PDB-7ch3: Crystal structure of Arabinose isomerase from hyper thermophilic ...

ID or keywords:

Entry

Database: PDB / ID: 7ch3

Title

Crystal structure of Arabinose isomerase from hyper thermophilic bacterium Thermotoga maritima (TMAI) triple mutant (K264A, E265A, K266A)

Components

L-arabinose isomerase

Keywords

ISOMERASE / Arabinose isomerase from hyperthermophile

Function / homology

Function and homology information

L-arabinose isomerase / L-arabinose isomerase activity / L-arabinose catabolic process to xylulose 5-phosphate / manganese ion binding / cytosol
Similarity search - Function

Biological species

Thermotoga maritima (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3.61 Å

Authors

Cao, T.P. / Dhanasingh, I. / Sung, J.Y. / Shin, S.M. / Lee, D.W. / Lee, S.H.

Citation

Journal: To Be Published
Title: Crystal structure of Arabinose isomerase from hyper thermophilic bacterium Thermotoga maritima (TMAI) triple mutant (K264A, E265A, K266A)
Authors: Cao, T.P. / Dhanasingh, I. / Sung, J.Y. / Shin, S.M. / Lee, D.W. / Lee, S.H.

History

Deposition	Jul 4, 2020	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Oct 20, 2021	Provider: repository / Type: Initial release
Revision 1.1	Nov 29, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._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

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	7ch3.cif.gz	2.3 MB	Display	PDBx/mmCIF format
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Validation report

Summary document	7ch3_validation.pdf.gz	5.7 MB	Display	wwPDB validaton report
Full document	7ch3_full_validation.pdf.gz	5.8 MB	Display
Data in XML	7ch3_validation.xml.gz	199 KB	Display
Data in CIF	7ch3_validation.cif.gz	264.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ch/7ch3 ftp://data.pdbj.org/pub/pdb/validation_reports/ch/7ch3	HTTPS FTP

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Related structure data

Related structure data	2hxgS S: Starting model for refinement
Similar structure data	7ch3-2 7cwv-2 7cyy-1 7cwv-1 4f2d-1 2hxg-1 7cxo-d 7chl-2 4r1p-d 2ajt-1 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

Deposited unit

A: L-arabinose isomerase

B: L-arabinose isomerase

C: L-arabinose isomerase

D: L-arabinose isomerase

E: L-arabinose isomerase

F: L-arabinose isomerase

G: L-arabinose isomerase

H: L-arabinose isomerase

I: L-arabinose isomerase

J: L-arabinose isomerase

K: L-arabinose isomerase

L: L-arabinose isomerase

hetero molecules

680 kDa, 12 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: L-arabinose isomerase

B: L-arabinose isomerase

C: L-arabinose isomerase

D: L-arabinose isomerase

F: L-arabinose isomerase

H: L-arabinose isomerase

hetero molecules

defined by author&software
Evidence: gel filtration
340 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

E: L-arabinose isomerase

G: L-arabinose isomerase

I: L-arabinose isomerase

J: L-arabinose isomerase

K: L-arabinose isomerase

L: L-arabinose isomerase

hetero molecules

defined by author&software
340 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	87.424, 113.913, 160.833
Angle α, β, γ (deg.)	81.080, 81.150, 88.890
Int Tables number	1
Space group name H-M	P1

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	chain A
2	1	(chain B and (resid 1 through 218 or resid 245 through 495))
3	1	(chain C and (resid 1 through 218 or resid 245 through 495))
4	1	(chain D and (resid 1 through 218 or resid 245 through 495))
5	1	(chain E and (resid 1 through 218 or resid 245 through 495))
6	1	(chain F and (resid 1 through 218 or resid 245 through 495))
7	1	(chain G and (resid 1 through 218 or resid 245 through 495))
8	1	(chain H and (resid 1 through 218 or resid 245 through 495))
9	1	(chain I and (resid 1 through 218 or resid 245 through 495))
10	1	(chain J and (resid 1 through 218 or resid 245 through 495))
11	1	(chain K and (resid 1 through 218 or resid 245 through 495))
12	1	(chain L and (resid 1 through 218 or resid 245 through 495))

