SAXSdb — 1ckm

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

MRNA CAPPING ENZYME

Paramecium bursaria Chlorella virus 1

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 1–330	Not recorded	GTP GUANOSINE-5'-TRIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；HANGING DROP VAPOR DIFFUSION. 10-15 MG/ML PROTEIN IN 50 MM TRIS-HCL, 0.5 M NACL, 10 MM MGCL2, 5MM GTP, 2 MM EDTA, 4 MM DTT, PH 7.5 WERE MIXED WITH AN EQUAL VOLUME OF AND EQUILIBRATED AGAINST 100 MM TRIS-HCL, 200 MM NACL, 200 MM AMMONIUM SULFATE 34% MEOPEG 5000, PH 7.5., vapor diffusion - hanging drop	Resolution 2.50 Å R-free 0.299
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 1–330	Not recorded	GTP GUANOSINE-5'-TRIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；HANGING DROP VAPOR DIFFUSION. 10-15 MG/ML PROTEIN IN 50 MM TRIS-HCL, 0.5 M NACL, 10 MM MGCL2, 5MM GTP, 2 MM EDTA, 4 MM DTT, PH 7.5 WERE MIXED WITH AN EQUAL VOLUME OF AND EQUILIBRATED AGAINST 100 MM TRIS-HCL, 200 MM NACL, 200 MM AMMONIUM SULFATE 34% MEOPEG 5000, PH 7.5., vapor diffusion - hanging drop	Resolution 2.50 Å R-free 0.299
3	Protein homooligomer Homooligomer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 1–330 Chain B； UniProt 1–330	Not recorded	GTP GUANOSINE-5'-TRIPHOSPHATE × 4	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；HANGING DROP VAPOR DIFFUSION. 10-15 MG/ML PROTEIN IN 50 MM TRIS-HCL, 0.5 M NACL, 10 MM MGCL2, 5MM GTP, 2 MM EDTA, 4 MM DTT, PH 7.5 WERE MIXED WITH AN EQUAL VOLUME OF AND EQUILIBRATED AGAINST 100 MM TRIS-HCL, 200 MM NACL, 200 MM AMMONIUM SULFATE 34% MEOPEG 5000, PH 7.5., vapor diffusion - hanging drop	Resolution 2.50 Å R-free 0.299
4	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 1–330 Chain B； UniProt 1–330	Not recorded	GTP GUANOSINE-5'-TRIPHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；HANGING DROP VAPOR DIFFUSION. 10-15 MG/ML PROTEIN IN 50 MM TRIS-HCL, 0.5 M NACL, 10 MM MGCL2, 5MM GTP, 2 MM EDTA, 4 MM DTT, PH 7.5 WERE MIXED WITH AN EQUAL VOLUME OF AND EQUILIBRATED AGAINST 100 MM TRIS-HCL, 200 MM NACL, 200 MM AMMONIUM SULFATE 34% MEOPEG 5000, PH 7.5., vapor diffusion - hanging drop	Resolution 2.50 Å R-free 0.299
5	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 1–330	Not recorded	GTP GUANOSINE-5'-TRIPHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；HANGING DROP VAPOR DIFFUSION. 10-15 MG/ML PROTEIN IN 50 MM TRIS-HCL, 0.5 M NACL, 10 MM MGCL2, 5MM GTP, 2 MM EDTA, 4 MM DTT, PH 7.5 WERE MIXED WITH AN EQUAL VOLUME OF AND EQUILIBRATED AGAINST 100 MM TRIS-HCL, 200 MM NACL, 200 MM AMMONIUM SULFATE 34% MEOPEG 5000, PH 7.5., vapor diffusion - hanging drop	Resolution 2.50 Å R-free 0.299

