PDB-1r2r: CRYSTAL STRUCTURE OF RABBIT MUSCLE TRIOSEPHOSPHATE ISOMERASE

ID or keywords:

Entry

Database: PDB / ID: 1r2r

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

Biological species

Oryctolagus cuniculus (rabbit)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.5 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	Feb 14, 2024	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_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4	Apr 3, 2024	Group: Refinement description / Category: pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	1r2r.cif.gz	227.6 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	1r2r_validation.pdf.gz	482.8 KB	Display	wwPDB validaton report
Full document	1r2r_full_validation.pdf.gz	494.1 KB	Display
Data in XML	1r2r_validation.xml.gz	50.5 KB	Display
Data in CIF	1r2r_validation.cif.gz	74.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/r2/1r2r ftp://data.pdbj.org/pub/pdb/validation_reports/r2/1r2r	HTTPS FTP

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Related structure data

Related structure data	1r2sC 1r2tC C: citing same article (ref.)
Similar structure data	6up8-d 1r2t-d 1tpc-d 1sq7-d 7tim-d 2jk2-d 6oog-1 2i9e-1 4zvj-d 3th6-d 1sw0-d 4nvt-2 4obt-d 1sw7-d 6upf-d 1wob-1 1tpu-d 6nlh-3 1su5-d 3pvf-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) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

Related structure data

1r2sC

1r2tC

C: citing same article (ref.)

Similar structure data

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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

C: Triosephosphate isomerase

D: Triosephosphate isomerase

hetero molecules

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

1

A: Triosephosphate isomerase

B: Triosephosphate isomerase

hetero molecules

defined by author&software
54 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: Triosephosphate isomerase

D: Triosephosphate isomerase

hetero molecules

defined by author&software
54.4 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	74.550, 75.952, 166.010
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:

Dom-ID	Component-ID	Ens-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	1	THR	THR	LYS	LYS	2	A	A	213 - 218	213 - 218
2	1	1	THR	THR	LYS	LYS	2	B	B	213 - 218	213 - 218
3	1	1	THR	THR	LYS	LYS	2	C	C	213 - 218	213 - 218
4	1	1	THR	THR	LYS	LYS	2	D	D	213 - 218	213 - 218
5	2	1	LEU	LEU	ASP	ASP	2	A	A	220 - 227	220 - 227
6	2	1	LEU	LEU	ASP	ASP	2	B	B	220 - 227	220 - 227
7	2	1	LEU	LEU	ASP	ASP	2	C	C	220 - 227	220 - 227
8	2	1	LEU	LEU	ASP	ASP	2	D	D	220 - 227	220 - 227
1	1	2	GLU	GLU	GLU	GLU	5	A	A	219	219
2	1	2	GLU	GLU	GLU	GLU	5	B	B	219	219
3	1	2	GLU	GLU	GLU	GLU	5	C	C	219	219
4	1	2	GLU	GLU	GLU	GLU	5	D	D	219	219
1	1	3	ARG	ARG	GLY	GLY	2	A	A	4 - 10	4 - 10
2	1	3	ARG	ARG	GLY	GLY	2	B	B	4 - 10	4 - 10
3	1	3	ARG	ARG	GLY	GLY	2	C	C	4 - 10	4 - 10
4	1	3	ARG	ARG	GLY	GLY	2	D	D	4 - 10	4 - 10
1	1	4	GLY	GLY	THR	THR	3	B	B	137 - 139	137 - 139
2	1	4	GLY	GLY	THR	THR	3	D	D	137 - 139	137 - 139

NCS ensembles :

ID
1
2
3
4

Details

The asymmetric unit contains two physiologically active dimers formed by chains {A,B} and {C,D}

#1: Protein	Triosephosphate isomerase / TIM Mass: 26658.398 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Tissue: muscle / References: UniProt: P00939, triose-phosphate isomerase
#2: Chemical	ChemComp-DMS / DIMETHYL SULFOXIDE Mass: 78.133 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: C₂H₆OS / Comment: DMSO, precipitant*YM
#3: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Mg
#4: Chemical	ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₄H₁₂NO₃ / Comment: pH buffer*YM
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1151 / 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: 2.2 Å³/Da / Density % sol: 44.17 %

