PDB-1r2t: CRYSTAL STRUCTURE OF RABBIT MUSCLE TRIOSEPHOSPHATE ISOMERASE

ID or keywords:

Entry

Database: PDB / ID: 1r2t

Title

CRYSTAL STRUCTURE OF RABBIT MUSCLE TRIOSEPHOSPHATE ISOMERASE

Components

Triosephosphate isomerase

Keywords

ISOMERASE / TIM / Closed loop conformation in the ligand-free state / Conformational heterogeneity / Tim-barrel

Function / homology

Function and homology information

methylglyoxal biosynthetic process / methylglyoxal synthase / methylglyoxal synthase activity / glyceraldehyde-3-phosphate biosynthetic process / glycerol catabolic process / triose-phosphate isomerase / triose-phosphate isomerase activity / canonical glycolysis / gluconeogenesis / ubiquitin protein ligase binding ...
Similarity search - Function

Biological species

Oryctolagus cuniculus (rabbit)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.25 Å

Authors

Aparicio, R. / Ferreira, S.T. / Polikarpov, I.

Citation

Journal: J.Mol.Biol. / Year: 2003
Title: Closed conformation of the active site loop of rabbit muscle triosephosphate isomerase in the absence of substrate: evidence of conformational heterogeneity.
Authors: Aparicio, R. / Ferreira, S.T. / Polikarpov, I.

History

Deposition	Sep 29, 2003	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Dec 23, 2003	Provider: repository / Type: Initial release
Revision 1.1	Apr 29, 2008	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.3	Aug 23, 2023	Group: Data collection / Database references / 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 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.end_auth_comp_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Validation report

Summary document	1r2t_validation.pdf.gz	432.7 KB	Display	wwPDB validaton report
Full document	1r2t_full_validation.pdf.gz	439.9 KB	Display
Data in XML	1r2t_validation.xml.gz	23.6 KB	Display
Data in CIF	1r2t_validation.cif.gz	34 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/r2/1r2t ftp://data.pdbj.org/pub/pdb/validation_reports/r2/1r2t	HTTPS FTP

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Related structure data

Related structure data	1r2rC 1r2sC 1htiS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	4unl-d 1r2s-1 2jk2-d 6nlh-4 1r2r-1 6nxw-1 6nlh-1 1tim-d 6nlh-3 2i9e-1 1sq7-d 4poc-d 6up8-d 1nf0-d 5i3g-1 4y96-1 6jox-d 4o4v-1 5i3g-2 4bi5-7 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	#50 - Feb 2004 Glycolytic Enzymes similarity (8)

Deposited unit

A: Triosephosphate isomerase

B: Triosephosphate isomerase

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	65.159, 72.035, 93.252
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:

Ens-ID: 1

Dom-ID	Component-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Refine code	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	ARG	ARG	GLY	GLY	2	A	A	4 - 22	4 - 22
2	1	ARG	ARG	GLY	GLY	2	B	B	4 - 22	4 - 22
3	2	LEU	LEU	ALA	ALA	2	A	A	24 - 31	24 - 31
4	2	LEU	LEU	ALA	ALA	2	B	B	24 - 31	24 - 31
5	3	LYS	LYS	LYS	LYS	3	A	A	32	32
6	3	LYS	LYS	LYS	LYS	3	B	B	32	32
7	4	VAL	VAL	LEU	LEU	2	A	A	33 - 55	33 - 55
8	4	VAL	VAL	LEU	LEU	2	B	B	33 - 55	33 - 55
9	5	ASP	ASP	ASP	ASP	3	A	A	56	56
10	5	ASP	ASP	ASP	ASP	3	B	B	56	56
11	6	PRO	PRO	ILE	ILE	2	A	A	57 - 83	57 - 83
12	6	PRO	PRO	ILE	ILE	2	B	B	57 - 83	57 - 83
13	7	LYS	LYS	LYS	LYS	3	A	A	84	84
14	7	LYS	LYS	LYS	LYS	3	B	B	84	84
15	8	ASP	ASP	ARG	ARG	2	A	A	85 - 134	85 - 134
16	8	ASP	ASP	ARG	ARG	2	B	B	85 - 134	85 - 134
17	9	GLU	GLU	GLU	GLU	3	A	A	135	135
18	9	GLU	GLU	GLU	GLU	3	B	B	135	135
19	10	ALA	ALA	PHE	PHE	2	A	A	136 - 144	136 - 144
20	10	ALA	ALA	PHE	PHE	2	B	B	136 - 144	136 - 144
21	11	GLU	GLU	GLU	GLU	3	A	A	145	145
22	11	GLU	GLU	GLU	GLU	3	B	B	145	145
23	12	GLN	GLN	VAL	VAL	2	A	A	146 - 161	146 - 161
24	12	GLN	GLN	VAL	VAL	2	B	B	146 - 161	146 - 161
25	13	LEU	LEU	LEU	LEU	3	A	A	162	162
26	13	LEU	LEU	LEU	LEU	3	B	B	162	162
27	14	ALA	ALA	TRP	TRP	2	A	A	163 - 168	163 - 168
28	14	ALA	ALA	TRP	TRP	2	B	B	163 - 168	163 - 168
29	15	ALA	ALA	THR	THR	5	A	A	169 - 172	169 - 172
30	15	ALA	ALA	THR	THR	5	B	B	169 - 172	169 - 172
31	16	THR	THR	ALA	ALA	5	A	A	175 - 176	175 - 176
32	16	THR	THR	ALA	ALA	5	B	B	175 - 176	175 - 176
33	17	THR	THR	PRO	PRO	2	A	A	177 - 178	177 - 178
34	17	THR	THR	PRO	PRO	2	B	B	177 - 178	177 - 178
35	18	GLN	GLN	GLN	GLN	3	A	A	179	179
36	18	GLN	GLN	GLN	GLN	3	B	B	179	179
37	19	GLN	GLN	GLN	GLN	2	A	A	180 - 182	180 - 182
38	19	GLN	GLN	GLN	GLN	2	B	B	180 - 182	180 - 182
39	20	GLU	GLU	GLU	GLU	3	A	A	183	183
40	20	GLU	GLU	GLU	GLU	3	B	B	183	183
41	21	VAL	VAL	HIS	HIS	2	A	A	184 - 185	184 - 185
42	21	VAL	VAL	HIS	HIS	2	B	B	184 - 185	184 - 185
43	22	GLU	GLU	GLU	GLU	3	A	A	186	186
44	22	GLU	GLU	GLU	GLU	3	B	B	186	186
45	23	LYS	LYS	LEU	LEU	3	A	A	187 - 192	187 - 192
46	23	LYS	LYS	LEU	LEU	3	B	B	187 - 192	187 - 192
47	24	LYS	LYS	GLN	GLN	5	A	A	193 - 202	193 - 202
48	24	LYS	LYS	GLN	GLN	5	B	B	193 - 202	193 - 202
49	25	SER	SER	THR	THR	3	A	A	203 - 213	203 - 213
50	25	SER	SER	THR	THR	3	B	B	203 - 213	203 - 213
51	26	GLY	GLY	ALA	ALA	2	A	A	214 - 246	214 - 246
52	26	GLY	GLY	ALA	ALA	2	B	B	214 - 246	214 - 246

Details

The asymmetric unit contains one physiologically active dimer formed by chains {A,B}

#1: Protein	Triosephosphate isomerase / TIM Mass: 26658.398 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Tissue: muscle / References: UniProt: P00939, triose-phosphate isomerase
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 335 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal

Density Matthews: 2.05 Å³/Da / Density % sol: 40.05 %

Crystal grow

Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG 4000, MgCl2, Tris-HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal grow

*PLUS

Method: vapor diffusion, hanging drop

Components of the solutions

*PLUS

ID	Conc.	Common name	Crystal-ID	Sol-ID	Chemical formula	Details
1	24 %(w/v)	PEG4000	1	reservoir
2	0.2 M		1	reservoir	MgCl2
3	0.1 M	Tris-HCl	1	reservoir		pH8.5
4	1.1 M	DMSO	1	reservoir
5	10 mg/ml	protein	1	drop

