1cer

DETERMINANTS OF ENZYME THERMOSTABILITY OBSERVED IN THE MOLECULAR STRUCTURE OF THERMUS AQUATICUS D-GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE AT 2.5 ANGSTROMS RESOLUTION

Method: X-RAY DIFFRACTION D_max: 165.0 Å Quality: GOOD

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

HOLO-D-GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE

Thermus aquaticus

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 × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain O； UniProt 1–331 Chain P； UniProt 1–331 Chain Q； UniProt 1–331 Chain R； UniProt 1–331	Not recorded	NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 4	X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions	Resolution 2.50 Å
2	Protein homooligomer Homooligomer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 1–331 Chain B； UniProt 1–331 Chain C； UniProt 1–331 Chain D； UniProt 1–331	Not recorded	NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 4	X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions	Resolution 2.50 Å

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 1CER	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2G82 High Resolution Structures of Thermus aquaticus Glyceraldehyde-3-Phosphate Dehydrogenase: Role of 220's Loop Motion in Catalysis Deposited 2006-03-01	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain O 1–331（331 aa） Chain P 1–331（331 aa） Chain Q 1–331（331 aa） Chain R 1–331（331 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 4 IPA ISOPROPYL ALCOHOL × 1 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.3；295 K；23% PEG 300, 0.1 M Hepes, 15% isopropanol, and 5% glycerol, pH 8.3, VAPOR DIFFUSION, SITTING DROP, temperature 295K	Resolution 1.65 Å R-free 0.172
2G82 High Resolution Structures of Thermus aquaticus Glyceraldehyde-3-Phosphate Dehydrogenase: Role of 220's Loop Motion in Catalysis Deposited 2006-03-01	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–331（331 aa） Chain B 1–331（331 aa） Chain C 1–331（331 aa） Chain D 1–331（331 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 4 IPA ISOPROPYL ALCOHOL × 1 GOL GLYCEROL × 1 NA SODIUM ION × 1 PGE TRIETHYLENE GLYCOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.3；295 K；23% PEG 300, 0.1 M Hepes, 15% isopropanol, and 5% glycerol, pH 8.3, VAPOR DIFFUSION, SITTING DROP, temperature 295K	Resolution 1.65 Å R-free 0.172

1 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	G3P_THEAQ
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–331； UniProt 1–331 Author chain B； PDBConstruct 1–331； UniProt 1–331 Author chain C； PDBConstruct 1–331； UniProt 1–331 Author chain D； PDBConstruct 1–331； UniProt 1–331 Author chain O； PDBConstruct 1–331； UniProt 1–331 Author chain P； PDBConstruct 1–331； UniProt 1–331 Author chain Q； PDBConstruct 1–331； UniProt 1–331 Author chain R； PDBConstruct 1–331； UniProt 1–331

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	1cer
Deposition date deposition_date	1995-11-11
Structure title title	DETERMINANTS OF ENZYME THERMOSTABILITY OBSERVED IN THE MOLECULAR STRUCTURE OF THERMUS AQUATICUS D-GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE AT 2.5 ANGSTROMS RESOLUTION
Keywords keywords	GLYCOLYSIS, OXIDOREDUCTASE, NAD, OXIDOREDUCTASE (ALDEHYDE(D)-NAD(A)); OXIDOREDUCTASE (ALDEHYDE(D)-NAD(A))
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	48.13 Å
Radius of gyration Rg (electron density) rg_electron	48.31 Å
Forward intensity I(0) i0	1178980000.00
Molecular weight molecular_weight	287270.0 kDa
Excluded volume excluded_volume	360620 Å³
Envelope volume envelope_volume	457850 Å³
Hydration-shell volume shell_volume	79238 Å³
Envelope diameter envelope_diameter	176.0 Å
Shell Rg shell_rg	51.51 Å
Envelope Rg envelope_rg	47.58 Å
Shape Rg shape_rg	48.32 Å
Total Rg total_rg	48.40 Å
Total atoms total_atoms	20226
Residues n_residues	2648
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	165.0 Å
Rg (real space) rg_real	48.37 Å
Rg uncertainty (real space) rg_real_error	1.72 Å
I(0) (real space) i0_real	1.1790e+09
I(0) uncertainty (real space) i0_real_error	2.2840e+07
Rg (reciprocal space) rg_reciprocal	48.13 Å
I(0) (reciprocal space) i0_reciprocal	1179000000.0000
Solution quality estimate total_estimate	0.8518
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	50.0 Å
Skewness Skewness skewness	0.440
Kurtosis Kurtosis kurtosis	-0.441
Angular range angular_range	— – 0.1650 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	111900000.0000
Real-space data points n_real_points	34
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.756; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.986; Smooth: 0.813

