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1d0k

THE ESCHERICHIA COLI LYTIC TRANSGLYCOSYLASE SLT35 IN COMPLEX WITH TWO MURODIPEPTIDES (GLCNAC-MURNAC-L-ALA-D-GLU)

Method: X-RAY DIFFRACTION Dmax: 82.6 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

35KD SOLUBLE LYTIC TRANSGLYCOSYLASE

Escherichia coli

UniProt P41052

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Other combination Monomer Protein × 1 其他Polymer 2 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 40–361 Mutation：L40M, L41V 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-N-acetyl-beta-muramic acid × 2 CA CALCIUM ION × 1 ALA ALANINE × 2 DGL D-GLUTAMIC ACID × 2 GOL GLYCEROL × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.8；295 K；BICINE-NAOH, ISOPROPANOL, PEG20K, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 295K Resolution 2.02 Å R-free 0.202

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 1D0K Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1D0L THE ESCHERICHIA COLI LYTIC TRANSGLYCOSYLASE SLT35 IN COMPLEX WITH BULGECIN A Deposited 1999-09-12 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 40–361（322 aa）
Mutation：L40M, L41V CA CALCIUM ION × 1 BLG 4-O-(4-O-SULFONYL-N-ACETYLGLUCOSAMININYL)-5-METHYLHYDROXY-L-PROLINE-TAURINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；295 K；BICINE-NAOH, ISOPRAPANOL, PEG20K, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Resolution 1.97 Å R-free 0.200
1D0M THE ESCHERICHIA COLI LYTIC TRANSGLYCOSYLASE SLT35 IN COMPLEX WITH BULGECIN A AND (GLCNAC)2 Deposited 1999-09-12 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric
Chain A 40–361（322 aa）
Mutation：L40M, L41V CA CALCIUM ION × 1 BLG 4-O-(4-O-SULFONYL-N-ACETYLGLUCOSAMININYL)-5-METHYLHYDROXY-L-PROLINE-TAURINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；295 K；BICINE-NAOH, ISOPROPANOL, PEG20K, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Resolution 2.47 Å R-free 0.241
1LTM ACCELERATED X-RAY STRUCTURE ELUCIDATION OF A 36 KDA MURAMIDASE/TRANSGLYCOSYLASE USING WARP Deposited 1997-09-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 42–361（320 aa） Fragment：SOLUBLE ACTIVE DOMAIN OF MLTB
Not recorded NA SODIUM ION × 1 BCN BICINE × 1 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；ROD-SHAPED CRYSTALS WERE GROWN AT 295 K IN 1 DAY TO 1 WEEK BY EQUILIBRATING A HANGING DROP, THAT CONSISTED OF 3 UL OF PROTEIN SOLUTION AND 3 UL OF RESERVOIR SOLUTION OF 100 MM BICINE-NAOH, PH 7.8-8.5 AND 0-6% PEG 20K., vapor diffusion - hanging drop
Resolution 1.70 Å R-free 0.221
1QDR 2.1 A RESOLUTION STRUCTURE OF ESCHERICHIA COLI LYTIC TRANSGLYCOSYLASE SLT35 Deposited 1999-07-10 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 40–361（322 aa） Fragment：SLT35
Mutation：L40M, L41V NA SODIUM ION × 1 BCN BICINE × 1 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；295 K；PEG 20K, BICINE-NAOH, ISOPROPANOL, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Resolution 2.10 Å R-free 0.210
1QDT 2.1 A RESOLUTION STRUCTURE OF ESCHERICHIA COLI LYTIC TRANSGLYCOYSLASE SLT35 IN COMPLEX WITH CALCIUM Deposited 1999-07-10 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 40–361（322 aa） Fragment：SLT35
Mutation：L40M, L41V CA CALCIUM ION × 1 EDO 1,2-ETHANEDIOL × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；295 K；PEG 20K, BICINE-NAOH, ISOPROPANOL, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Resolution 2.10 Å R-free 0.206
1QUS 1.7 A RESOLUTION STRUCTURE OF THE SOLUBLE LYTIC TRANSGLYCOSYLASE SLT35 FROM ESCHERICHIA COLI Deposited 1999-07-03 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 40–361（322 aa） Fragment：SLT35
Mutation：L40M, L41V NA SODIUM ION × 1 BCN BICINE × 1 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；295 K；BICINE-NAOH, PEG 20K, ISOPROPANOL, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Resolution 1.70 Å R-free 0.207
1QUT THE SOLUBLE LYTIC TRANSGLYCOSYLASE SLT35 FROM ESCHERICHIA COLI IN COMPLEX WITH N-ACETYLGLUCOSAMINE Deposited 1999-07-03 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 40–361（322 aa） Fragment：SLT35
Mutation：L40M, L41V NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 NA SODIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；295 K；BICINE-NAOH, PEG 20K, ISOPROPANOL, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Resolution 2.44 Å R-free 0.256

7 other PDB entries and 7 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name MLTB_ECOLI
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–322； UniProt 40–361

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 1d0k

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1d0k
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1d0k
Deposition date deposition_date1999-09-12
Structure title titleTHE ESCHERICHIA COLI LYTIC TRANSGLYCOSYLASE SLT35 IN COMPLEX WITH TWO MURODIPEPTIDES (GLCNAC-MURNAC-L-ALA-D-GLU)
Keywords keywordsALPHA-HELICAL PROTEIN WITH A FIVE-STRANDED ANTIPARALLEL BETA-SHEET, GLYCOSYLTRANSFERASE, EF-HAND, TRANSFERASE; TRANSFERASE
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier22.94 Å
Radius of gyration Rg (electron density) rg_electron21.97 Å
Forward intensity I(0) i023357100.00
Molecular weight molecular_weight36626.0 kDa
Excluded volume excluded_volume45661 ų
Envelope volume envelope_volume53907 ų
Hydration-shell volume shell_volume21228 ų
Envelope diameter envelope_diameter84.0 Å
Shell Rg shell_rg27.96 Å
Envelope Rg envelope_rg22.54 Å
Shape Rg shape_rg21.95 Å
Total Rg total_rg22.79 Å
Total atoms total_atoms2585
Residues n_residues314
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 dmax82.6 Å
Rg (real space) rg_real23.03 Å
Rg uncertainty (real space) rg_real_error0.82 Å
I(0) (real space) i0_real2.3360e+07
I(0) uncertainty (real space) i0_real_error3.7000e+05
Rg (reciprocal space) rg_reciprocal23.01 Å
I(0) (reciprocal space) i0_reciprocal23360000.0000
Solution quality estimate total_estimate0.8420
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary24.1 Å
Skewness Skewness skewness0.489
Kurtosis Kurtosis kurtosis-0.092
Angular range angular_range— – 0.3450 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha5906000.0000
Real-space data points n_real_points66
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.695; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.870; Smooth: 0.988
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (7)

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7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd1d0ka_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.2 — Lysozyme-like
Superfamily Superfamily superfamilyd.2.1 — Lysozyme-like
Family Family familyd.2.1.6 — Bacterial muramidase, catalytic domain

CATH v4.4 (2 domains)

Domain ID domain_id1d0kA01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily350 — Bacterial muramidase
Domain ID domain_id1d0kA02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology530 — Lysozyme
Homologous superfamily homologous superfamily10 —
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8. Citations (1)

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9. Files and Curves (10)