PDB-3nuz: Crystal structure of a putative acetyl xylan esterase (BF1801) fr...

ID or keywords:

Entry

Database: PDB / ID: 3nuz

Title

Crystal structure of a putative acetyl xylan esterase (BF1801) from Bacteroides fragilis NCTC 9343 at 2.30 A resolution

Components

Putative acetyl xylan esterase

Keywords

HYDROLASE / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-BIOLOGY

Function / homology

Abhydrolase, bacterial / Abhydrolase family / : / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / Abhydrolase family

Function and homology information

Biological species

Bacteroides fragilis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MAD / Resolution: 2.3 Å

Authors

Joint Center for Structural Genomics (JCSG)

Citation

Journal: To be published
Title: Crystal structure of a putative acetyl xylan esterase (BF1801) from Bacteroides fragilis NCTC 9343 at 2.30 A resolution
Authors: Joint Center for Structural Genomics (JCSG)

History

Deposition	Jul 7, 2010	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 4, 2010	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance
Revision 1.2	Jul 20, 2011	Group: Structure summary
Revision 1.3	Oct 25, 2017	Group: Author supporting evidence / Refinement description / Category: pdbx_struct_assembly_auth_evidence / software / Item: _software.classification / _software.name
Revision 1.4	Jul 3, 2019	Group: Data collection / Derived calculations / Refinement description Category: software / struct_conn Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.5	Nov 20, 2024	Group: Data collection / Database references / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ref_seq_dif Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _struct_ref_seq_dif.details

Structure viewer	Molecule: MolmilJmol/JSmol

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Validation report

Summary document	3nuz_validation.pdf.gz	450.7 KB	Display	wwPDB validaton report
Full document	3nuz_full_validation.pdf.gz	465.4 KB	Display
Data in XML	3nuz_validation.xml.gz	85.2 KB	Display
Data in CIF	3nuz_validation.cif.gz	112.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/nu/3nuz ftp://data.pdbj.org/pub/pdb/validation_reports/nu/3nuz	HTTPS FTP

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Related structure data

Similar structure data	4go3-4 6wmm-d 3byh-d 4q5j-d 6p3j-d 4brr-d 2w9z-d 3g8y-1 3k3e-d 6p3k-2 Search similar-shape structures by Omokage search (details) 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 - HomologyF&H Search
Other databases	TargetDB: 393240

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Putative acetyl xylan esterase

B: Putative acetyl xylan esterase

C: Putative acetyl xylan esterase

D: Putative acetyl xylan esterase

E: Putative acetyl xylan esterase

F: Putative acetyl xylan esterase

278 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Putative acetyl xylan esterase

B: Putative acetyl xylan esterase

defined by author&software
Evidence: gel filtration, light scattering
92.7 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: Putative acetyl xylan esterase

D: Putative acetyl xylan esterase

defined by author&software
Evidence: gel filtration, light scattering
92.7 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

E: Putative acetyl xylan esterase

F: Putative acetyl xylan esterase

defined by author&software
Evidence: gel filtration, light scattering
92.7 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	125.612, 125.612, 162.639
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	145
Space group name H-M	P3₂