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 32 domains

SCOP 2.08 (16 domains)

Domain ID domain_id	d1cera1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.2 — NAD(P)-binding Rossmann-fold domains
Superfamily Superfamily superfamily	c.2.1 — NAD(P)-binding Rossmann-fold domains
Family Family family	c.2.1.3 — Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminal domain

Domain ID domain_id	d1cera2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.81 — FwdE/GAPDH domain-like
Superfamily Superfamily superfamily	d.81.1 — Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain
Family Family family	d.81.1.1 — GAPDH-like

Domain ID domain_id	d1cerb1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.2 — NAD(P)-binding Rossmann-fold domains
Superfamily Superfamily superfamily	c.2.1 — NAD(P)-binding Rossmann-fold domains
Family Family family	c.2.1.3 — Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminal domain

Domain ID domain_id	d1cerb2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.81 — FwdE/GAPDH domain-like
Superfamily Superfamily superfamily	d.81.1 — Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain
Family Family family	d.81.1.1 — GAPDH-like

Domain ID domain_id	d1cerc1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.2 — NAD(P)-binding Rossmann-fold domains
Superfamily Superfamily superfamily	c.2.1 — NAD(P)-binding Rossmann-fold domains
Family Family family	c.2.1.3 — Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminal domain

Domain ID domain_id	d1cerc2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.81 — FwdE/GAPDH domain-like
Superfamily Superfamily superfamily	d.81.1 — Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain
Family Family family	d.81.1.1 — GAPDH-like

Domain ID domain_id	d1cerd1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.2 — NAD(P)-binding Rossmann-fold domains
Superfamily Superfamily superfamily	c.2.1 — NAD(P)-binding Rossmann-fold domains
Family Family family	c.2.1.3 — Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminal domain

Domain ID domain_id	d1cerd2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.81 — FwdE/GAPDH domain-like
Superfamily Superfamily superfamily	d.81.1 — Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain
Family Family family	d.81.1.1 — GAPDH-like

Domain ID domain_id	d1cero1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.2 — NAD(P)-binding Rossmann-fold domains
Superfamily Superfamily superfamily	c.2.1 — NAD(P)-binding Rossmann-fold domains
Family Family family	c.2.1.3 — Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminal domain

Domain ID domain_id	d1cero2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.81 — FwdE/GAPDH domain-like
Superfamily Superfamily superfamily	d.81.1 — Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain
Family Family family	d.81.1.1 — GAPDH-like

Domain ID domain_id	d1cerp1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.2 — NAD(P)-binding Rossmann-fold domains
Superfamily Superfamily superfamily	c.2.1 — NAD(P)-binding Rossmann-fold domains
Family Family family	c.2.1.3 — Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminal domain

Domain ID domain_id	d1cerp2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.81 — FwdE/GAPDH domain-like
Superfamily Superfamily superfamily	d.81.1 — Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain
Family Family family	d.81.1.1 — GAPDH-like

Domain ID domain_id	d1cerq1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.2 — NAD(P)-binding Rossmann-fold domains
Superfamily Superfamily superfamily	c.2.1 — NAD(P)-binding Rossmann-fold domains
Family Family family	c.2.1.3 — Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminal domain

Domain ID domain_id	d1cerq2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.81 — FwdE/GAPDH domain-like
Superfamily Superfamily superfamily	d.81.1 — Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain
Family Family family	d.81.1.1 — GAPDH-like

Domain ID domain_id	d1cerr1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.2 — NAD(P)-binding Rossmann-fold domains
Superfamily Superfamily superfamily	c.2.1 — NAD(P)-binding Rossmann-fold domains
Family Family family	c.2.1.3 — Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminal domain

Domain ID domain_id	d1cerr2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.81 — FwdE/GAPDH domain-like
Superfamily Superfamily superfamily	d.81.1 — Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain
Family Family family	d.81.1.1 — GAPDH-like

