9 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5872	0	0	835	6707

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009	6012
X-RAY DIFFRACTION	f_angle_d	1.225	8122
X-RAY DIFFRACTION	f_dihedral_angle_d	13.114	2224
X-RAY DIFFRACTION	f_chiral_restr	0.074	868
X-RAY DIFFRACTION	f_plane_restr	0.007	1020

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 (%)
1.6-1.6196	0.2248	156	0.1944	3165	X-RAY DIFFRACTION	97
1.6196-1.6387	0.2591	160	0.1962	3253	X-RAY DIFFRACTION	100
1.6387-1.6586	0.2323	176	0.1906	3241	X-RAY DIFFRACTION	100
1.6586-1.6796	0.204	178	0.1823	3204	X-RAY DIFFRACTION	99
1.6796-1.7017	0.234	186	0.175	3237	X-RAY DIFFRACTION	100
1.7017-1.725	0.2202	153	0.1659	3277	X-RAY DIFFRACTION	100
1.725-1.7497	0.1943	201	0.161	3184	X-RAY DIFFRACTION	100
1.7497-1.7758	0.1814	190	0.1528	3283	X-RAY DIFFRACTION	100
1.7758-1.8035	0.1672	176	0.1467	3213	X-RAY DIFFRACTION	100
1.8035-1.833	0.1892	201	0.1448	3245	X-RAY DIFFRACTION	100
1.833-1.8646	0.197	164	0.1376	3263	X-RAY DIFFRACTION	100
1.8646-1.8985	0.1562	167	0.1341	3259	X-RAY DIFFRACTION	100
1.8985-1.935	0.1757	186	0.1338	3231	X-RAY DIFFRACTION	100
1.935-1.9744	0.1665	186	0.1345	3286	X-RAY DIFFRACTION	100
1.9744-2.0173	0.1732	175	0.1262	3231	X-RAY DIFFRACTION	100
2.0173-2.0642	0.1465	161	0.1217	3297	X-RAY DIFFRACTION	100
2.0642-2.1158	0.1619	162	0.1177	3288	X-RAY DIFFRACTION	100
2.1158-2.1729	0.1459	161	0.1173	3266	X-RAY DIFFRACTION	100
2.1729-2.2368	0.1448	170	0.1139	3304	X-RAY DIFFRACTION	100
2.2368-2.3089	0.1477	185	0.1114	3269	X-RAY DIFFRACTION	100
2.3089-2.3913	0.1411	183	0.1142	3257	X-RAY DIFFRACTION	100
2.3913-2.4868	0.147	155	0.1194	3295	X-RAY DIFFRACTION	100
2.4868-2.5998	0.1505	158	0.1217	3319	X-RAY DIFFRACTION	100
2.5998-2.7365	0.1535	149	0.1203	3327	X-RAY DIFFRACTION	100
2.7365-2.9075	0.1574	158	0.125	3343	X-RAY DIFFRACTION	100
2.9075-3.1312	0.1696	160	0.1335	3338	X-RAY DIFFRACTION	100
3.1312-3.4448	0.164	179	0.1374	3329	X-RAY DIFFRACTION	100
3.4448-3.94	0.1487	179	0.1267	3358	X-RAY DIFFRACTION	100
3.94-4.9514	0.1369	187	0.1294	3376	X-RAY DIFFRACTION	100
4.9514-19.9358	0.1817	175	0.1912	3540	X-RAY DIFFRACTION	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	1.9335	0.4406	0.255	1.311	0.3042	1.6797	-0.0168	-0.0287	0.1418	0.0139	0.0748	-0.0087	-0.136	0.07	-0.0434	0.1552	-0.0051	-0.0033	0.1316	0.0063	0.1484	26.409	56.8941	26.4825
2	2.4805	0.4155	0.0177	2.3109	0.0074	1.2204	-0.0887	0.0242	0.4242	-0.0717	0.0855	0.3067	-0.1954	-0.2506	0.0152	0.1595	0.0246	0.0051	0.1956	0.0449	0.1794	12.5809	57.6678	26.5805
3	1.8248	0.5688	-0.1399	2.5887	0.6859	1.5116	0.0153	-0.09	0.1116	0.1173	-0.0527	0.2656	0.0247	-0.1929	0.0497	0.1229	-0.0018	0.0054	0.1871	0.0296	0.1605	8.8993	46.8175	30.5103
4	0.9837	-0.1941	-0.4693	0.9551	0.3441	1.5706	-0.0752	0.0147	-0.1198	-0.008	0.0178	0.0678	0.208	-0.1269	0.0651	0.1578	-0.0337	0.0054	0.1478	0.0244	0.1717	16.2233	32.3252	24.3762
5	1.69	0.0804	-1.0419	0.8497	-0.2386	1.976	-0.0932	-0.2039	-0.1325	0.0578	0.0607	0.0453	0.1702	0.0592	0.0101	0.1589	0.0006	-0.0039	0.1639	0.0292	0.1362	25.1241	33.9056	33.7322
6	1.1685	0.0912	-0.3084	0.7714	-0.4369	1.8254	-0.0469	-0.0755	-0.0118	0.0447	0.0232	-0.122	0.0839	0.2308	0.027	0.1123	0.0177	-0.0057	0.1643	0.0089	0.1402	37.5038	40.165	25.3002
7	3.1716	2.8302	1.0401	5.0863	1.8812	1.7928	-0.1438	0.0422	0.1452	-0.2348	0.0534	0.162	-0.1119	0.0335	0.1002	0.1618	-0.0147	-0.0047	0.1486	0.0311	0.1066	28.2353	48.5156	13.2553
8	0.7023	0.0027	0.1316	0.9757	0.3954	0.9587	-0.0641	-0.0554	0.0159	0.0334	0.0389	-0.0105	0.036	0.0107	0.0204	0.1458	-0.0162	0.0042	0.1504	0.0286	0.1313	30.3095	45.5445	20.3478
9	1.1837	0.005	0.0923	2.8554	0.6289	2.1539	0.0503	0.0679	-0.1512	0.0133	0.0131	-0.0054	0.2191	-0.0723	-0.0483	0.1494	-0.0216	-0.0139	0.1429	-0.0106	0.1479	27.3118	44.0618	-12.6374
10	1.6945	-0.1276	0.254	3.2427	0.2339	1.279	0.1267	0.0836	-0.0605	-0.1323	-0.2361	0.3164	0.0357	-0.2842	0.106	0.1425	-0.0021	-0.0067	0.2097	-0.0072	0.124	20.2771	54.867	-17.3786
11	1.3374	0.6157	0.5903	1.377	0.7363	1.4083	-0.0077	0.1355	0.0608	-0.104	0.009	0.1118	-0.0584	-0.0437	0.001	0.1473	0.0087	0.0019	0.1548	0.0195	0.1336	31.8973	63.6268	-18.1659
12	0.741	0.0036	-0.3345	0.9447	0.3341	1.5472	0.0262	0.0405	0.0071	-0.0246	0.0402	-0.0941	-0.1071	0.0153	-0.0657	0.1162	-0.0065	0.0054	0.1213	0.0022	0.1428	46.1082	63.3495	-10.4877
13	1.1789	-0.9103	1.6321	2.2845	-2.9617	7.5656	-0.0208	0.0766	-0.0593	0.0143	-0.0537	-0.242	-0.0628	0.3818	0.083	0.1337	-0.0002	0.0169	0.148	-0.0226	0.1914	53.397	54.0797	-13.2824
14	0.7796	0.1372	-0.0949	1.0032	0.3	1.1972	0.0081	0.0089	-0.1076	0.0448	0.0163	-0.087	0.1679	0.0549	-0.0229	0.1301	0.0071	-0.0079	0.0941	0.0103	0.1257	40.8796	46.0618	-3.5185

