PDB-3u0h: The Structure of a Xylose Isomerase domain protein from Alicyclob...

ID or keywords:

Entry

Database: PDB / ID: 3u0h

Title

The Structure of a Xylose Isomerase domain protein from Alicyclobacillus acidocaldarius subsp. acidocaldarius.

Components

Xylose isomerase domain protein

Keywords

ISOMERASE / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG / Tim Barrel / putative xylose isomerase

Function / homology

Function and homology information

isomerase activity
Similarity search - Function

Biological species

Alicyclobacillus acidocaldarius subsp. acidocaldarius (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MAD / Resolution: 2.3 Å

Authors

Cuff, M.E. / Chhor, G. / Bearden, J. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)

Citation

Journal: TO BE PUBLISHED
Title: The Structure of a Xylose Isomerase domain protein from Alicyclobacillus acidocaldarius subsp. acidocaldarius.
Authors: Cuff, M.E. / Chhor, G. / Bearden, J. / Joachimiak, A.

History

Deposition	Sep 28, 2011	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 9, 2011	Provider: repository / Type: Initial release
Revision 1.1	Nov 8, 2017	Group: Refinement description / Category: software
Revision 1.2	Oct 9, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _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	3u0h.cif.gz	131.2 KB	Display	PDBx/mmCIF format
PDB format	pdb3u0h.ent.gz	100.2 KB	Display	PDB format
PDBx/mmJSON format	3u0h.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	3u0h_validation.pdf.gz	467.1 KB	Display	wwPDB validaton report
Full document	3u0h_full_validation.pdf.gz	472.2 KB	Display
Data in XML	3u0h_validation.xml.gz	28.4 KB	Display
Data in CIF	3u0h_validation.cif.gz	38.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/u0/3u0h ftp://data.pdbj.org/pub/pdb/validation_reports/u0/3u0h	HTTPS FTP

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Related structure data

Similar structure data	7bbi-1 7bb4-1 4il3-d 4h45-1 2yyt-d 7b7e-1 5c9o-1 2x4s-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: apc100342

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#74 - Feb 2006 alpha-Amylase similarity (3)

Deposited unit

A: Xylose isomerase domain protein

B: Xylose isomerase domain protein

hetero molecules

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

1

A: Xylose isomerase domain protein

B: Xylose isomerase domain protein

hetero molecules

A: Xylose isomerase domain protein

B: Xylose isomerase domain protein

hetero molecules

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

2

Idetical with deposited unit
defined by software

Unit cell

Length a, b, c (Å)	53.555, 240.329, 113.356
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	20
Space group name H-M	C222₁

Details

Likely AB dimer of the AU, or A2B2 tetramer x,y,z -x,y,-z+1/2

#1: Protein	Xylose isomerase domain protein Mass: 31895.814 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Alicyclobacillus acidocaldarius subsp. acidocaldarius (bacteria) Strain: DSM 446 / Gene: Aaci_2157 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) magic / References: UniProt: C8WQZ7
#2: Chemical	ChemComp-PO4 / PHOSPHATE ION Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO₄
#3: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 249 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.86 Å³/Da / Density % sol: 56.98 %
Crystal grow	Temperature: 297 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 0.1M Tris:HCl, 1.0M Amonium phosphate, pH 8.0, 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: 0.97921, 0.97937

Detector

Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 3, 2011

Radiation

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

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	0.97921	1
2	0.97937	1

Reflection

Redundancy: 5 % / Av σ(I) over netI: 21.3 / Number: 165632 / R_merge(I) obs: 0.087 / Χ²: 1.33 / D res high: 2.3 Å / D res low: 50 Å / Num. obs: 32970 / % possible obs: 99.9

Diffraction reflection shell

Highest resolution (Å)	Lowest resolution (Å)	% possible obs (%)	ID	R_merge(I) obs	Chi squared	Redundancy
6.24	50	98.2	1	0.055	3.897	4.7
4.95	6.24	99.7	1	0.062	2.559	4.8
4.33	4.95	99.9	1	0.058	2.311	4.9
3.93	4.33	99.9	1	0.066	2.259	5
3.65	3.93	100	1	0.069	1.851	5
3.44	3.65	100	1	0.073	1.457	5.1
3.26	3.44	99.9	1	0.08	1.213	5.1
3.12	3.26	100	1	0.1	1.065	5.1
3	3.12	100	1	0.122	0.978	5.1
2.9	3	99.9	1	0.148	0.925	5.1
2.81	2.9	100	1	0.194	0.908	5.1
2.73	2.81	100	1	0.214	0.898	5.1
2.66	2.73	99.9	1	0.239	0.87	5.1
2.59	2.66	100	1	0.303	0.834	5.1
2.53	2.59	100	1	0.357	0.796	5.1
2.48	2.53	100	1	0.359	0.806	5.1
2.43	2.48	100	1	0.408	0.78	5.1
2.38	2.43	100	1	0.49	0.766	5
2.34	2.38	100	1	0.506	0.741	5.1
2.3	2.34	100	1	0.581	0.776	5