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 1CKM	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1CKN STRUCTURE OF GUANYLYLATED MRNA CAPPING ENZYME COMPLEXED WITH GTP Deposited 1997-04-20	Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–330（330 aa）	Not recorded	GTP GUANOSINE-5'-TRIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；HANGING DROP VAPOR DIFFUSION. 10-15 MG/ML PROTEIN IN 50 MM TRIS-HCL, 0.5 M NACL, 10 MM MGCL2, 5MM GTP, 2 MM EDTA, 4 MM DTT, PH 7.5 WERE MIXED WITH AN EQUAL VOLUME OF AND EQUILIBRATED AGAINST 100 MM TRIS- HCL, 200 MM NACL, 200 MM AMMONIUM SULFATE, 34% MEOPEG 5000, PH 7.5. THE CRYSTALS WERE SOAKED IN EQUILIBRATION SOLUTION WITH 100 MM MANGANESE(II)CHLORIDE AND 5 MM GTP FOR 4 HOURS PRIOR TO DATA COLLECTION., vapor diffusion - hanging drop	Resolution 2.50 Å R-free 0.299
1CKN STRUCTURE OF GUANYLYLATED MRNA CAPPING ENZYME COMPLEXED WITH GTP Deposited 1997-04-20	Different mutation/modification Different ligand/ion Different experimental conditions	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–330（330 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	MN MANGANESE (II) ION × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；HANGING DROP VAPOR DIFFUSION. 10-15 MG/ML PROTEIN IN 50 MM TRIS-HCL, 0.5 M NACL, 10 MM MGCL2, 5MM GTP, 2 MM EDTA, 4 MM DTT, PH 7.5 WERE MIXED WITH AN EQUAL VOLUME OF AND EQUILIBRATED AGAINST 100 MM TRIS- HCL, 200 MM NACL, 200 MM AMMONIUM SULFATE, 34% MEOPEG 5000, PH 7.5. THE CRYSTALS WERE SOAKED IN EQUILIBRATION SOLUTION WITH 100 MM MANGANESE(II)CHLORIDE AND 5 MM GTP FOR 4 HOURS PRIOR TO DATA COLLECTION., vapor diffusion - hanging drop	Resolution 2.50 Å R-free 0.299
1CKN STRUCTURE OF GUANYLYLATED MRNA CAPPING ENZYME COMPLEXED WITH GTP Deposited 1997-04-20	Different mutation/modification Different ligand/ion Different experimental conditions	Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–330（330 aa） Chain B 1–330（330 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MN MANGANESE (II) ION × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；HANGING DROP VAPOR DIFFUSION. 10-15 MG/ML PROTEIN IN 50 MM TRIS-HCL, 0.5 M NACL, 10 MM MGCL2, 5MM GTP, 2 MM EDTA, 4 MM DTT, PH 7.5 WERE MIXED WITH AN EQUAL VOLUME OF AND EQUILIBRATED AGAINST 100 MM TRIS- HCL, 200 MM NACL, 200 MM AMMONIUM SULFATE, 34% MEOPEG 5000, PH 7.5. THE CRYSTALS WERE SOAKED IN EQUILIBRATION SOLUTION WITH 100 MM MANGANESE(II)CHLORIDE AND 5 MM GTP FOR 4 HOURS PRIOR TO DATA COLLECTION., vapor diffusion - hanging drop	Resolution 2.50 Å R-free 0.299
1CKN STRUCTURE OF GUANYLYLATED MRNA CAPPING ENZYME COMPLEXED WITH GTP Deposited 1997-04-20	Different experimental conditions	Assembly 4 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–330（330 aa）	Not recorded	GTP GUANOSINE-5'-TRIPHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；HANGING DROP VAPOR DIFFUSION. 10-15 MG/ML PROTEIN IN 50 MM TRIS-HCL, 0.5 M NACL, 10 MM MGCL2, 5MM GTP, 2 MM EDTA, 4 MM DTT, PH 7.5 WERE MIXED WITH AN EQUAL VOLUME OF AND EQUILIBRATED AGAINST 100 MM TRIS- HCL, 200 MM NACL, 200 MM AMMONIUM SULFATE, 34% MEOPEG 5000, PH 7.5. THE CRYSTALS WERE SOAKED IN EQUILIBRATION SOLUTION WITH 100 MM MANGANESE(II)CHLORIDE AND 5 MM GTP FOR 4 HOURS PRIOR TO DATA COLLECTION., vapor diffusion - hanging drop	Resolution 2.50 Å R-free 0.299
1CKO STRUCTURE OF MRNA CAPPING ENZYME IN COMPLEX WITH THE CAP ANALOG GPPPG Deposited 1997-09-06	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–330（330 aa）	Not recorded	ZN ZINC ION × 1 GP3 DIGUANOSINE-5'-TRIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；HANGING DROP VAPOR DIFFUSION. 15 MG/ML PROTEIN IN 50 MM TRIS-HCL, 1.3 MM CAP ANALOG (GPPPG) 0.4 M NACL, 2 MM EDTA, 4 MM DTT, PH 7.5 WERE MIXED WITH AN EQUAL VOLUME OF AND EQUILIBRATED AGAINST 50 MM POTASSIUM PHOSPHATE, 5-10% PEG 8000, 2MM ZNCL2 PH 6.5., vapor diffusion - hanging drop	Resolution 3.10 Å R-free 0.314
1CKO STRUCTURE OF MRNA CAPPING ENZYME IN COMPLEX WITH THE CAP ANALOG GPPPG Deposited 1997-09-06	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–330（330 aa）	Not recorded	ZN ZINC ION × 2 GP3 DIGUANOSINE-5'-TRIPHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；HANGING DROP VAPOR DIFFUSION. 15 MG/ML PROTEIN IN 50 MM TRIS-HCL, 1.3 MM CAP ANALOG (GPPPG) 0.4 M NACL, 2 MM EDTA, 4 MM DTT, PH 7.5 WERE MIXED WITH AN EQUAL VOLUME OF AND EQUILIBRATED AGAINST 50 MM POTASSIUM PHOSPHATE, 5-10% PEG 8000, 2MM ZNCL2 PH 6.5., vapor diffusion - hanging drop	Resolution 3.10 Å R-free 0.314