Crystal grow

Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG 4000, MgCl2, DMSO, 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: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å
Detector	Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 20, 2001 / Details: Toroidal Zerodur mirror
Radiation	Monochromator: [111] Diamond crystals / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.933 Å / Relative weight: 1
Reflection	Resolution: 1.5→33 Å / Num. all: 152459 / Num. obs: 135276 / % possible obs: 88.7 % / Observed criterion σ(I): 2 / Redundancy: 3.81 % / R_merge(I) obs: 0.066 / Net I/σ(I): 18.34
Reflection shell	Resolution: 1.5→1.52 Å / Redundancy: 2.06 % / R_merge(I) obs: 0.327 / Mean I/σ(I) obs: 2.25 / Num. unique all: 6005 / % possible all: 65.8
Reflection	PLUS Lowest resolution: 32.79 Å / R_merge(I) obs*: 0.067

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Processing

Software

Name	Version	Classification
REFMAC	5.1.24	refinement
DENZO		data reduction
SCALEPACK		data scaling
AMoRE		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: A partially refined dimer of rabbit muscle TIM structure (crystal form B)

Resolution: 1.5→32.79 Å / Cor.coef. F_o:F_c: 0.969 / Cor.coef. F_o:F_c free: 0.956 / SU B: 1.42 / SU ML: 0.051 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.078 / ESU R Free: 0.079 / Stereochemistry target values: MAXIMUM LIKELIHOOD

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.18954	6747	5 %	RANDOM
R_work	0.15942	-	-	-
all	0.16091	-	-	-
obs	0.16091	127887	89.1 %	-

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: 11.459 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.28 Å²	0 Å²	0 Å²
2-	-	-0.44 Å²	0 Å²
3-	-	-	0.72 Å²

Refinement step

Cycle: LAST / Resolution: 1.5→32.79 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7469	0	93	1151	8713

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.011	0.021	7745
X-RAY DIFFRACTION	r_bond_other_d	0.003	0.02	7132
X-RAY DIFFRACTION	r_angle_refined_deg	1.393	1.957	10494
X-RAY DIFFRACTION	r_angle_other_deg	0.834	3	16641
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.844	5	983
X-RAY DIFFRACTION	r_chiral_restr	0.084	0.2	1198
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	8561
X-RAY DIFFRACTION	r_gen_planes_other	0.003	0.02	1437
X-RAY DIFFRACTION	r_nbd_refined	0.215	0.2	1636
X-RAY DIFFRACTION	r_nbd_other	0.255	0.2	8199
X-RAY DIFFRACTION	r_nbtor_other	0.085	0.2	4147
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.174	0.2	791
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.248	0.2	23
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.264	0.2	74
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.208	0.2	77
X-RAY DIFFRACTION	r_mcbond_it	0.764	1.5	4920
X-RAY DIFFRACTION	r_mcangle_it	1.341	2	7928
X-RAY DIFFRACTION	r_scbond_it	2.074	3	2825
X-RAY DIFFRACTION	r_scangle_it	3.426	4.5	2561