Reflection

Resolution: 2.3→50 Å / Num. all: 32970 / Num. obs: 32970 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 5 % / B_iso Wilson estimate: 44 Å² / R_merge(I) obs: 0.087 / Χ²: 1.33 / Net I/σ(I): 7.3

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique all	Χ²	Diffraction-ID	% possible all
2.3-2.34	5	0.581	1621	0.776	1	100
2.34-2.38	5.1	0.506	1617	0.741	1	100
2.38-2.43	5	0.49	1659	0.766	1	100
2.43-2.48	5.1	0.408	1600	0.78	1	100
2.48-2.53	5.1	0.359	1632	0.806	1	100
2.53-2.59	5.1	0.357	1606	0.796	1	100
2.59-2.66	5.1	0.303	1666	0.834	1	100
2.66-2.73	5.1	0.239	1615	0.87	1	99.9
2.73-2.81	5.1	0.214	1631	0.898	1	100
2.81-2.9	5.1	0.194	1630	0.908	1	100
2.9-3	5.1	0.148	1659	0.925	1	99.9
3-3.12	5.1	0.122	1623	0.978	1	100
3.12-3.26	5.1	0.1	1637	1.065	1	100
3.26-3.44	5.1	0.08	1658	1.213	1	99.9
3.44-3.65	5.1	0.073	1644	1.457	1	100
3.65-3.93	5	0.069	1657	1.851	1	100
3.93-4.33	5	0.066	1662	2.259	1	99.9
4.33-4.95	4.9	0.058	1691	2.311	1	99.9
4.95-6.24	4.8	0.062	1691	2.559	1	99.7
6.24-50	4.7	0.055	1771	3.897	1	98.2

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Phasing

Phasing

Method:

MAD

Phasing MAD

D res high: 2.25 Å / D res low: 41.44 Å / FOM : 0.156 / FOM acentric: 0.162 / FOM centric: 0.099 / Reflection: 35211 / Reflection acentric: 31695 / Reflection centric: 3516

Phasing MAD set

Highest resolution: 2.25 Å / Lowest resolution: 41.44 Å

ID	R cullis acentric	R cullis centric	Loc acentric	Loc centric	Power acentric	Power centric	Reflection acentric	Reflection centric
1	1.96	1	0.1	0.1	0	0	31695	3516
2	0.99	0.96	41.2	49.1	0.23	0.23	18129	2423

Phasing MAD set shell

ID	Resolution (Å)	R cullis acentric	R cullis centric	Loc acentric	Loc centric	Power acentric	Power centric	Reflection acentric	Reflection centric
1	13.04-41.44	1.61	1	0.5	0.3	0	0	119	82
1	7.74-13.04	1.43	1	0.4	0.2	0	0	557	185
1	5.5-7.74	2.46	1	0.4	0.2	0	0	1331	286
1	4.27-5.5	1.51	1	0.2	0.1	0	0	2422	398
1	3.49-4.27	1.45	1	0.1	0.1	0	0	3849	493
1	2.95-3.49	2.36	1	0.1	0	0	0	5616	589
1	2.55-2.95	7.82	1	0	0	0	0	7706	696
1	2.25-2.55	2.08	1	0	0	0	0	10095	787
2	13.04-41.44	0.99	0.87	56.9	49.4	0.73	0.66	119	81
2	7.74-13.04	0.91	0.9	43.8	46.4	0.75	0.68	557	185
2	5.5-7.74	0.94	0.9	40.7	46.9	0.59	0.44	1331	285
2	4.27-5.5	0.98	0.96	47.8	57.4	0.32	0.25	2420	397
2	3.49-4.27	0.99	0.98	46.7	54.1	0.2	0.15	3848	491
2	2.95-3.49	1	1	38.3	47.6	0.13	0.09	5613	589
2	2.55-2.95	1	1	35.6	39.3	0.08	0.06	4241	395
2	2.25-2.55	0	0	0	0	0	0	0	0

Phasing MAD set site

Atom type symbol: Se

ID	B iso	Fract x	Fract y	Fract z	Occupancy	Occupancy iso
1	79.8484	-0.74	-0.195	-0.123	3.986	0
2	81.8221	-1.036	-0.04	0.115	4.533	0
3	52.8958	-0.581	-0.258	-0.199	3.727	0
4	62.6271	-1.129	-0.083	0.244	3.533	0
5	64.3376	-0.688	-0.145	0.059	2.699	0
6	73.9374	-0.758	-0.213	-0.302	3.023	0
7	61.9173	-0.804	-0.183	0.026	2.609	0
8	83.0161	-1.339	-0.018	0.216	3.358	0
9	67.2426	-0.739	-0.194	-0.123	1.836	-0.139
10	70.7936	-1.036	-0.04	0.115	2.564	-0.142
11	51.9109	-0.58	-0.258	-0.2	2.119	-0.181
12	52.0643	-1.132	-0.083	0.246	1.836	-0.111
13	78.2114	-0.688	-0.146	0.059	1.363	-0.123
14	60.8264	-0.757	-0.213	-0.301	1.956	-0.136
15	122.4555	-0.807	-0.182	0.027	1.723	-0.122
16	48.6422	-1.338	-0.018	0.215	1.456	-0.095