2 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	MCE_CHVP1
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–330； UniProt 1–330 Author chain B； PDBConstruct 1–330； UniProt 1–330

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	1ckm
Deposition date deposition_date	1997-04-20
Structure title title	STRUCTURE OF TWO DIFFERENT CONFORMATIONS OF MRNA CAPPING ENZYME IN COMPLEX WITH GTP
Keywords keywords	MRNA, CAPPING ENZYME, NUCLEOTIDYLTRANSFERASE; CAPPING ENZYME
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	27.62 Å
Radius of gyration Rg (electron density) rg_electron	26.99 Å
Forward intensity I(0) i0	83166800.00
Molecular weight molecular_weight	73713.0 kDa
Excluded volume excluded_volume	93297 Å³
Envelope volume envelope_volume	113940 Å³
Hydration-shell volume shell_volume	34846 Å³
Envelope diameter envelope_diameter	87.6 Å
Shell Rg shell_rg	34.77 Å
Envelope Rg envelope_rg	26.77 Å
Shape Rg shape_rg	26.98 Å
Total Rg total_rg	27.83 Å
Total atoms total_atoms	5186
Residues n_residues	634
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	86.2 Å
Rg (real space) rg_real	27.55 Å
Rg uncertainty (real space) rg_real_error	0.47 Å
I(0) (real space) i0_real	8.3170e+07
I(0) uncertainty (real space) i0_real_error	1.1350e+06
Rg (reciprocal space) rg_reciprocal	27.58 Å
I(0) (reciprocal space) i0_reciprocal	83170000.0000
Solution quality estimate total_estimate	0.9029
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	31.8 Å
Skewness Skewness skewness	0.288
Kurtosis Kurtosis kurtosis	-0.452
Angular range angular_range	— – 0.2850 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	27980000.0000
Real-space data points n_real_points	58
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.935; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.928

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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	MRNA CAPPING ENZYME
Molecular weight formula_weight	37885.0 kDa
EC 编号 ec_number	2.7.7.50
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	5546

