PDB-4nx0: Crystal structure of Abp-WT, a GH27-b-L-arabinopyranosidase from ...

ID or keywords:

Entry

Database: PDB / ID: 4nx0

Title

Crystal structure of Abp-WT, a GH27-b-L-arabinopyranosidase from Geobacillus stearothermophilus

Components

Abp, a GH27 beta-L-arabinopyranosidase

Keywords

HYDROLASE / Tim Barrel / Glycoside Hydrolase

Function / homology

Golgi alpha-mannosidase II / Aldolase class I / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta / CITRIC ACID

Function and homology information

Biological species

Geobacillus stearothermophilus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.28 Å

Authors

Lansky, S. / Solomon, H.V. / Salama, R. / Belrhali, H. / Shoham, Y. / Shoham, G.

Citation

Journal: Acta Crystallogr.,Sect.D / Year: 2014
Title: Structure-specificity relationships in Abp, a GH27 beta-L-arabinopyranosidase from Geobacillus stearothermophilus T6
Authors: Lansky, S. / Salama, R. / Solomon, H.V. / Feinberg, H. / Belrhali, H. / Shoham, Y. / Shoham, G.

History

Deposition	Dec 8, 2013	Deposition site: RCSB / Processing site: PDBJ
Revision 1.0	Dec 3, 2014	Provider: repository / Type: Initial release
Revision 1.1	Nov 8, 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 / struct_ncs_dom_lim / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _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	4nx0.cif.gz	799 KB	Display	PDBx/mmCIF format
PDB format	pdb4nx0.ent.gz	654.9 KB	Display	PDB format
PDBx/mmJSON format	4nx0.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	4nx0_validation.pdf.gz	577.8 KB	Display	wwPDB validaton report
Full document	4nx0_full_validation.pdf.gz	640.1 KB	Display
Data in XML	4nx0_validation.xml.gz	175.8 KB	Display
Data in CIF	4nx0_validation.cif.gz	259.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/nx/4nx0 ftp://data.pdbj.org/pub/pdb/validation_reports/nx/4nx0	HTTPS FTP

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Related structure data

Related structure data	4nxkC 4nzfC 3cc1S S: Starting model for refinement C: citing same article (ref.)
Similar structure data	4nzf-2 4nxk-1 4nzf-1 4nxk-2 0510 2fg6-d 2exh-d 6nts-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) 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

Related structure data

4nxkC

4nzfC

3cc1S

S: Starting model for refinement

C: citing same article (ref.)

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Abp, a GH27 beta-L-arabinopyranosidase

B: Abp, a GH27 beta-L-arabinopyranosidase

C: Abp, a GH27 beta-L-arabinopyranosidase

D: Abp, a GH27 beta-L-arabinopyranosidase

E: Abp, a GH27 beta-L-arabinopyranosidase

F: Abp, a GH27 beta-L-arabinopyranosidase

G: Abp, a GH27 beta-L-arabinopyranosidase

H: Abp, a GH27 beta-L-arabinopyranosidase

hetero molecules

423 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Abp, a GH27 beta-L-arabinopyranosidase

B: Abp, a GH27 beta-L-arabinopyranosidase

C: Abp, a GH27 beta-L-arabinopyranosidase

D: Abp, a GH27 beta-L-arabinopyranosidase

hetero molecules

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

2

E: Abp, a GH27 beta-L-arabinopyranosidase

F: Abp, a GH27 beta-L-arabinopyranosidase

G: Abp, a GH27 beta-L-arabinopyranosidase

H: Abp, a GH27 beta-L-arabinopyranosidase

hetero molecules

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

3

A: Abp, a GH27 beta-L-arabinopyranosidase

B: Abp, a GH27 beta-L-arabinopyranosidase

E: Abp, a GH27 beta-L-arabinopyranosidase

F: Abp, a GH27 beta-L-arabinopyranosidase

hetero molecules

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

4

C: Abp, a GH27 beta-L-arabinopyranosidase

D: Abp, a GH27 beta-L-arabinopyranosidase

G: Abp, a GH27 beta-L-arabinopyranosidase

H: Abp, a GH27 beta-L-arabinopyranosidase

hetero molecules

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

Unit cell

Length a, b, c (Å)	107.708, 202.156, 287.289
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Component-ID: _ / Refine code: _

