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- PDB-1ltm: ACCELERATED X-RAY STRUCTURE ELUCIDATION OF A 36 KDA MURAMIDASE/TR... -

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Basic information

Entry
Database: PDB / ID: 1ltm
TitleACCELERATED X-RAY STRUCTURE ELUCIDATION OF A 36 KDA MURAMIDASE/TRANSGLYCOSYLASE USING WARP
Components36 KDA SOLUBLE LYTIC TRANSGLYCOSYLASE
KeywordsGLYCOSYLTRANSFERASE / MURAMIDASE / TRANSGLYCOSYLASE / PEPTIDOGLYCAN MATURATION / LYSOZYME / PERIPLASMIC
Function / homology
Function and homology information


lytic endotransglycosylase activity / : / lytic transglycosylase activity / sodium ion binding / peptidoglycan catabolic process / cell outer membrane / cell wall organization / outer membrane-bounded periplasmic space / calcium ion binding
Similarity search - Function
Bacterial muramidase / Lytic transglycosylase MltB / Transglycosylase SLT domain 2 / Membrane-bound lytic murein transglycosylase B-like / Transglycosylase SLT domain / Helicase, Ruva Protein; domain 3 / Lysozyme - #10 / Lysozyme / Prokaryotic membrane lipoprotein lipid attachment site profile. / Lysozyme-like domain superfamily ...Bacterial muramidase / Lytic transglycosylase MltB / Transglycosylase SLT domain 2 / Membrane-bound lytic murein transglycosylase B-like / Transglycosylase SLT domain / Helicase, Ruva Protein; domain 3 / Lysozyme - #10 / Lysozyme / Prokaryotic membrane lipoprotein lipid attachment site profile. / Lysozyme-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Membrane-bound lytic murein transglycosylase B
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 1.7 Å
AuthorsVan Asselt, E.J. / Dijkstra, B.W.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 1998
Title: Accelerated X-ray structure elucidation of a 36 kDa muramidase/transglycosylase using wARP.
Authors: Van Asselt, E.J. / Perrakis, A. / Kalk, K.H. / Lamzin, V.S. / Dijkstra, B.W.
History
DepositionSep 26, 1997Processing site: BNL
Revision 1.0Nov 11, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 36 KDA SOLUBLE LYTIC TRANSGLYCOSYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,0984
Polymers35,8491
Non-polymers2483
Water5,891327
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.329, 67.883, 98.853
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein 36 KDA SOLUBLE LYTIC TRANSGLYCOSYLASE / 35 KD SOLUBLE LYTIC TRANSGLYCOSYLASE / SLT35


Mass: 35849.336 Da / Num. of mol.: 1 / Fragment: SOLUBLE ACTIVE DOMAIN OF MLTB
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: 122-1 / Cell line: BL21 / Cellular location: PERIPLASM / Gene: MLTB / Plasmid: PAD115 / Species (production host): Escherichia coli / Cellular location (production host): CYTOPLASM / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3)
References: UniProt: P41052, Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-BCN / BICINE


Mass: 163.172 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4 / Comment: pH buffer*YM
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 327 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.72 Å3/Da / Density % sol: 55 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 8.5
Details: 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, ...Details: 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
PH range: 7.8-8.5
Crystal grow
*PLUS
Temperature: 295 K / pH: 7.2 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
17.0 mg/mlprotein1drop
210 mMTris-HCl1drop
31 %isopropanol1drop
41 mMPMSF1drop
5100 mMBicine-NaOH1reservoir
60-6 %PEG200001reservoir

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.92
DetectorDetector: CCD / Date: Apr 8, 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.7→29.6 Å / Num. obs: 41653 / % possible obs: 94.4 % / Observed criterion σ(I): 0 / Redundancy: 5 % / Biso Wilson estimate: 18.4 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 24.4
Reflection shellResolution: 1.7→1.73 Å / Rmerge(I) obs: 0.261 / Mean I/σ(I) obs: 3.5 / % possible all: 91.8
Reflection
*PLUS
Num. measured all: 206582

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Processing

Software
NameVersionClassification
ARP/wARPmodel building
PHASESphasing
X-PLOR3.843model building
X-PLOR3.843refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.843phasing
RefinementMethod to determine structure: MIRAS / Resolution: 1.7→20 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 100000 / Data cutoff low absF: 0.0001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.221 4214 10.2 %RANDOM
Rwork0.186 ---
obs0.186 41498 94.5 %-
Displacement parametersBiso mean: 23.6 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.21 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.18 Å0.19 Å
Refinement stepCycle: LAST / Resolution: 1.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2826 0 16 0 2842
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.4
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d22.1
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.22
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.371.5
X-RAY DIFFRACTIONx_mcangle_it2.182
X-RAY DIFFRACTIONx_scbond_it2.432
X-RAY DIFFRACTIONx_scangle_it3.812.5
LS refinement shellResolution: 1.7→1.81 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.277 644 10.4 %
Rwork0.278 5523 -
obs--85.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARHCSD_SUGAR.SOLTOPH19.SOL
X-RAY DIFFRACTION3PARAM19.WAT
Software
*PLUS
Name: X-PLOR / Version: 3.843 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.189 / Rfactor Rwork: 0.187
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg22.1
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.22

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