MVPPTINTGKNITTERAVLTLNGLQIKLHKVVGESRDDIVAKMKDLAMDDHKFPRLPGPNPVSIERKDFEKLKQNKYVVSEKTDGIRFMMFFTRVFGFKVCTIIDRAMTVYLLPFKNIPRVLFQGSIFDGELCVDIVEKKFAFVLFDAVVVSGVTVSQMDLASRFFAMKRSLKEFKNVPEDPAILRYKEWIPLEHPTIIKDHLKKANAIYHTDGLIIMSVDEPVIYGRNFNLFKLKPGTHHTIDFIIMSEDGTIGIFDPNLRKNVPVGKLDGYYNKGSIVECGFADGTWKYIQGRSDKNQANDRLTYEKTLLNIEENITIDELLDLFKWE

来源 Source

来源生物 organism	Paramecium bursaria Chlorella virus 1
NCBI Class编号 ncbi_taxonomy_id	10506
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	GUANOSINE-5'-TRIPHOSPHATE
Molecular weight formula_weight	523.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	360

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7. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1ckma1
Class class	b — All beta proteins
Fold Fold fold	b.40 — OB-fold
Superfamily Superfamily superfamily	b.40.4 — Nucleic acid-binding proteins
Family Family family	b.40.4.6 — DNA ligase/mRNA capping enzyme postcatalytic domain

Domain ID domain_id	d1ckma2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.142 — ATP-grasp
Superfamily Superfamily superfamily	d.142.2 — DNA ligase/mRNA capping enzyme, catalytic domain
Family Family family	d.142.2.3 — mRNA capping enzyme

Domain ID domain_id	d1ckmb1
Class class	b — All beta proteins
Fold Fold fold	b.40 — OB-fold
Superfamily Superfamily superfamily	b.40.4 — Nucleic acid-binding proteins
Family Family family	b.40.4.6 — DNA ligase/mRNA capping enzyme postcatalytic domain

Domain ID domain_id	d1ckmb2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.142 — ATP-grasp
Superfamily Superfamily superfamily	d.142.2 — DNA ligase/mRNA capping enzyme, catalytic domain
Family Family family	d.142.2.3 — mRNA capping enzyme

CATH v4.4 (6 domains)

Domain ID domain_id	1ckmA01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	470 — D-amino Acid Aminotransferase; Chain A, domain 1
Homologous superfamily homologous superfamily	30 — DNA ligase/mRNA capping enzyme

Domain ID domain_id	1ckmA02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	140 — Nucleic acid-binding proteins

Domain ID domain_id	1ckmA03
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	87 — mRNA Capping Enzyme; Chain
Homologous superfamily homologous superfamily	10 — mRNA Capping Enzyme; domain 3

Domain ID domain_id	1ckmB01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	470 — D-amino Acid Aminotransferase; Chain A, domain 1
Homologous superfamily homologous superfamily	30 — DNA ligase/mRNA capping enzyme

Domain ID domain_id	1ckmB02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	140 — Nucleic acid-binding proteins

Domain ID domain_id	1ckmB03
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	87 — mRNA Capping Enzyme; Chain
Homologous superfamily homologous superfamily	10 — mRNA Capping Enzyme; domain 3

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8. Citations (2)

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Unit-cell length a length_a	93.332 Å
Unit-cell length b length_b	214.931 Å
Unit-cell length c length_c	105.752 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	16

Space group space_group	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	2.500 Å
Low-resolution limit resolution_low	10.000 Å
R factor r_factor	0.2180
R_work r_work	0.2180
R_free r_free	0.2990

fit	/app/data/saxs_computation/ck/1ckm/1ckm.fit
pddf	/app/data/pr_computation/ck/1ckm/1ckm.pr.out
profile	/app/data/saxs_computation/ck/1ckm/1ckm.dat

STRUCTURE OF TWO DIFFERENT CONFORMATIONS OF MRNA CAPPING ENZYME IN COMPLEX WITH GTP

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

MRNA CAPPING ENZYME

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

Diffraction experiment Diffraction