Dom-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	SER	SER	VAL	VAL	A	A	15 - 444	15 - 444
2	1	SER	SER	VAL	VAL	B	B	15 - 444	15 - 444
1	2	SER	SER	ALA	ALA	A	A	15 - 443	15 - 443
2	2	SER	SER	ALA	ALA	C	C	15 - 443	15 - 443
1	3	SER	SER	ALA	ALA	A	A	15 - 443	15 - 443
2	3	SER	SER	ALA	ALA	D	D	15 - 443	15 - 443
1	4	SER	SER	VAL	VAL	A	A	15 - 444	15 - 444
2	4	SER	SER	VAL	VAL	E	E	15 - 444	15 - 444
1	5	SER	SER	VAL	VAL	A	A	15 - 444	15 - 444
2	5	SER	SER	VAL	VAL	F	F	15 - 444	15 - 444
1	6	SER	SER	VAL	VAL	A	A	15 - 444	15 - 444
2	6	SER	SER	VAL	VAL	G	G	15 - 444	15 - 444
1	7	SER	SER	VAL	VAL	A	A	15 - 444	15 - 444
2	7	SER	SER	VAL	VAL	H	H	15 - 444	15 - 444
1	8	SER	SER	ALA	ALA	B	B	15 - 443	15 - 443
2	8	SER	SER	ALA	ALA	C	C	15 - 443	15 - 443
1	9	SER	SER	ALA	ALA	B	B	15 - 443	15 - 443
2	9	SER	SER	ALA	ALA	D	D	15 - 443	15 - 443
1	10	SER	SER	VAL	VAL	B	B	15 - 444	15 - 444
2	10	SER	SER	VAL	VAL	E	E	15 - 444	15 - 444
1	11	SER	SER	VAL	VAL	B	B	15 - 444	15 - 444
2	11	SER	SER	VAL	VAL	F	F	15 - 444	15 - 444
1	12	SER	SER	VAL	VAL	B	B	15 - 444	15 - 444
2	12	SER	SER	VAL	VAL	G	G	15 - 444	15 - 444
1	13	SER	SER	VAL	VAL	B	B	15 - 444	15 - 444
2	13	SER	SER	VAL	VAL	H	H	15 - 444	15 - 444
1	14	ALA	ALA	ALA	ALA	C	C	14 - 443	14 - 443
2	14	ALA	ALA	ALA	ALA	D	D	14 - 443	14 - 443
1	15	SER	SER	ALA	ALA	C	C	15 - 443	15 - 443
2	15	SER	SER	ALA	ALA	E	E	15 - 443	15 - 443
1	16	SER	SER	ALA	ALA	C	C	15 - 443	15 - 443
2	16	SER	SER	ALA	ALA	F	F	15 - 443	15 - 443
1	17	SER	SER	ALA	ALA	C	C	15 - 443	15 - 443
2	17	SER	SER	ALA	ALA	G	G	15 - 443	15 - 443
1	18	SER	SER	ALA	ALA	C	C	15 - 443	15 - 443
2	18	SER	SER	ALA	ALA	H	H	15 - 443	15 - 443
1	19	SER	SER	ALA	ALA	D	D	15 - 443	15 - 443
2	19	SER	SER	ALA	ALA	E	E	15 - 443	15 - 443
1	20	SER	SER	ALA	ALA	D	D	15 - 443	15 - 443
2	20	SER	SER	ALA	ALA	F	F	15 - 443	15 - 443
1	21	SER	SER	ALA	ALA	D	D	15 - 443	15 - 443
2	21	SER	SER	ALA	ALA	G	G	15 - 443	15 - 443
1	22	SER	SER	ALA	ALA	D	D	15 - 443	15 - 443
2	22	SER	SER	ALA	ALA	H	H	15 - 443	15 - 443
1	23	SER	SER	VAL	VAL	E	E	15 - 444	15 - 444
2	23	SER	SER	VAL	VAL	F	F	15 - 444	15 - 444
1	24	SER	SER	VAL	VAL	E	E	15 - 444	15 - 444
2	24	SER	SER	VAL	VAL	G	G	15 - 444	15 - 444
1	25	SER	SER	VAL	VAL	E	E	15 - 444	15 - 444
2	25	SER	SER	VAL	VAL	H	H	15 - 444	15 - 444
1	26	SER	SER	VAL	VAL	F	F	15 - 444	15 - 444
2	26	SER	SER	VAL	VAL	G	G	15 - 444	15 - 444
1	27	SER	SER	VAL	VAL	F	F	15 - 444	15 - 444
2	27	SER	SER	VAL	VAL	H	H	15 - 444	15 - 444
1	28	SER	SER	VAL	VAL	G	G	15 - 444	15 - 444
2	28	SER	SER	VAL	VAL	H	H	15 - 444	15 - 444

NCS ensembles :

#1: Protein	Abp, a GH27 beta-L-arabinopyranosidase Mass: 51241.176 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Geobacillus stearothermophilus (bacteria) Production host: Escherichia coli (E. coli)
#2: Chemical	... ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 40 / Source method: obtained synthetically / Formula: C₃H₈O₃
#3: Chemical	... ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 85 / Source method: obtained synthetically / Formula: SO₄
#4: Chemical	ChemComp-CIT / CITRIC ACID Mass: 192.124 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₆H₈O₇
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 4204 / Source method: isolated from a natural source / Formula: H₂O
Sequence details	THE UNP SEQUENCE DATABASE REFERENCES FOR THIS PROTEIN DOES NOT CURRENTLY EXIST.