NCS domain segments:

Ens-ID: 1

Dom-ID	Component-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	MET	MET	LYS	LYS	chain A	A	A	1 - 495	1 - 495
2	1	MET	MET	VAL	VAL	(chain B and (resid 1 through 218 or resid 245 through 495))	B	B	1 - 218	1 - 218
2	2	SER	SER	LYS	LYS	(chain B and (resid 1 through 218 or resid 245 through 495))	B	B	245 - 495	245 - 495
3	1	MET	MET	VAL	VAL	(chain C and (resid 1 through 218 or resid 245 through 495))	C	C	1 - 218	1 - 218
3	2	SER	SER	LYS	LYS	(chain C and (resid 1 through 218 or resid 245 through 495))	C	C	245 - 495	245 - 495
4	1	MET	MET	VAL	VAL	(chain D and (resid 1 through 218 or resid 245 through 495))	D	D	1 - 218	1 - 218
4	2	SER	SER	LYS	LYS	(chain D and (resid 1 through 218 or resid 245 through 495))	D	D	245 - 495	245 - 495
5	1	MET	MET	VAL	VAL	(chain E and (resid 1 through 218 or resid 245 through 495))	E	E	1 - 218	1 - 218
5	2	SER	SER	LYS	LYS	(chain E and (resid 1 through 218 or resid 245 through 495))	E	E	245 - 495	245 - 495
6	1	MET	MET	VAL	VAL	(chain F and (resid 1 through 218 or resid 245 through 495))	F	F	1 - 218	1 - 218
6	2	SER	SER	LYS	LYS	(chain F and (resid 1 through 218 or resid 245 through 495))	F	F	245 - 495	245 - 495
7	1	MET	MET	VAL	VAL	(chain G and (resid 1 through 218 or resid 245 through 495))	G	G	1 - 218	1 - 218
7	2	SER	SER	LYS	LYS	(chain G and (resid 1 through 218 or resid 245 through 495))	G	G	245 - 495	245 - 495
8	1	MET	MET	VAL	VAL	(chain H and (resid 1 through 218 or resid 245 through 495))	H	H	1 - 218	1 - 218
8	2	SER	SER	LYS	LYS	(chain H and (resid 1 through 218 or resid 245 through 495))	H	H	245 - 495	245 - 495
9	1	MET	MET	VAL	VAL	(chain I and (resid 1 through 218 or resid 245 through 495))	I	I	1 - 218	1 - 218
9	2	SER	SER	LYS	LYS	(chain I and (resid 1 through 218 or resid 245 through 495))	I	I	245 - 495	245 - 495
10	1	MET	MET	VAL	VAL	(chain J and (resid 1 through 218 or resid 245 through 495))	J	J	1 - 218	1 - 218
10	2	SER	SER	LYS	LYS	(chain J and (resid 1 through 218 or resid 245 through 495))	J	J	245 - 495	245 - 495
11	1	MET	MET	VAL	VAL	(chain K and (resid 1 through 218 or resid 245 through 495))	K	K	1 - 218	1 - 218
11	2	SER	SER	LYS	LYS	(chain K and (resid 1 through 218 or resid 245 through 495))	K	K	245 - 495	245 - 495
12	1	MET	MET	VAL	VAL	(chain L and (resid 1 through 218 or resid 245 through 495))	L	L	1 - 218	1 - 218
12	2	SER	SER	LYS	LYS	(chain L and (resid 1 through 218 or resid 245 through 495))	L	L	245 - 495	245 - 495

#1: Protein	L-arabinose isomerase Mass: 56561.984 Da / Num. of mol.: 12 / Mutation: K264A, E265A, K266A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099) (bacteria) Gene: araA, TM_0276 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9WYB3, L-arabinose isomerase
#2: Chemical	ChemComp-MN / MANGANESE (II) ION Mass: 54.938 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 19 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	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: 2.3 Å³/Da / Density % sol: 46.6 %
Crystal grow	Temperature: 310 K / Method: vapor diffusion, hanging drop / Details: 100mM Tris pH 8.5, 2% Tacismate pH 8, 15% PEG 3350