Phasing MAD shell

Resolution (Å)	FOM	FOM acentric	FOM centric	Reflection	Reflection acentric	Reflection centric
13.04-41.44	0.469	0.604	0.273	201	119	82
7.74-13.04	0.55	0.617	0.345	742	557	185
5.5-7.74	0.527	0.578	0.289	1617	1331	286
4.27-5.5	0.396	0.43	0.189	2820	2422	398
3.49-4.27	0.27	0.291	0.11	4342	3849	493
2.95-3.49	0.16	0.17	0.06	6205	5616	589
2.55-2.95	0.069	0.073	0.02	8402	7706	696
2.25-2.55	0.026	0.029	0	10882	10095	787

Phasing dm

Method: Solvent flattening and Histogram matching / Reflection: 35211

Phasing dm shell

Resolution (Å)	Delta phi final	FOM	Reflection
9.59-100	65.2	0.619	508
7.54-9.59	62.6	0.82	510
6.41-7.54	60.4	0.808	619
5.68-6.41	55.9	0.811	704
5.15-5.68	62.4	0.792	770
4.74-5.15	60.6	0.827	842
4.42-4.74	60.7	0.828	904
4.15-4.42	64.8	0.822	953
3.93-4.15	64.9	0.803	1019
3.74-3.93	69.8	0.81	1063
3.58-3.74	70	0.817	1109
3.43-3.58	69.7	0.816	1173
3.31-3.43	72.1	0.794	1201
3.19-3.31	73.9	0.792	1253
3.09-3.19	76.4	0.784	1285
2.99-3.09	80.3	0.769	1312
2.91-2.99	79.3	0.76	1389
2.83-2.91	78.8	0.733	1389
2.75-2.83	82.6	0.751	1446
2.69-2.75	83.8	0.774	1448
2.62-2.69	83.6	0.757	1534
2.56-2.62	83	0.744	1533
2.51-2.56	85.4	0.746	1580
2.46-2.51	84.8	0.745	1618
2.41-2.46	87.4	0.743	1639
2.36-2.41	87.2	0.774	1671
2.32-2.36	87	0.759	1694
2.25-2.32	87.5	0.743	3045

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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:

MAD / Resolution: 2.3→40.05 Å / Cor.coef. F_o:F_c: 0.962 / Cor.coef. F_o:F_c free: 0.945 / WR_factor R_free: 0.2161 / WR_factor R_work: 0.1692 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8711 / SU B: 11.468 / SU ML: 0.144 / SU R Cruickshank DPI: 0.2593 / SU R_free: 0.2061 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.206
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2252	1669	5.1 %	RANDOM
R_work	0.1773	-	-	-
all	0.1798	32850	-	-
obs	0.1798	32850	99.26 %	-

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: 89.44 Å² / B_iso mean: 30.6011 Å² / B_iso min: 14.83 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.88 Å²	0 Å²	0 Å²
2-	-	2.79 Å²	0 Å²
3-	-	-	-1.91 Å²

Refinement step

Cycle: LAST / Resolution: 2.3→40.05 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4440	0	23	249	4712

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.016	0.019	4604
X-RAY DIFFRACTION	r_bond_other_d	0.003	0.02	3212
X-RAY DIFFRACTION	r_angle_refined_deg	1.759	1.984	6268
X-RAY DIFFRACTION	r_angle_other_deg	1.015	3	7732
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.671	5	564
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	33.142	21.892	222
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.595	15	737
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	21.05	15	56
X-RAY DIFFRACTION	r_chiral_restr	0.094	0.2	686
X-RAY DIFFRACTION	r_gen_planes_refined	0.009	0.021	5134
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1002

LS refinement shell

Resolution: 2.301→2.361 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.254	114	-
R_work	0.21	2061	-
all	-	2175	-
obs	-	-	96.75 %

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	1.0661	-0.0071	-0.0232	0.7366	0.341	1.4328	0.0889	-0.1252	0.0949	0.0595	-0.003	0.0106	-0.289	0.083	-0.0859	0.1722	-0.0411	0.0332	0.1331	-0.0269	0.0219	5.3145	61.8178	44.1242
2	1.5515	0.0902	0.4866	1.7916	0.2798	1.5649	0.1627	-0.2205	-0.8116	0.3214	0.0687	-0.1369	0.4034	0.0638	-0.2314	0.2108	0.0131	-0.1324	0.1638	0.0985	0.499	10.5203	16.5465	41.3318

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	-10 - 9999
2	X-RAY DIFFRACTION	2	B	-10 - 9999

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