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
3	1	C
4	1	D
5	1	E
6	1	F

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Refine code	Auth asym-ID	Auth seq-ID
1	1	1	1	A	25 - 53
2	1	1	1	B	25 - 53
3	1	1	1	C	25 - 53
4	1	1	1	D	25 - 53
5	1	1	1	E	25 - 53
6	1	1	1	F	25 - 53
1	2	1	3	A	54 - 89
2	2	1	3	B	54 - 89
3	2	1	3	C	54 - 89
4	2	1	3	D	54 - 89
5	2	1	3	E	54 - 89
6	2	1	3	F	54 - 89
1	3	1	3	A	90 - 114
2	3	1	3	B	90 - 114
3	3	1	3	C	90 - 114
4	3	1	3	D	90 - 114
5	3	1	3	E	90 - 114
6	3	1	3	F	90 - 114
1	4	1	1	A	115 - 130
2	4	1	1	B	115 - 130
3	4	1	1	C	115 - 130
4	4	1	1	D	115 - 130
5	4	1	1	E	115 - 130
6	4	1	1	F	115 - 130
1	5	1	3	A	131 - 132
2	5	1	3	B	131 - 132
3	5	1	3	C	131 - 132
4	5	1	3	D	131 - 132
5	5	1	3	E	131 - 132
6	5	1	3	F	131 - 132
1	6	1	2	A	133 - 157
2	6	1	2	B	133 - 157
3	6	1	2	C	133 - 157
4	6	1	2	D	133 - 157
5	6	1	2	E	133 - 157
6	6	1	2	F	133 - 157
1	7	1	4	A	158 - 169
2	7	1	4	B	158 - 169
3	7	1	4	C	158 - 169
4	7	1	4	D	158 - 169
5	7	1	4	E	158 - 169
6	7	1	4	F	158 - 169
1	8	1	1	A	170 - 241
2	8	1	1	B	170 - 241
3	8	1	1	C	170 - 241
4	8	1	1	D	170 - 241
5	8	1	1	E	170 - 241
6	8	1	1	F	170 - 241
1	9	1	3	A	242 - 247
2	9	1	3	B	242 - 247
3	9	1	3	C	242 - 247
4	9	1	3	D	242 - 247
5	9	1	3	E	242 - 247
6	9	1	3	F	242 - 247
1	10	1	1	A	248 - 303
2	10	1	1	B	248 - 303
3	10	1	1	C	248 - 303
4	10	1	1	D	248 - 303
5	10	1	1	E	248 - 303
6	10	1	1	F	248 - 303
1	11	1	3	A	304 - 308
2	11	1	3	B	304 - 308
3	11	1	3	C	304 - 308
4	11	1	3	D	304 - 308
5	11	1	3	E	304 - 308
6	11	1	3	F	304 - 308
1	12	1	1	A	309 - 349
2	12	1	1	B	309 - 349
3	12	1	1	C	309 - 349
4	12	1	1	D	309 - 349
5	12	1	1	E	309 - 349
6	12	1	1	F	309 - 349
1	13	1	4	A	350 - 357
2	13	1	4	B	350 - 357
3	13	1	4	C	350 - 357
4	13	1	4	D	350 - 357
5	13	1	4	E	350 - 357
6	13	1	4	F	350 - 357
1	14	1	1	A	358 - 409
2	14	1	1	B	358 - 409
3	14	1	1	C	358 - 409
4	14	1	1	D	358 - 409
5	14	1	1	E	358 - 409
6	14	1	1	F	358 - 409
1	15	1	5	A	410 - 413
2	15	1	5	B	410 - 413
3	15	1	5	C	410 - 413
4	15	1	5	D	410 - 413
5	15	1	5	E	410 - 413
6	15	1	5	F	410 - 413

Details

CRYSTAL PACKING ANALYSIS AND SIZE-EXCLUSION CHROMATOGRAPHY COUPLED WITH STATIC LIGHT SCATTERING SUPPORT THE ASSIGNMENT OF A DIMER AS THE SIGNIFICANT OLIGOMERIC FORM IN SOLUTION.

#1: Protein	Putative acetyl xylan esterase Mass: 46372.391 Da / Num. of mol.: 6 / Fragment: sequence database residues 20-416 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacteroides fragilis (bacteria) / Strain: ATCC 25285 / NCTC 9343 / Gene: BF1801 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q5LEF1
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 253 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y
Sequence details	THIS CONSTRUCT (RESIDUES 20-416) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG ...THIS CONSTRUCT (RESIDUES 20-416) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.66 Å³/Da / Density % sol: 53.8 % Description: THE STRUCTURE WAS INITIALLY SOLVED BY MAD IN THE APPARENT SPACE GROUP P3221 WITH TWO MOLECULES PER ASYMMETRIC UNIT AND TWINNED WITH THE TWIN LAW (-H, -K, L). THE RESULTING STRUCTURE ...Description: THE STRUCTURE WAS INITIALLY SOLVED BY MAD IN THE APPARENT SPACE GROUP P3221 WITH TWO MOLECULES PER ASYMMETRIC UNIT AND TWINNED WITH THE TWIN LAW (-H, -K, L). THE RESULTING STRUCTURE SUGGESTED A THIRD MOLECULE IN THE ASYMMETRIC UNIT. HOWEVER, DENSITY FOR THIS MOLECULE WAS UNINTERPRETABLE. FURTHER EXAMINATION SUGGESTED THE CORRECT SPACE GROUP WAS P32 WITH 6 MOLECULES PER ASYMMETRIC UNIT AND 4 TWIN DOMAINS. EXPERIMENTAL PHASES WERE RECALCULATED IN THE CORRECT SPACE GROUP P32.
Crystal grow	Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4 Details: 40.0000% MPD, 0.1M Citrate pH 4.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal

Density Matthews: 2.66 Å³/Da / Density % sol: 53.8 %
Description: THE STRUCTURE WAS INITIALLY SOLVED BY MAD IN THE APPARENT SPACE GROUP P3221 WITH TWO MOLECULES PER ASYMMETRIC UNIT AND TWINNED WITH THE TWIN LAW (-H, -K, L). THE RESULTING STRUCTURE ...