CATH v4.4 (16 domains)

Domain ID domain_id	1cerA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	720 — NAD(P)-binding Rossmann-like Domain

Domain ID domain_id	1cerA02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	360 — Dihydrodipicolinate Reductase; domain 2
Homologous superfamily homologous superfamily	10 — Dihydrodipicolinate Reductase; domain 2

Domain ID domain_id	1cerB01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	720 — NAD(P)-binding Rossmann-like Domain

Domain ID domain_id	1cerB02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	360 — Dihydrodipicolinate Reductase; domain 2
Homologous superfamily homologous superfamily	10 — Dihydrodipicolinate Reductase; domain 2

Domain ID domain_id	1cerC01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	720 — NAD(P)-binding Rossmann-like Domain

Domain ID domain_id	1cerC02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	360 — Dihydrodipicolinate Reductase; domain 2
Homologous superfamily homologous superfamily	10 — Dihydrodipicolinate Reductase; domain 2

Domain ID domain_id	1cerD01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	720 — NAD(P)-binding Rossmann-like Domain

Domain ID domain_id	1cerD02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	360 — Dihydrodipicolinate Reductase; domain 2
Homologous superfamily homologous superfamily	10 — Dihydrodipicolinate Reductase; domain 2

Domain ID domain_id	1cerO01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	720 — NAD(P)-binding Rossmann-like Domain

Domain ID domain_id	1cerO02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	360 — Dihydrodipicolinate Reductase; domain 2
Homologous superfamily homologous superfamily	10 — Dihydrodipicolinate Reductase; domain 2

Domain ID domain_id	1cerP01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	720 — NAD(P)-binding Rossmann-like Domain

Domain ID domain_id	1cerP02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	360 — Dihydrodipicolinate Reductase; domain 2
Homologous superfamily homologous superfamily	10 — Dihydrodipicolinate Reductase; domain 2

Domain ID domain_id	1cerQ01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	720 — NAD(P)-binding Rossmann-like Domain

Domain ID domain_id	1cerQ02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	360 — Dihydrodipicolinate Reductase; domain 2
Homologous superfamily homologous superfamily	10 — Dihydrodipicolinate Reductase; domain 2

Domain ID domain_id	1cerR01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	720 — NAD(P)-binding Rossmann-like Domain

Domain ID domain_id	1cerR02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	360 — Dihydrodipicolinate Reductase; domain 2
Homologous superfamily homologous superfamily	10 — Dihydrodipicolinate Reductase; domain 2

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8. Citations (2)

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Unit-cell length a length_a	144.770 Å
Unit-cell length b length_b	148.770 Å
Unit-cell length c length_c	149.500 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	32

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.500 Å
Low-resolution limit resolution_low	12.000 Å
R factor r_factor	0.2050
R_work r_work	0.2050
R_free r_free	—

Description description	HOLO-D-GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE
Molecular weight formula_weight	35941.3 kDa
EC 编号 ec_number	1.2.1.12
Source method src_method	man
Copy count entity_count	8

Polymer type type	polypeptide(L)
Chain IDs strand_id	O,P,Q,R,A,B,C,D
Atom count atom_count	20226

DETERMINANTS OF ENZYME THERMOSTABILITY OBSERVED IN THE MOLECULAR STRUCTURE OF THERMUS AQUATICUS D-GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE AT 2.5 ANGSTROMS RESOLUTION

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

HOLO-D-GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

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

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

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 non-polymer

7. Fold Classification (SCOP + CATH) 32 domains

SCOP 2.08 (16 domains)

CATH v4.4 (16 domains)

8. Citations (2)

9. Files and Curves (10)

Files (7)

Curves (3)

来源生物 organism	Thermus aquaticus
NCBI Class编号 ncbi_taxonomy_id	271
宿主生物 host_organism	Escherichia coli

Description description	NICOTINAMIDE-ADENINE-DINUCLEOTIDE
Molecular weight formula_weight	663.4 kDa
Source method src_method	syn
Copy count entity_count	8

fit	/app/data/saxs_computation/ce/1cer/1cer.fit
pddf	/app/data/pr_computation/ce/1cer/1cer.pr.out
profile	/app/data/saxs_computation/ce/1cer/1cer.dat