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 3.81 Å³/Da / Density % sol: 67.76 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 1.8M ammonium sulfate, 0.1M citrate buffer, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.954 Å
Detector	Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 11, 2012
Radiation	Monochromator: Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.954 Å / Relative weight: 1
Reflection	Resolution: 2.28→29.9 Å / Num. all: 284269 / Num. obs: 261171 / % possible obs: 96.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.9 % / R_merge(I) obs: 0.073
Reflection shell	Resolution: 2.28→2.32 Å / Redundancy: 5.9 % / R_merge(I) obs: 0.073 / Mean I/σ(I) obs: 9.6 / Num. unique all: 284269 / % possible all: 96.7

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Processing

Software

Name	Version	Classification
HKL-2000		data collection
MOLREP		phasing
REFMAC	5.7.0029	refinement
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3cc1

3cc1

Resolution: 2.28→29.9 Å / Cor.coef. F_o:F_c: 0.964 / Cor.coef. F_o:F_c free: 0.948 / SU B: 3.565 / SU ML: 0.088 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.172 / ESU R Free: 0.147 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.17671	13898	5.1 %	RANDOM
R_work	0.14565	-	-	-
all	0.14722	284269	-	-
obs	0.14722	261171	96.76 %	-

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 mean: 28.297 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.41 Å²	0 Å²	0 Å²
2-	-	0.79 Å²	0 Å²
3-	-	-	-0.38 Å²

Refinement step

Cycle: LAST / Resolution: 2.28→29.9 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	27795	0	730	4204	32729

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.018	0.019	29346
X-RAY DIFFRACTION	r_bond_other_d	0.012	0.02	26813
X-RAY DIFFRACTION	r_angle_refined_deg	1.892	1.955	39847
X-RAY DIFFRACTION	r_angle_other_deg	1.864	3	61722
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.818	5	3478
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	36.376	23.801	1410
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.948	15	4761
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	16.445	15	177
X-RAY DIFFRACTION	r_chiral_restr	0.181	0.2	4155
X-RAY DIFFRACTION	r_gen_planes_refined	0.013	0.021	32760
X-RAY DIFFRACTION	r_gen_planes_other	0.01	0.02	6981
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined
X-RAY DIFFRACTION	r_long_range_B_other
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-ID	Dom-ID	Auth asym-ID	Number	Rms dev position (Å)
1	1	A	27533	0.08
1	2	B	27533	0.08
2	1	A	27574	0.08
2	2	C	27574	0.08
3	1	A	27518	0.08
3	2	D	27518	0.08
4	1	A	27596	0.08
4	2	E	27596	0.08
5	1	A	27585	0.08
5	2	F	27585	0.08
6	1	A	27095	0.09
6	2	G	27095	0.09
7	1	A	27611	0.08
7	2	H	27611	0.08
8	1	B	27807	0.07
8	2	C	27807	0.07
9	1	B	27407	0.08
9	2	D	27407	0.08
10	1	B	27656	0.08
10	2	E	27656	0.08
11	1	B	27326	0.09
11	2	F	27326	0.09
12	1	B	26870	0.09
12	2	G	26870	0.09
13	1	B	27561	0.08
13	2	H	27561	0.08
14	1	C	27762	0.07
14	2	D	27762	0.07
15	1	C	27654	0.07
15	2	E	27654	0.07
16	1	C	27390	0.08
16	2	F	27390	0.08
17	1	C	26869	0.09
17	2	G	26869	0.09
18	1	C	27532	0.07
18	2	H	27532	0.07
19	1	D	27745	0.07
19	2	E	27745	0.07
20	1	D	27550	0.08
20	2	F	27550	0.08
21	1	D	27079	0.08
21	2	G	27079	0.08
22	1	D	27646	0.08
22	2	H	27646	0.08
23	1	E	27662	0.08
23	2	F	27662	0.08
24	1	E	27176	0.09
24	2	G	27176	0.09
25	1	E	27647	0.08
25	2	H	27647	0.08
26	1	F	26841	0.09
26	2	G	26841	0.09
27	1	F	27471	0.08
27	2	H	27471	0.08
28	1	G	27117	0.09
28	2	H	27117	0.09

LS refinement shell

Resolution: 2.281→2.34 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.234	800	-
R_work	0.184	14736	-
obs	-	-	74.43 %

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