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site: PAL/PLS

/ Beamline: 7A (6B, 6C1) / Wavelength: 0.97933 Å

Detector

Type: ADSC QUANTUM 270 / Detector: CCD / Date: Mar 23, 2016

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.97933 Å / Relative weight: 1

Reflection

Resolution: 3.6→50 Å / Num. obs: 68198 / % possible obs: 98.6 % / Redundancy: 3.7 % / R_merge(I) obs: 0.087 / R_pim(I) all: 0.053 / R_rim(I) all: 0.102 / Χ²: 0.707 / Net I/σ(I): 9 / Num. measured all: 252359

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique obs	CC_1/2	R_pim(I) all	R_rim(I) all	Χ²	% possible all
3.6-3.66	3.6	0.486	3369	0.632	0.297	0.571	1	97.3
3.66-3.73	3.7	0.411	3374	0.686	0.254	0.485	1.015	97.8
3.73-3.8	3.6	0.347	3428	0.854	0.211	0.407	0.794	97.9
3.8-3.88	3.7	0.367	3359	0.888	0.223	0.431	0.819	98.1
3.88-3.96	3.7	0.274	3452	0.92	0.166	0.321	0.767	98.2
3.96-4.05	3.7	0.226	3365	0.932	0.138	0.265	0.764	98.6
4.05-4.16	3.7	0.199	3394	0.947	0.121	0.233	0.79	98.5
4.16-4.27	3.7	0.168	3400	0.929	0.102	0.198	0.849	99
4.27-4.39	3.7	0.138	3494	0.89	0.085	0.163	1.039	99.2
4.39-4.54	3.8	0.099	3425	0.97	0.06	0.116	0.733	99.3
4.54-4.7	3.8	0.075	3402	0.98	0.045	0.087	0.768	99.2
4.7-4.89	3.8	0.062	3469	0.979	0.036	0.072	0.629	99.4
4.89-5.11	3.8	0.058	3430	0.981	0.034	0.067	0.584	99.5
5.11-5.38	3.8	0.056	3433	0.98	0.033	0.065	0.57	99.5
5.38-5.71	3.8	0.057	3448	0.973	0.034	0.067	0.568	99.6
5.71-6.15	3.8	0.048	3450	0.976	0.028	0.056	0.502	99.6
6.15-6.77	3.8	0.038	3458	0.983	0.022	0.044	0.481	99.7
6.77-7.75	3.7	0.026	3426	0.989	0.016	0.031	0.457	99.7
7.75-9.75	3.6	0.021	3443	0.988	0.012	0.024	0.491	99.1
9.75-50	3.2	0.022	3179	0.989	0.014	0.026	0.543	92.1

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Processing

Software

Name	Version	Classification
PHENIX	1.17.1_3660	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PDB_EXTRACT	3.25	data extraction
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 2HXG

2hxg

Resolution: 3.61→33.11 Å / SU ML: 0.48 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 28.49 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2799	3336	4.98 %
R_work	0.2316	63677	-
obs	0.2341	67013	96.08 %

Solvent computation

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

Displacement parameters

B_iso max: 204.2 Å² / B_iso mean: 73.6774 Å² / B_iso min: 15.86 Å²

Refinement step

Cycle: final / Resolution: 3.61→33.11 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	47398	0	18	19	47435
B_iso mean	-	-	90.91	35.7	-
Num. residues	-	-	-	-	5914

