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- PDB-2pi8: Crystal structure of E. coli MltA with bound chitohexaose -

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Basic information

Entry
Database: PDB / ID: 2pi8
TitleCrystal structure of E. coli MltA with bound chitohexaose
ComponentsMembrane-bound lytic murein transglycosylase A
KeywordsHYDROLASE / double-psi beta-barrel / protein-sugar complex / lytic transglycosylase
Function / homology
Function and homology information


: / lytic transglycosylase activity / peptidoglycan turnover / peptidoglycan metabolic process / hydrolase activity, hydrolyzing O-glycosyl compounds / peptidoglycan catabolic process / cell outer membrane / cell wall organization / outer membrane-bounded periplasmic space
Similarity search - Function
Barwin-like endoglucanases / Lytic transglycosylase MltA, domain B / Membrane-bound lytic murein transglycosylase A / MltA specific insert domain / MltA specific insert domain / 3D domain / 3D domain / RlpA-like domain / RlpA-like domain superfamily / Ribosomal Protein L25; Chain P ...Barwin-like endoglucanases / Lytic transglycosylase MltA, domain B / Membrane-bound lytic murein transglycosylase A / MltA specific insert domain / MltA specific insert domain / 3D domain / 3D domain / RlpA-like domain / RlpA-like domain superfamily / Ribosomal Protein L25; Chain P / Barwin-like endoglucanases / Prokaryotic membrane lipoprotein lipid attachment site profile. / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
PHOSPHATE ION / Membrane-bound lytic murein transglycosylase A
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.25 Å
Authorsvan Straaten, K.E. / Barends, T.R.M. / Dijkstra, B.W. / Thunnissen, A.M.W.H.
Citation
Journal: J.Biol.Chem. / Year: 2007
Title: Structure of Escherichia coli Lytic transglycosylase MltA with bound chitohexaose: implications for peptidoglycan binding and cleavage
Authors: van Straaten, K.E. / Barends, T.R.M. / Dijkstra, B.W. / Thunnissen, A.M.W.H.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2005
Title: Escherichia coli MltA: MAD phasing and refinement of a tetartohedrally twinned protein crystal structure
Authors: Barends, T.R.M. / de Jong, R.M. / van Straaten, K.E. / Thunnissen, A.M.W.H. / Dijkstra, B.W.
#2: Journal: J.Mol.Biol. / Year: 2005
Title: Crystal structure of MltA from Escherichia coli reveals a unique lytic transglycosylase fold
Authors: van Straaten, K.E. / Dijkstra, B.W. / Vollmer, W. / Thunnissen, A.M.W.H.
#3: Journal: Acta Crystallogr.,Sect.D / Year: 2004
Title: Purification, crystallization and preliminary X-ray analysis of the lytic transglycosylase MltA from Escherichia coli
Authors: van Straaten, K.E. / Dijkstra, B.W. / Thunnissen, A.M.W.H.
History
DepositionApr 13, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 8, 2007Provider: repository / Type: Initial release
Revision 1.1Nov 19, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Jun 13, 2012Group: Other
Revision 1.4Oct 18, 2017Group: Refinement description / Category: software
Revision 1.5Mar 14, 2018Group: Data collection / Database references / Category: diffrn_source / struct_ref_seq_dif
Item: _diffrn_source.pdbx_synchrotron_site / _struct_ref_seq_dif.details
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Membrane-bound lytic murein transglycosylase A
B: Membrane-bound lytic murein transglycosylase A
C: Membrane-bound lytic murein transglycosylase A
D: Membrane-bound lytic murein transglycosylase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)160,03314
Polymers154,5154
Non-polymers5,51910
Water3,567198
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)91.0, 91.0, 187.2
Angle α, β, γ (deg.)90.0, 90.0, 120.0
Int Tables number144
Space group name H-MP31
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.9999, -0.0112, 0.0031), (0.0108, -0.7932, 0.6089), (-0.0044, 0.6089, 0.7932)174.4428, -1.514, 0.7045

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Components

#1: Protein
Membrane-bound lytic murein transglycosylase A / E.C.3.2.1.- / Murein hydrolase A / Mlt38


Mass: 38628.730 Da / Num. of mol.: 4 / Mutation: D308A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: mltA, mlt / Plasmid: pMSS / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
References: UniProt: P0A935, Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds
#2: Polysaccharide
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1237.172 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-4DGlcpNAcb1-4DGlcpNAcb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,6,5/[a2122h-1b_1-5_2*NCC/3=O]/1-1-1-1-1-1/a4-b1_b4-c1_c4-d1_d4-e1_e4-f1WURCSPDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}}}}LINUCSPDB-CARE
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 198 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.89 Å3/Da / Density % sol: 57.51 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop, cocrystallization / pH: 4.2
Details: 1.5-2.0 M ammonium sulfate, 100mM phosphate/citrate buffer, 15mg/ml hexa-N-acetyl glucosamine, pH 4.2, vapor diffusion, hanging drop, cocrystallization, temperature 298K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
31
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONESRF ID14-110.934
SYNCHROTRONEMBL/DESY, HAMBURG BW7A20.9792, 0.9794, 0.9393
Detector
TypeIDDetector
ADSC QUANTUM 41CCD
MAR CCD 165 mm2CCD
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2MADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.9341
20.97921
30.97941
40.93931
Reflection

