1aw1

TRIOSEPHOSPHATE ISOMERASE OF VIBRIO MARINUS COMPLEXED WITH 2-PHOSPHOGLYCOLATE

Method: X-RAY DIFFRACTION D_max: 174.4 Å Quality: REASONABLE

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1. Protein Identity and Related Structures Protein Identity & Related Structures

TRIOSEPHOSPHATE ISOMERASE

Moritella marina

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 1–256 Chain B； UniProt 1–256	Not recorded	PGA 2-PHOSPHOGLYCOLIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions：pH 7.5；100MM TRIETHANOLAMINE/HCL 2.OM AMMONIUM SULFATE, 1MM DTT, EDTA, NAN3 20MM PGA PH 7.5	Resolution 2.70 Å R-free 0.215
2	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain D； UniProt 1–256 Chain E； UniProt 1–256	Not recorded	PGA 2-PHOSPHOGLYCOLIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions：pH 7.5；100MM TRIETHANOLAMINE/HCL 2.OM AMMONIUM SULFATE, 1MM DTT, EDTA, NAN3 20MM PGA PH 7.5	Resolution 2.70 Å R-free 0.215
3	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain G； UniProt 1–256 Chain H； UniProt 1–256	Not recorded	PGA 2-PHOSPHOGLYCOLIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions：pH 7.5；100MM TRIETHANOLAMINE/HCL 2.OM AMMONIUM SULFATE, 1MM DTT, EDTA, NAN3 20MM PGA PH 7.5	Resolution 2.70 Å R-free 0.215
4	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain J； UniProt 1–256 Chain K； UniProt 1–256	Not recorded	PGA 2-PHOSPHOGLYCOLIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions：pH 7.5；100MM TRIETHANOLAMINE/HCL 2.OM AMMONIUM SULFATE, 1MM DTT, EDTA, NAN3 20MM PGA PH 7.5	Resolution 2.70 Å R-free 0.215

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 1AW1	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1AW2 TRIOSEPHOSPHATE ISOMERASE OF VIBRIO MARINUS Deposited 1997-10-09	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–256（256 aa） Chain B 1–256（256 aa）	Not recorded	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；100MM TRIETHANOLAMINE/HCL 100MM AMMONIUM SULFATE, 1MM DTT, EDTA, NAN3 1.26M SODIUM CITRATE PH 7.0	Resolution 2.65 Å R-free 0.219
1AW2 TRIOSEPHOSPHATE ISOMERASE OF VIBRIO MARINUS Deposited 1997-10-09	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain D 1–256（256 aa） Chain E 1–256（256 aa）	Not recorded	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；100MM TRIETHANOLAMINE/HCL 100MM AMMONIUM SULFATE, 1MM DTT, EDTA, NAN3 1.26M SODIUM CITRATE PH 7.0	Resolution 2.65 Å R-free 0.219
1AW2 TRIOSEPHOSPHATE ISOMERASE OF VIBRIO MARINUS Deposited 1997-10-09	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain G 1–256（256 aa） Chain H 1–256（256 aa）	Not recorded	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；100MM TRIETHANOLAMINE/HCL 100MM AMMONIUM SULFATE, 1MM DTT, EDTA, NAN3 1.26M SODIUM CITRATE PH 7.0	Resolution 2.65 Å R-free 0.219
1AW2 TRIOSEPHOSPHATE ISOMERASE OF VIBRIO MARINUS Deposited 1997-10-09	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain J 1–256（256 aa） Chain K 1–256（256 aa）	Not recorded	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；100MM TRIETHANOLAMINE/HCL 100MM AMMONIUM SULFATE, 1MM DTT, EDTA, NAN3 1.26M SODIUM CITRATE PH 7.0	Resolution 2.65 Å R-free 0.219

1 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	TPIS_VIBMA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–256； UniProt 1–256 Author chain B； PDBConstruct 1–256； UniProt 1–256 Author chain D； PDBConstruct 1–256； UniProt 1–256 Author chain E； PDBConstruct 1–256； UniProt 1–256 Author chain G； PDBConstruct 1–256； UniProt 1–256 Author chain H； PDBConstruct 1–256； UniProt 1–256 Author chain J； PDBConstruct 1–256； UniProt 1–256 Author chain K； PDBConstruct 1–256； UniProt 1–256

