1ef2

CRYSTAL STRUCTURE OF MANGANESE-SUBSTITUTED KLEBSIELLA AEROGENES UREASE

Method: X-RAY DIFFRACTION Dmax: 97.7 Å Quality: GOOD

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

UREASE ALPHA SUBUNIT

Klebsiella aerogenes

UniProt P18314

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 heterocomplex Heteromer Protein × 9 PDB declaration: nonameric(9) Consistent with protein copy count Chain A; UniProt 2–567 Non-standard monomer:Yes (specific site not provided by mmCIF) UREASE BETA SUBUNIT × 3 (P18315) UREASE GAMMA SUBUNIT × 3 (P18316) MN MANGANESE (II) ION × 6 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.5;298 K;lithium sulfate, HEPES, EDTA, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K 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.

30 other PDB entries and 30 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name URE1_KLEAE
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–566; UniProt 2–567

UREASE BETA SUBUNIT

Klebsiella aerogenes

UniProt P18315

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 heterocomplex Heteromer Protein × 9 PDB declaration: nonameric(9) Consistent with protein copy count Chain B; UniProt 1–101 Not recorded UREASE ALPHA SUBUNIT × 3 (P18314) UREASE GAMMA SUBUNIT × 3 (P18316) MN MANGANESE (II) ION × 6 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.5;298 K;lithium sulfate, HEPES, EDTA, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K 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.

30 other PDB entries and 30 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name URE2_KLEAE
Isoform
PDB entities 2
Chains and sequence ranges Author chain B; PDBConstruct 1–101; UniProt 1–101

UREASE GAMMA SUBUNIT

Klebsiella aerogenes

UniProt P18316

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 heterocomplex Heteromer Protein × 9 PDB declaration: nonameric(9) Consistent with protein copy count Chain C; UniProt 1–100 Not recorded UREASE ALPHA SUBUNIT × 3 (P18314) UREASE BETA SUBUNIT × 3 (P18315) MN MANGANESE (II) ION × 6 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.5;298 K;lithium sulfate, HEPES, EDTA, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K 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.

30 other PDB entries and 30 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name URE3_KLEAE
Isoform
PDB entities 3
Chains and sequence ranges Author chain C; PDBConstruct 1–100; UniProt 1–100

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

SAXS profile for 1ef2

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1ef2
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1ef2
Deposition date deposition_date2000-02-05
Structure title titleCRYSTAL STRUCTURE OF MANGANESE-SUBSTITUTED KLEBSIELLA AEROGENES UREASE
Keywords keywordsalpha-beta barrel, metalloenzyme, HYDROLASE; HYDROLASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier29.84
Radius of gyration Rg (electron density) rg_electron28.95
Forward intensity I(0) i0111693000.00
Molecular weight molecular_weight82497.0 kDa
Excluded volume excluded_volume102840 ų
Envelope volume envelope_volume123930 ų
Hydration-shell volume shell_volume36079 ų
Envelope diameter envelope_diameter104.3
Shell Rg shell_rg35.86
Envelope Rg envelope_rg29.21
Shape Rg shape_rg28.96
Total Rg total_rg29.53
Total atoms total_atoms5792
Residues n_residues766
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3

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

Maximum dimension Dmax dmax97.7
Rg (real space) rg_real29.85
Rg uncertainty (real space) rg_real_error0.62
I(0) (real space) i0_real1.1170e+08
I(0) uncertainty (real space) i0_real_error1.6360e+06
Rg (reciprocal space) rg_reciprocal29.85
I(0) (reciprocal space) i0_reciprocal111700000.0000
Solution quality estimate total_estimate0.8831
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary35.0
Skewness Skewness skewness0.360
Kurtosis Kurtosis kurtosis-0.284
Angular range angular_range— – 0.2650 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha28390000.0000
Real-space data points n_real_points54
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.894; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.991; Smooth: 0.803

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (5)

7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_idd1ef2a1
Class classb — All beta proteins
Fold Fold foldb.92 — Composite domain of metallo-dependent hydrolases
Superfamily Superfamily superfamilyb.92.1 — Composite domain of metallo-dependent hydrolases
Family Family familyb.92.1.1 — alpha-Subunit of urease
Domain ID domain_idd1ef2a2
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamilyc.1.9 — Metallo-dependent hydrolases
Family Family familyc.1.9.2 — alpha-subunit of urease, catalytic domain
Domain ID domain_idd1ef2b_
Class classb — All beta proteins
Fold Fold foldb.85 — beta-clip
Superfamily Superfamily superfamilyb.85.3 — Urease, beta-subunit
Family Family familyb.85.3.1 — Urease, beta-subunit
Domain ID domain_idd1ef2c_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.8 — Urease, gamma-subunit
Superfamily Superfamily superfamilyd.8.1 — Urease, gamma-subunit
Family Family familyd.8.1.1 — Urease, gamma-subunit

CATH v4.4 (4 domains)

Domain ID domain_id1ef2A01
Class class2 — Mainly Beta
Architecture architecture30 — Roll
Topology topology40 — Urease, subunit C; domain 1
Homologous superfamily homologous superfamily10 — Urease, subunit C, domain 1
Domain ID domain_id1ef2A02
Class class3 — Alpha Beta
Architecture architecture20 — Alpha-Beta Barrel
Topology topology20 — TIM Barrel
Homologous superfamily homologous superfamily140 — Metal-dependent hydrolases
Domain ID domain_id1ef2B00
Class class2 — Mainly Beta
Architecture architecture10 — Ribbon
Topology topology150 — Urease, subunit B
Homologous superfamily homologous superfamily10 — Urease, beta subunit
Domain ID domain_id1ef2C00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology280 — Urease; subunit A
Homologous superfamily homologous superfamily10 — Urease, gamma-like subunit

8. Citations (1)

9. Files and Curves (10)