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1vkr

STRUCTURE OF IIB DOMAIN OF THE MANNITOL-SPECIFIC PERMEASE ENZYME II

Method: SOLUTION NMR Dmax: 46.3 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

mannitol-specific PTS system enzyme IIABC components

Escherichia coli

UniProt P00550

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 367–489 Fragment：IIB DOMAIN No other associated polymer SOLUTION NMR NMR measurement conditions：pH 7.1；308 K；Ionic strength (raw mmCIF value) 40 mM SODIUM PHOSPHATE Resolution not provided

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 1VKR Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1A3A CRYSTAL STRUCTURE OF IIA MANNITOL FROM ESCHERICHIA COLI Deposited 1998-01-19 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 491–637（147 aa） Fragment：IIA DOMAIN, RESIDUES 491 - 637
Chain C 491–637（147 aa） Fragment：IIA DOMAIN, RESIDUES 491 - 637
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；pH 7.5
Resolution 1.80 Å R-free 0.242
1A3A CRYSTAL STRUCTURE OF IIA MANNITOL FROM ESCHERICHIA COLI Deposited 1998-01-19 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain B 491–637（147 aa） Fragment：IIA DOMAIN, RESIDUES 491 - 637
Chain D 491–637（147 aa） Fragment：IIA DOMAIN, RESIDUES 491 - 637
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；pH 7.5
Resolution 1.80 Å R-free 0.242
1J6T COMPLEX OF ENZYME IIAMTL AND THE HISTIDINE-CONTAINING PHOSPHOCARRIER PROTEIN HPR FROM ESCHERICHIA COLI NMR, RESTRAINED REGULARIZED MEAN STRUCTURE Deposited 2002-08-14 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 491–637（147 aa） Fragment：EIIA DOMAIN
Not recorded PO3 PHOSPHITE ION × 1 SOLUTION NMR
NMR measurement conditions pH 7；308 K；Ionic strength (raw mmCIF value) 10 mM SODIUM PHOSPHATE
Resolution not provided
1VRV Structure of phosphorylated IIB (C384(SEP)) domain of the mannitol-specific permease enzyme II Deposited 2005-06-17 Different construct Different mutation/modification Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 375–475（101 aa） Fragment：IIB DOMAIN
Mutation：C384(SEP) Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7.4；303 K；Ionic strength (raw mmCIF value) 0 EXCEPT FOR RDC MEASUREMENTS IN PHAGE PF1 WHERE IT WAS 0.5M
Resolution not provided
2FEW Complex of enzyme IIAMTL and phosphorylated enzyme IIBMTL from Escherichia coli NMR, restrained regularized mean structure Deposited 2005-12-16 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 491–637（147 aa） Fragment：EIIA-MTL, PHOSPHOTRANSFERASE ENZYME II, A DOMAIN COMPONENT
Mutation：H65Q No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7.4；303 K；Ionic strength (raw mmCIF value) 20 mM TRIS-D11
Resolution not provided

4 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name PTM3C_ECOLI
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 3–125； UniProt 367–489

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 1vkr

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id1vkr
Deposition date deposition_date2004-06-14
Structure title titleSTRUCTURE OF IIB DOMAIN OF THE MANNITOL-SPECIFIC PERMEASE ENZYME II
Keywords keywordsPHOSPHOTRANSFERASE, TRANSFERASE, KINASE, SUGAR TRANSPORT; TRANSFERASE
Experimental Method methodSOLUTION NMR
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier14.56 Å
Radius of gyration Rg (electron density) rg_electron12.86 Å
Forward intensity I(0) i02568540.00
Molecular weight molecular_weight10462.0 kDa
Excluded volume excluded_volume12976 ų
Envelope volume envelope_volume15789 ų
Hydration-shell volume shell_volume10565 ų
Envelope diameter envelope_diameter43.3 Å
Shell Rg shell_rg18.39 Å
Envelope Rg envelope_rg13.16 Å
Shape Rg shape_rg12.84 Å
Total Rg total_rg14.25 Å
Total atoms total_atoms1483
Residues n_residues97
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−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
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax46.3 Å
Rg (real space) rg_real14.46 Å
Rg uncertainty (real space) rg_real_error0.30 Å
I(0) (real space) i0_real2.5690e+06
I(0) uncertainty (real space) i0_real_error3.2980e+04
Rg (reciprocal space) rg_reciprocal14.47 Å
I(0) (reciprocal space) i0_reciprocal2569000.0000
Solution quality estimate total_estimate0.8873
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary19.3 Å
Skewness Skewness skewness0.092
Kurtosis Kurtosis kurtosis-0.377
Angular range angular_range— – 0.5000 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha493900.0000
Real-space data points n_real_points80
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.849; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.993; Smooth: 0.993
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd1vkra_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.44 — Phosphotyrosine protein phosphatases I-like
Superfamily Superfamily superfamilyc.44.2 — PTS system IIB component-like
Family Family familyc.44.2.1 — PTS system, Lactose/Cellobiose specific IIB subunit

CATH v4.4 (1 domains)

Domain ID domain_id1vkrA00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily2300 — Response regulator
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8. Citations (1)

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9. Files and Curves (10)