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Data collection

Diffraction	Mean temperature: 85 K
Diffraction source	Source: SYNCHROTRON / Site: LNLS / Beamline: D03B-MX1 / Wavelength: 1.31 Å
Detector	Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 7, 1999 / Details: Mirror
Radiation	Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.31 Å / Relative weight: 1
Reflection	Resolution: 2.25→15.65 Å / Num. all: 21372 / Num. obs: 20842 / % possible obs: 97.5 % / Observed criterion σ(I): 2 / Redundancy: 2.93 % / R_merge(I) obs: 0.104 / Net I/σ(I): 10.16
Reflection shell	Resolution: 2.25→2.29 Å / Redundancy: 2.83 % / R_merge(I) obs: 0.379 / Mean I/σ(I) obs: 2.63 / Num. unique all: 1044 / % possible all: 99.7
Reflection	PLUS Lowest resolution: 13.5 Å / R_merge(I) obs*: 0.107
Reflection shell	PLUS Lowest resolution: 2.3 Å / R_merge(I) obs: 0.366 / Mean I/σ(I) obs*: 2.14

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Processing

Software

Name	Version	Classification
REFMAC	5.1.19	refinement
DENZO		data reduction
SCALEPACK		data scaling
AMoRE		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1HTI

1hti

Resolution: 2.25→15.54 Å / Cor.coef. F_o:F_c: 0.953 / Cor.coef. F_o:F_c free: 0.938 / SU B: 6.964 / SU ML: 0.171 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.453 / ESU R Free: 0.23 / Stereochemistry target values: MAXIMUM LIKELIHOOD

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.21999	1032	5 %	RANDOM
R_work	0.18218	-	-	-
all	0.18409	-	-	-
obs	0.18409	19784	97.53 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK

Displacement parameters

B_iso mean: 20.385 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.14 Å²	0 Å²	0 Å²
2-	-	-0.78 Å²	0 Å²
3-	-	-	-0.36 Å²

Refinement step

Cycle: LAST / Resolution: 2.25→15.54 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3731	0	0	335	4066

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.011	0.021	3801
X-RAY DIFFRACTION	r_angle_refined_deg	1.309	1.946	5148
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.684	5	489
X-RAY DIFFRACTION	r_chiral_restr	0.084	0.2	589
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.02	2828
X-RAY DIFFRACTION	r_nbd_refined	0.201	0.2	1897
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.16	0.2	304
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.223	0.2	43
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.267	0.2	22
X-RAY DIFFRACTION	r_mcbond_it	0.568	1.5	2433
X-RAY DIFFRACTION	r_mcangle_it	1.071	2	3911
X-RAY DIFFRACTION	r_scbond_it	1.613	3	1368
X-RAY DIFFRACTION	r_scangle_it	2.731	4.5	1237

Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Number	Type	Rms dev position (Å)	Weight position
1663	tight positional	0.06	0.05
106	medium positional	0.53	0.5
1663	tight thermal	0.76	0.5
106	medium thermal	2.15	2

LS refinement shell

Resolution: 2.251→2.308 Å / Total num. of bins used: 20 /

	R_factor	Num. reflection
R_free	0.302	76
R_work	0.221	1417

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	2.636	-1.8382	0.0567	3.4047	-0.6351	0.6004	0.1777	0.2704	-0.5115	-0.3536	-0.2154	0.3754	0.0602	0.0432	0.0377	0.0732	0.0035	-0.0388	0.1052	-0.0676	0.0898	1.3392	19.0229	-8.6251
2	1.6683	-0.236	0.2604	2.4442	0.9084	1.9469	-0.1896	-0.2055	0.2521	0.1909	0.0506	0.1044	-0.2266	-0.201	0.139	0.1433	0.0486	-0.0326	0.1067	-0.0272	0.0696	-0.9931	48.5565	8.7683

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	X-RAY DIFFRACTION	1	A	A	3 - 248	3 - 248
2	X-RAY DIFFRACTION	2	B	B	2 - 248	2 - 248

Refinement

*PLUS

Lowest resolution: 13.5 Å / % reflection R_free: 5 % / R_factor obs: 0.1841 / R_factor R_free: 0.22 / R_factor R_work: 0.1822

Solvent computation

*PLUS

Displacement parameters

*PLUS

Refine LS restraints

*PLUS

Refine-ID	Type	Dev ideal
X-RAY DIFFRACTION	r_bond_d	0.011
X-RAY DIFFRACTION	r_angle_d
X-RAY DIFFRACTION	r_angle_deg	1.309

LS refinement shell

*PLUS

Highest resolution: 2.25 Å / Lowest resolution: 2.3 Å

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