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	( CHAIN A AND RESID 2:41 )	A	2 - 41
2	X-RAY DIFFRACTION	2	( CHAIN A AND RESID 42:73 )	A	42 - 73
3	X-RAY DIFFRACTION	3	( CHAIN A AND RESID 74:117 )	A	74 - 117
4	X-RAY DIFFRACTION	4	( CHAIN A AND RESID 118:198 )	A	118 - 198
5	X-RAY DIFFRACTION	5	( CHAIN A AND RESID 199:240 )	A	199 - 240
6	X-RAY DIFFRACTION	6	( CHAIN A AND RESID 241:305 )	A	241 - 305
7	X-RAY DIFFRACTION	7	( CHAIN A AND RESID 306:328 )	A	306 - 328
8	X-RAY DIFFRACTION	8	( CHAIN A AND RESID 329:361 )	A	329 - 361
9	X-RAY DIFFRACTION	9	( CHAIN B AND RESID 2:41 )	B	2 - 41
10	X-RAY DIFFRACTION	10	( CHAIN B AND RESID 42:73 )	B	42 - 73
11	X-RAY DIFFRACTION	11	( CHAIN B AND RESID 74:148 )	B	74 - 148
12	X-RAY DIFFRACTION	12	( CHAIN B AND RESID 149:222 )	B	149 - 222
13	X-RAY DIFFRACTION	13	( CHAIN B AND RESID 223:240 )	B	223 - 240
14	X-RAY DIFFRACTION	14	( CHAIN B AND RESID 241:361 )	B	241 - 361

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