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1ltm

ACCELERATED X-RAY STRUCTURE ELUCIDATION OF A 36 KDA MURAMIDASE/TRANSGLYCOSYLASE USING WARP

Method: X-RAY DIFFRACTION Dmax: 80.5 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

36 KDA 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 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 42–361 Fragment：SOLUBLE ACTIVE DOMAIN OF MLTB 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

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 1LTM Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1D0K THE ESCHERICHIA COLI LYTIC TRANSGLYCOSYLASE SLT35 IN COMPLEX WITH TWO MURODIPEPTIDES (GLCNAC-MURNAC-L-ALA-D-GLU) Deposited 1999-09-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions 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 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
1D0L THE ESCHERICHIA COLI LYTIC TRANSGLYCOSYLASE SLT35 IN COMPLEX WITH BULGECIN A Deposited 1999-09-12 Different construct Different mutation/modification 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 construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions 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
1QDR 2.1 A RESOLUTION STRUCTURE OF ESCHERICHIA COLI LYTIC TRANSGLYCOSYLASE SLT35 Deposited 1999-07-10 Different construct Different mutation/modification 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 mutation/modification 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 mutation/modification 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 mutation/modification 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 1–320； UniProt 42–361

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 1ltm

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id1ltm
Deposition date deposition_date1997-09-26
Structure title titleACCELERATED X-RAY STRUCTURE ELUCIDATION OF A 36 KDA MURAMIDASE/TRANSGLYCOSYLASE USING WARP
Keywords keywordsGLYCOSYLTRANSFERASE, MURAMIDASE, TRANSGLYCOSYLASE, PEPTIDOGLYCAN MATURATION, LYSOZYME, PERIPLASMIC; GLYCOSYLTRANSFERASE
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_guinier23.15 Å
Radius of gyration Rg (electron density) rg_electron22.13 Å
Forward intensity I(0) i021162800.00
Molecular weight molecular_weight34970.0 kDa
Excluded volume excluded_volume43654 ų
Envelope volume envelope_volume52006 ų
Hydration-shell volume shell_volume20406 ų
Envelope diameter envelope_diameter81.4 Å
Shell Rg shell_rg28.05 Å
Envelope Rg envelope_rg22.47 Å
Shape Rg shape_rg22.10 Å
Total Rg total_rg22.96 Å
Total atoms total_atoms2471
Residues n_residues309
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 dmax80.5 Å
Rg (real space) rg_real23.22 Å
Rg uncertainty (real space) rg_real_error0.65 Å
I(0) (real space) i0_real2.1160e+07
I(0) uncertainty (real space) i0_real_error3.1270e+05
Rg (reciprocal space) rg_reciprocal23.21 Å
I(0) (reciprocal space) i0_reciprocal21160000.0000
Solution quality estimate total_estimate0.6964
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary23.5 Å
Skewness Skewness skewness0.433
Kurtosis Kurtosis kurtosis-0.247
Angular range angular_range— – 0.3450 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha4605000.0000
Real-space data points n_real_points66
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.792; Stabil: 1.000; Sysdev: 0.307; Positv: 1.000; Valcen: 0.900; Smooth: 0.852
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

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7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd1ltma_
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_id1ltmA01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily350 — Bacterial muramidase
Domain ID domain_id1ltmA02
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)