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-ID	Dom-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	1	A	82	tight positional	0.06	0.05
1	2	B	82	tight positional	0.06	0.05
1	3	C	82	tight positional	0.05	0.05
1	4	D	82	tight positional	0.05	0.05
3	1	A	40	tight positional	0.03	0.05
3	2	B	40	tight positional	0.03	0.05
3	3	C	40	tight positional	0.05	0.05
3	4	D	40	tight positional	0.03	0.05
4	1	B	17	tight positional	0.02	0.05
1	1	A	94	medium positional	0.14	0.5
1	2	B	94	medium positional	0.15	0.5
1	3	C	94	medium positional	0.1	0.5
1	4	D	94	medium positional	0.1	0.5
2	1	A	6	medium positional	0.02	0.5
2	2	B	6	medium positional	0.07	0.5
2	3	C	6	medium positional	0.02	0.5
2	4	D	6	medium positional	0.03	0.5
3	1	A	73	medium positional	0.09	0.5
3	2	B	73	medium positional	0.11	0.5
3	3	C	73	medium positional	0.1	0.5
3	4	D	73	medium positional	0.08	0.5
2	1	A	9	loose positional	0.63	5
2	2	B	9	loose positional	1.86	5
2	3	C	9	loose positional	0.61	5
2	4	D	9	loose positional	0.65	5
4	1	B	22	loose positional	0.07	5
1	1	A	82	tight thermal	0.19	0.5
1	2	B	82	tight thermal	0.19	0.5
1	3	C	82	tight thermal	0.13	0.5
1	4	D	82	tight thermal	0.2	0.5
3	1	A	40	tight thermal	0.14	0.5
3	2	B	40	tight thermal	0.14	0.5
3	3	C	40	tight thermal	0.14	0.5
3	4	D	40	tight thermal	0.14	0.5
4	1	B	17	tight thermal	0.32	0.5
1	1	A	94	medium thermal	0.47	2
1	2	B	94	medium thermal	0.39	2
1	3	C	94	medium thermal	0.52	2
1	4	D	94	medium thermal	0.54	2
2	1	A	6	medium thermal	0.24	2
2	2	B	6	medium thermal	0.77	2
2	3	C	6	medium thermal	0.16	2
2	4	D	6	medium thermal	0.69	2
3	1	A	73	medium thermal	0.49	2
3	2	B	73	medium thermal	0.45	2
3	3	C	73	medium thermal	0.36	2
3	4	D	73	medium thermal	0.44	2
2	1	A	9	loose thermal	0.29	10
2	2	B	9	loose thermal	0.47	10
2	3	C	9	loose thermal	0.79	10
2	4	D	9	loose thermal	0.85	10
4	1	B	22	loose thermal	0.61	10

LS refinement shell

Resolution: 1.5→1.539 Å / Total num. of bins used: 20 /

	R_factor	Num. reflection
R_free	0.254	388
R_work	0.224	7502

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	0.5501	0.1914	-0.1999	1.0004	-0.0303	0.5012	-0.0229	0.0069	-0.1086	0.0194	-0.0126	-0.01	0.097	0.0407	0.0355	0.0737	0.0005	0.0235	0.0664	-0.0013	0.0386	14.3163	4.1275	34.0504
2	0.589	0.2161	-0.2311	1.1137	-0.7038	1.2346	0.1282	-0.0528	0.14	0.2251	-0.083	0.0658	-0.2995	0.1815	-0.0452	0.116	-0.0563	0.0426	0.0741	-0.0275	0.0438	21.2097	37.5952	31.631
3	0.524	0.3185	0.0841	1.218	-0.017	0.2898	-0.0303	0.0312	0.097	-0.0872	0.0501	0.1582	-0.0231	-0.0157	-0.0199	0.0079	-0.0058	-0.0064	0.0427	0.0251	0.0513	16.3125	59.5057	-6.9678
4	0.5164	0.1596	-0.0853	1.013	-0.1579	0.2481	-0.0391	0.029	-0.0709	-0.1584	0.051	0.0829	0.0596	0.0023	-0.0119	0.0299	-0.0085	-0.0043	0.0376	-0.0081	0.0517	13.267	25.2639	-5.2322

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
3	X-RAY DIFFRACTION	3	C	C	2 - 248	2 - 248
4	X-RAY DIFFRACTION	4	D	D	2 - 248	2 - 248

Refinement

*PLUS

R_factor obs: 0.1609 / R_factor R_free: 0.1895 / R_factor R_work: 0.1594

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	1.393

LS refinement shell

*PLUS

Highest resolution: 1.5 Å / Lowest resolution: 1.52 Å

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