Crystal grow

Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4
Details: 40.0000% MPD, 0.1M Citrate pH 4.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

SSRL

/ Beamline: BL9-2 / Wavelength: 0.91837,0.97934,0.97920

Detector

Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 14, 2009 / Details: Flat collimating mirror, toroid focusing mirror

Radiation

Monochromator: Double crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	0.91837	1
2	0.97934	1
3	0.9792	1

Reflection twin

Crystal-ID	ID	Operator	Domain-ID	Fraction
1	1	H, K, L	1	0.382
1	1	-H, H+K, -L	2	0.136
1	1	-h,-k,l	3	0.162
1	1	K, H, -L	4	0.32

Reflection

Resolution: 2.3→29.665 Å / Num. obs: 126358 / % possible obs: 81.6 % / Observed criterion σ(I): -3 / B_iso Wilson estimate: 36.371 Å² / R_merge(I) obs: 0.09 / Net I/σ(I): 8

Reflection shell

Resolution (Å)	R_merge(I) obs	Mean I/σ(I) obs	Num. measured obs	Num. unique obs	Diffraction-ID	% possible all
2.3-2.38	0.495	1.4	22823	18492	1	74.4
2.38-2.48	0.416	1.7	25729	20938	1	78.3
2.48-2.59	0.325	2	23923	19634	1	79
2.59-2.73	0.244	2.5	25095	20822	1	79.8
2.73-2.9	0.179	3.5	24462	20432	1	80.6
2.9-3.12	0.123	5	24236	20474	1	81.8
3.12-3.43	0.075	7.8	24540	20979	1	83
3.43-3.93	0.044	12.7	25065	21782	1	84.4
3.93-4.93	0.027	18.3	24568	21755	1	86.3
4.93-29.665	0.022	21.7	25120	22946	1	88.5

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Phasing

Phasing	Method: MAD

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Processing

Software

Name	Version	Classification
REFMAC	5.5.0110	refinement
MolProbity	3beta29	model building
PHENIX		refinement
SHELX		phasing
XSCALE		data scaling
PDB_EXTRACT	3.006	data extraction
XDS		data reduction
SHELXD		phasing
autoSHARP		phasing

Refinement

Method to determine structure:

MAD / Resolution: 2.3→29.665 Å / Cor.coef. F_o:F_c: 0.957 / Cor.coef. F_o:F_c free: 0.938 / Occupancy max: 1 / Occupancy min: 0.2 / SU B: 8.385 / SU ML: 0.098 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.05 / ESU R Free: 0.036 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: 1.HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2.A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.182	6616	5.2 %	THIN SHELLS
R_work	0.152	-	-	-
obs	0.153	126305	99.23 %	-

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: 72.44 Å² / B_iso mean: 33.793 Å² / B_iso min: 5.6 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	10.11 Å²	0 Å²	0 Å²
2-	-	10.11 Å²	0 Å²
3-	-	-	-20.22 Å²

Refinement step

Cycle: LAST / Resolution: 2.3→29.665 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	18820	0	0	253	19073

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.009	0.022	19407
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	13638
X-RAY DIFFRACTION	r_angle_refined_deg	1.44	1.967	26346
X-RAY DIFFRACTION	r_angle_other_deg	0.97	3	33023
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	3.084	5	2329
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	27.571	23.24	932
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	10.966	15	3256
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	9.547	15	153
X-RAY DIFFRACTION	r_chiral_restr	0.09	0.2	2766
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.021	21478
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	4109
X-RAY DIFFRACTION	r_mcbond_it	0.791	3	11667
X-RAY DIFFRACTION	r_mcbond_other	0.334	3	4622
X-RAY DIFFRACTION	r_mcangle_it	1.307	5	18908
X-RAY DIFFRACTION	r_scbond_it	2.628	8	7740
X-RAY DIFFRACTION	r_scangle_it	3.395	11	7430

Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	A	4196	TIGHT POSITIONAL	0.23	0.05
2	B	4196	TIGHT POSITIONAL	0.23	0.05
3	C	4196	TIGHT POSITIONAL	0.25	0.05
4	D	4196	TIGHT POSITIONAL	0.24	0.05
5	E	4196	TIGHT POSITIONAL	0.23	0.05
6	F	4196	TIGHT POSITIONAL	0.23	0.05
1	A	387	MEDIUM POSITIONAL	0.39	0.5
2	B	387	MEDIUM POSITIONAL	0.39	0.5
3	C	387	MEDIUM POSITIONAL	0.32	0.5
4	D	387	MEDIUM POSITIONAL	0.37	0.5
5	E	387	MEDIUM POSITIONAL	0.4	0.5
6	F	387	MEDIUM POSITIONAL	0.28	0.5
1	A	674	LOOSE POSITIONAL	0.42	5
2	B	674	LOOSE POSITIONAL	0.48	5
3	C	674	LOOSE POSITIONAL	0.45	5
4	D	674	LOOSE POSITIONAL	0.4	5
5	E	674	LOOSE POSITIONAL	0.39	5
6	F	674	LOOSE POSITIONAL	0.4	5
1	A	4196	TIGHT THERMAL	0.48	0.5
2	B	4196	TIGHT THERMAL	0.5	0.5
3	C	4196	TIGHT THERMAL	0.5	0.5
4	D	4196	TIGHT THERMAL	0.5	0.5
5	E	4196	TIGHT THERMAL	0.45	0.5
6	F	4196	TIGHT THERMAL	0.46	0.5
1	A	387	MEDIUM THERMAL	0.44	2
2	B	387	MEDIUM THERMAL	0.39	2
3	C	387	MEDIUM THERMAL	0.4	2
4	D	387	MEDIUM THERMAL	0.41	2
5	E	387	MEDIUM THERMAL	0.46	2
6	F	387	MEDIUM THERMAL	0.36	2
1	A	674	LOOSE THERMAL	0.48	10
2	B	674	LOOSE THERMAL	0.45	10
3	C	674	LOOSE THERMAL	0.49	10
4	D	674	LOOSE THERMAL	0.44	10
5	E	674	LOOSE THERMAL	0.41	10
6	F	674	LOOSE THERMAL	0.44	10

LS refinement shell

Resolution: 2.301→2.36 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_work	0.163	9066	-
obs	-	-	96.33 %

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	0.5642	0.2245	-0.0158	0.8554	0.165	0.9026	-0.0372	0.0137	-0.1134	0.0258	0.0036	0.0051	0.2129	-0.0151	0.0336	0.0846	-0.0143	-0.0006	0.0081	-0.0024	0.0623	53.5174	-52.3946	34.4374
2	0.4979	0.2326	0.0348	0.8842	0.2279	0.8011	-0.0055	0.0325	0.0837	-0.0213	0.0478	-0.077	-0.1441	0.1781	-0.0423	0.0727	-0.0442	0.0097	0.0551	-0.0177	0.0756	71.3249	-19.6992	26.2958
3	0.5705	0.3187	-0.1098	0.5558	-0.0273	0.8117	-0.0098	0.0247	-0.0596	0.001	0.0048	0.0916	0.1266	-0.1527	0.0049	0.0633	-0.0374	-0.0019	0.0458	0.0097	0.0713	53.4167	20.2093	21.1636
4	0.4981	0.2185	-0.0244	0.8825	-0.1649	0.7882	0.0276	-0.0093	0.1201	0.0702	0.0072	-0.0029	-0.2068	0.0515	-0.0348	0.0959	-0.0289	0.0231	0.0199	0.001	0.0534	72.8938	51.9931	29.259
5	0.5833	-0.0666	-0.0284	0.1911	-0.0314	0.4232	-0.0254	0.0084	-0.0335	0.0176	0.0207	-0.0502	0.0335	0.0402	0.0047	0.1295	-0.0153	0.0023	0.09	-0.006	0.2319	15.5589	-10.3202	36.8891
6	0.3392	-0.2119	-0.0807	0.5472	0.0554	0.467	0.0348	0.0086	-0.0133	0.0198	0.0008	0.1159	-0.0174	-0.1118	-0.0356	0.1131	-0.031	0.006	0.1208	0.0118	0.2321	-16.0584	9.6118	28.5767

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	25 - 415
2	X-RAY DIFFRACTION	2	B	25 - 415
3	X-RAY DIFFRACTION	3	C	25 - 415
4	X-RAY DIFFRACTION	4	D	25 - 415
5	X-RAY DIFFRACTION	5	E	25 - 413
6	X-RAY DIFFRACTION	6	F	25 - 413

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+About Yorodumi

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-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

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Movie

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Structure viewers

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Viewer log

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This page

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This web site

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Options

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Open data

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Basic information

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Structure visualization

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Downloads & links

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Download

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Validation report

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Related structure data

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Links

-
Assembly

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Components

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Experimental details

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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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Processing

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About Yorodumi

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News

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Feb 9, 2022. New format data for meta-information of EMDB entries

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Aug 12, 2020. Covid-19 info

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Mar 5, 2020. Novel coronavirus structure data

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Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

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Jul 12, 2017. Major update of PDB

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Yorodumi