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	1aw1
Deposition date deposition_date	1997-10-09
Structure title title	TRIOSEPHOSPHATE ISOMERASE OF VIBRIO MARINUS COMPLEXED WITH 2-PHOSPHOGLYCOLATE
Keywords keywords	ISOMERASE, PSYCHROPHILIC, VIBRIO MARINUS; ISOMERASE
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	52.03 Å
Radius of gyration Rg (electron density) rg_electron	52.08 Å
Forward intensity I(0) i0	687111000.00
Molecular weight molecular_weight	213660.0 kDa
Excluded volume excluded_volume	265740 Å³
Envelope volume envelope_volume	358650 Å³
Hydration-shell volume shell_volume	59802 Å³
Envelope diameter envelope_diameter	181.0 Å
Shell Rg shell_rg	51.22 Å
Envelope Rg envelope_rg	51.61 Å
Shape Rg shape_rg	52.09 Å
Total Rg total_rg	52.04 Å
Total atoms total_atoms	15016
Residues n_residues	2036
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	174.4 Å
Rg (real space) rg_real	52.16 Å
Rg uncertainty (real space) rg_real_error	2.12 Å
I(0) (real space) i0_real	6.8710e+08
I(0) uncertainty (real space) i0_real_error	1.2670e+07
Rg (reciprocal space) rg_reciprocal	51.91 Å
I(0) (reciprocal space) i0_reciprocal	686900000.0000
Solution quality estimate total_estimate	0.6251
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	63.9 Å
Skewness Skewness skewness	0.318
Kurtosis Kurtosis kurtosis	-0.403
Angular range angular_range	— – 0.1500 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	22160000.0000
Real-space data points n_real_points	31
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.879; Stabil: 1.000; Sysdev: 0.007; Positv: 1.000; Valcen: 0.979; Smooth: 0.486

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	TRIOSEPHOSPHATE ISOMERASE
Molecular weight formula_weight	26766.2 kDa
EC 编号 ec_number	5.3.1.1
Source method src_method	man
Copy count entity_count	8

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,D,E,G,H,J,K
Atom count atom_count	15324

MRHPVVMGNWKLNGSKEMVVDLLNGLNAELEGVTGVDVAVAPPALFVDLAERTLTEAGSAIILGAQNTDLNNSGAFTGDMSPAMLKEFGATHIIIGHSERREYHAESDEFVAKKFAFLKENGLTPVLCIGESDAQNEAGETMAVCARQLDAVINTQGVEALEGAIIAYEPIWAIGTGKAATAEDAQRIHAQIRAHIAEKSEAVAKNVVIQYGGSVKPENAAAYFAQPDIDGALVGGAALDAKSFAAIAKAAAEAKA

来源 Source

来源生物 organism	Moritella marina
NCBI Class编号 ncbi_taxonomy_id	90736
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	2-PHOSPHOGLYCOLIC ACID
Molecular weight formula_weight	156.0 kDa
Source method src_method	man
Copy count entity_count	8

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	308

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7. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d1aw1a_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.1 — Triosephosphate isomerase (TIM)
Family Family family	c.1.1.1 — Triosephosphate isomerase (TIM)

Domain ID domain_id	d1aw1b_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.1 — Triosephosphate isomerase (TIM)
Family Family family	c.1.1.1 — Triosephosphate isomerase (TIM)

Domain ID domain_id	d1aw1d_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.1 — Triosephosphate isomerase (TIM)
Family Family family	c.1.1.1 — Triosephosphate isomerase (TIM)

Domain ID domain_id	d1aw1e_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.1 — Triosephosphate isomerase (TIM)
Family Family family	c.1.1.1 — Triosephosphate isomerase (TIM)

Domain ID domain_id	d1aw1g_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.1 — Triosephosphate isomerase (TIM)
Family Family family	c.1.1.1 — Triosephosphate isomerase (TIM)

Domain ID domain_id	d1aw1h_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.1 — Triosephosphate isomerase (TIM)
Family Family family	c.1.1.1 — Triosephosphate isomerase (TIM)

Domain ID domain_id	d1aw1j_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.1 — Triosephosphate isomerase (TIM)
Family Family family	c.1.1.1 — Triosephosphate isomerase (TIM)

Domain ID domain_id	d1aw1k_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.1 — Triosephosphate isomerase (TIM)
Family Family family	c.1.1.1 — Triosephosphate isomerase (TIM)

CATH v4.4 (8 domains)

Domain ID domain_id	1aw1A00
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	70 — Aldolase class I

Domain ID domain_id	1aw1B00
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	70 — Aldolase class I

Domain ID domain_id	1aw1D00
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	70 — Aldolase class I

Domain ID domain_id	1aw1E00
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	70 — Aldolase class I

Domain ID domain_id	1aw1G00
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	70 — Aldolase class I

Domain ID domain_id	1aw1H00
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	70 — Aldolase class I

Domain ID domain_id	1aw1J00
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	70 — Aldolase class I

Domain ID domain_id	1aw1K00
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	70 — Aldolase class I

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8. Citations (1)

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Unit-cell length a length_a	89.508 Å
Unit-cell length b length_b	138.076 Å
Unit-cell length c length_c	89.524 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	91.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	16

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.700 Å
Low-resolution limit resolution_low	8.000 Å
R factor r_factor	0.1920
R_work r_work	0.1920
R_free r_free	0.2150

fit	/app/data/saxs_computation/aw/1aw1/1aw1.fit
pddf	/app/data/pr_computation/aw/1aw1/1aw1.pr.out
profile	/app/data/saxs_computation/aw/1aw1/1aw1.dat