2mjp

STRUCTURE-BASED IDENTIFICATION OF THE BIOCHEMICAL FUNCTION OF A HYPOTHETICAL PROTEIN FROM METHANOCOCCUS JANNASCHII:MJ0226

Method: X-RAY DIFFRACTION D_max: 76.5 Å Quality: EXCELLENT

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

PYROPHOSPHATASE

OrganismNot specified

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 10–193 Chain B； UniProt 10–193	Not recorded	ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1	X-RAY DIFFRACTION X-ray crystallization conditions：pH 6.5；pH 6.5	Resolution 2.20 Å R-free 0.259

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 2MJP	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1B78 STRUCTURE-BASED IDENTIFICATION OF THE BIOCHEMICAL FUNCTION OF A HYPOTHETICAL PROTEIN FROM METHANOCOCCUS JANNASCHII:MJ0226 Deposited 1999-01-27	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–193（193 aa） Chain B 1–193（193 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；pH 6.50	Resolution 2.20 Å R-free 0.267

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

View Construct and Data Evidence

UniProt name	NTPA_METJA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–193； UniProt 10–193 Author chain B； PDBConstruct 1–193； UniProt 10–193

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	2mjp
Deposition date deposition_date	1999-01-27
Structure title title	STRUCTURE-BASED IDENTIFICATION OF THE BIOCHEMICAL FUNCTION OF A HYPOTHETICAL PROTEIN FROM METHANOCOCCUS JANNASCHII:MJ0226
Keywords keywords	;STRUCTURAL GENOMICS, PYROPHOSPHATASE, HYPERTHERMAL PROTEIN, BSGC structure funded by NIH, Protein Structure Initiative, PSI, Berkeley Structural Genomics Center ;; STRUCTURAL GENOMICS
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	24.47 Å
Radius of gyration Rg (electron density) rg_electron	23.67 Å
Forward intensity I(0) i0	28688000.00
Molecular weight molecular_weight	42751.0 kDa
Excluded volume excluded_volume	54172 Å³
Envelope volume envelope_volume	63753 Å³
Hydration-shell volume shell_volume	22832 Å³
Envelope diameter envelope_diameter	77.5 Å
Shell Rg shell_rg	29.98 Å
Envelope Rg envelope_rg	23.71 Å
Shape Rg shape_rg	23.62 Å
Total Rg total_rg	24.61 Å
Total atoms total_atoms	3021
Residues n_residues	368
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	76.5 Å
Rg (real space) rg_real	24.46 Å
Rg uncertainty (real space) rg_real_error	0.42 Å
I(0) (real space) i0_real	2.8690e+07
I(0) uncertainty (real space) i0_real_error	3.9010e+05
Rg (reciprocal space) rg_reciprocal	24.46 Å
I(0) (reciprocal space) i0_reciprocal	28690000.0000
Solution quality estimate total_estimate	0.9070
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	23.1 Å
Skewness Skewness skewness	0.262
Kurtosis Kurtosis kurtosis	-0.579
Angular range angular_range	— – 0.3250 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	12740000.0000
Real-space data points n_real_points	64
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.947; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.969; Smooth: 0.978

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d2mjpa_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.51 — Anticodon-binding domain-like
Superfamily Superfamily superfamily	c.51.4 — ITPase-like
Family Family family	c.51.4.1 — ITPase (Ham1)

Domain ID domain_id	d2mjpb_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.51 — Anticodon-binding domain-like
Superfamily Superfamily superfamily	c.51.4 — ITPase-like
Family Family family	c.51.4.1 — ITPase (Ham1)

CATH v4.4 (2 domains)

Domain ID domain_id	2mjpA00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	950 — Maf protein
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	2mjpB00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	950 — Maf protein
Homologous superfamily homologous superfamily	10 —

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8. Citations (1)

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Unit-cell length a length_a	44.360 Å
Unit-cell length b length_b	72.130 Å
Unit-cell length c length_c	140.530 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	8

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

Resolution resolution	2.200 Å
Low-resolution limit resolution_low	8.000 Å
R factor r_factor	—
R_work r_work	0.2040
R_free r_free	0.2590

Description description	PYROPHOSPHATASE
Molecular weight formula_weight	22232.5 kDa
Source method src_method	nat
Copy count entity_count	2

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	3182

STRUCTURE-BASED IDENTIFICATION OF THE BIOCHEMICAL FUNCTION OF A HYPOTHETICAL PROTEIN FROM METHANOCOCCUS JANNASCHII:MJ0226

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

PYROPHOSPHATASE

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

6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

Description description	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
Molecular weight formula_weight	506.2 kDa
Source method src_method	syn
Copy count entity_count	1

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	161

fit	/app/data/saxs_computation/mj/2mjp/2mjp.fit
pddf	/app/data/pr_computation/mj/2mjp/2mjp.pr.out
profile	/app/data/saxs_computation/mj/2mjp/2mjp.dat