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Number	Refine-ID	Rms	Type
1	1	A	17076	X-RAY DIFFRACTION	7.063	TORSIONAL
1	2	B	17076	X-RAY DIFFRACTION	7.063	TORSIONAL
1	3	C	17076	X-RAY DIFFRACTION	7.063	TORSIONAL
1	4	D	17076	X-RAY DIFFRACTION	7.063	TORSIONAL
1	5	E	17076	X-RAY DIFFRACTION	7.063	TORSIONAL
1	6	F	17076	X-RAY DIFFRACTION	7.063	TORSIONAL
1	7	G	17076	X-RAY DIFFRACTION	7.063	TORSIONAL
1	8	H	17076	X-RAY DIFFRACTION	7.063	TORSIONAL
1	9	I	17076	X-RAY DIFFRACTION	7.063	TORSIONAL
1	10	J	17076	X-RAY DIFFRACTION	7.063	TORSIONAL
1	11	K	17076	X-RAY DIFFRACTION	7.063	TORSIONAL
1	12	L	17076	X-RAY DIFFRACTION	7.063	TORSIONAL

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0 / Total num. of bins used: 24

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
3.61-3.66	0.3004	98	0.2867	1835	1933	65
3.66-3.71	0.3425	128	0.2906	2336	2464	85
3.71-3.77	0.3388	118	0.2776	2488	2606	90
3.77-3.83	0.3029	151	0.2816	2627	2778	95
3.83-3.9	0.3195	142	0.2773	2633	2775	96
3.9-3.97	0.2989	143	0.2769	2740	2883	97
3.97-4.05	0.3005	127	0.2601	2671	2798	98
4.05-4.13	0.3252	128	0.2634	2714	2842	98
4.13-4.22	0.3135	144	0.2703	2725	2869	98
4.22-4.32	0.3398	147	0.2724	2710	2857	99
4.32-4.42	0.2917	146	0.2499	2709	2855	98
4.42-4.54	0.2683	131	0.2262	2767	2898	99
4.54-4.68	0.2745	156	0.2128	2712	2868	99
4.68-4.83	0.2834	148	0.213	2743	2891	99
4.83-5	0.2678	133	0.2142	2742	2875	99
5-5.2	0.2379	156	0.2073	2760	2916	100
5.2-5.43	0.3229	128	0.2222	2760	2888	99
5.43-5.72	0.2623	140	0.2301	2740	2880	100
5.72-6.07	0.2748	156	0.2265	2726	2882	100
6.07-6.54	0.3059	138	0.2401	2746	2884	100
6.54-7.19	0.2595	169	0.2156	2749	2918	100
7.19-8.22	0.2057	138	0.1779	2740	2878	100
8.22-10.3	0.2129	155	0.1659	2724	2879	99
10.3-33.11	0.2836	116	0.212	2580	2696	93

Refinement TLS params.

Method: refined / Origin x: -18.4847 Å / Origin y: -4.1574 Å / Origin z: -16.3098 Å

	11	12	13	21	22	23	31	32	33
T	0.1153 Å²	0.0087 Å²	0.1375 Å²	-	0.1342 Å²	-0.0956 Å²	-	-	0.2946 Å²
L	0.5814 °²	-0.1722 °²	0.4299 °²	-	0.3642 °²	-0.2957 °²	-	-	1.007 °²
S	-0.0247 Å °	0.0513 Å °	0.043 Å °	-0.0501 Å °	-0.0062 Å °	-0.0464 Å °	0.1275 Å °	-0.086 Å °	0.0153 Å °

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	all	A	1 - 495
2	X-RAY DIFFRACTION	1	all	B	1 - 495
3	X-RAY DIFFRACTION	1	all	C	1 - 495
4	X-RAY DIFFRACTION	1	all	D	1 - 495
5	X-RAY DIFFRACTION	1	all	E	1 - 495
6	X-RAY DIFFRACTION	1	all	F	1 - 495
7	X-RAY DIFFRACTION	1	all	G	1 - 495
8	X-RAY DIFFRACTION	1	all	H	1 - 495
9	X-RAY DIFFRACTION	1	all	I	1 - 495
10	X-RAY DIFFRACTION	1	all	J	1 - 495
11	X-RAY DIFFRACTION	1	all	K	1 - 495
12	X-RAY DIFFRACTION	1	all	L	1 - 495
13	X-RAY DIFFRACTION	1	all	M	1 - 18
14	X-RAY DIFFRACTION	1	all	N	1 - 19

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