D res high: 2.5 Å / D res low: 15 Å / % possible obs: 100

IDAv σ(I) over netINumberRmerge(I) obsΧ2Num. obs
116.75841700.0580.9759614
215.33462750.0490.9559705
317.53415520.0470.9359754
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squared
5.311510010.0451.053
4.255.3110010.0371.032
3.724.2510010.040.994
3.393.7210010.0520.93
3.143.3910010.0660.968
2.963.1410010.0940.953
2.812.9610010.1240.943
2.692.8199.910.1720.942
2.592.6999.910.2290.93
2.52.5999.910.3060.941
5.311510020.0251.044
4.255.3110020.0270.938
3.724.2510020.0331.057
3.393.7210020.0470.971
3.143.3910020.0640.955
2.963.1410020.0960.831
2.812.9610020.1310.907
2.692.8199.920.1870.944
2.592.6999.920.2540.949
2.52.5999.920.3430.95
5.311510030.0350.903
4.255.3110030.0290.939
3.724.2510030.0320.947
3.393.7210030.0431.017
3.143.3910030.0560.927
2.963.1410030.080.924
2.812.9610030.1080.933
2.692.8199.930.1480.913
2.592.6999.930.1990.904
2.52.5910030.2640.921
Reflection twinType: hemihedral / Operator: &STRIP%twin_oper / Fraction: 0.5
ReflectionResolution: 2.15→40 Å / Num. all: 278139 / Num. obs: 93064 / % possible obs: 99.1 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.092 / Χ2: 1.049 / Net I/σ(I): 8.7
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.15-2.230.69285610.9871,291.6
2.23-2.320.6894081.0221,299.7
2.32-2.420.51893411.0791,2100
2.42-2.550.3993891.0921,2100
2.55-2.710.26993901.1561,2100
2.71-2.920.17294091.1261,2100
2.92-3.210.1193951.051,2100
3.21-3.680.0793610.9851,2100
3.68-4.630.05494120.9361,2100
4.63-400.05993981.0371,299.9

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Phasing

PhasingMethod: MAD
Phasing set
ID
1
2
3
Phasing MAD set
Clust-IDExpt-IDSet-IDWavelength (Å)F double prime refinedF prime refined
13 wavelength10.98074.15-8.02
13 wavelength20.9811.69-8.74
13 wavelength30.97333.05-4.81
Phasing MAD set site
IDAtom type symbolB isoFract xFract yFract zOccupancy
1Se600.0830.8940.0020.904
2Se54.690.9030.0010.1320.625
3Se600.2520.7730.0020.88
4Se58.5980.2370.6690.2570.614
5Se600.080.1860.0540.88
6Se600.1130.1420.2630.805
7Se600.3010.5270.1270.729
8Se57.7370.0320.1420.1260.678
9Se18.9670.5550.4160.0980.259
10Se600.2530.4790.0540.868
11Se51.4280.2250.5270.2620.656
12Se56.070.4310.6680.1330.61
13Se51.5030.09810.2570.567
14Se600.1520.7040.2640.505
15Se38.0310.8630.4140.2910.339
16Se45.4440.790.2570.0780.392
Phasing dmFOM : 0.81 / FOM acentric: 0.81 / FOM centric: 0 / Reflection: 38228 / Reflection acentric: 38228 / Reflection centric: 0
Phasing dm shell
Resolution (Å)FOM FOM acentricReflectionReflection acentric
8.3-14.9920.940.9413651365
5.2-8.30.90.951405140
4.1-5.20.930.9364206420
3.6-4.10.90.965206520
3.1-3.60.780.781160511605
2.9-3.10.570.5771787178

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SOLVE2.05phasing
RESOLVE2.05phasing
CNSrefinement
PDB_EXTRACT2data extraction
ProDCdata collection
RefinementMethod to determine structure: MAD / Resolution: 2.25→36 Å / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: REFLECTION DATA ARE TETARTOHEDRALLY TWINNED. REFINEMENT REQUIRED SPECIAL TWIN-ADAPTED REFINEMENT SCRIPTS FOR CNS
RfactorNum. reflection% reflectionSelection details
Rfree0.226 5887 7.2 %thin resolution shells
Rwork0.182 ---
all0.184 82094 --
obs0.184 82094 100 %-
Solvent computationBsol: 29.404 Å2
Displacement parametersBiso mean: 37.25 Å2
Baniso -1Baniso -2Baniso -3
1--0.504 Å2-1.707 Å20 Å2
2---0.504 Å20 Å2
3---1.008 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.25 Å
Luzzati d res low-5 Å
Refinement stepCycle: LAST / Resolution: 2.25→36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10475 0 370 198 11043
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1
X-RAY DIFFRACTIONc_dihedral_angle_d23
X-RAY DIFFRACTIONc_improper_angle_d0.8
X-RAY DIFFRACTIONc_mcbond_it1.1071.5
X-RAY DIFFRACTIONc_mcangle_it1.8962
X-RAY DIFFRACTIONc_scbond_it1.4762
X-RAY DIFFRACTIONc_scangle_it2.2632.5
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs
2.25-2.350.3235370.29965710194
2.35-2.480.2819190.27939710316
2.48-2.630.2584820.258977510257
2.63-2.830.2548520.218941810270
2.83-3.120.2549610.2929410255
3.12-3.570.2356760.177958310259
3.57-4.50.1827220.138957110293
4.5-360.2047380.153951210250
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein.param
X-RAY DIFFRACTION2param_peptidogl_sugars.dat
X-RAY DIFFRACTION3CNS_TOPPAR:water.param
X-RAY DIFFRACTION4CNS_TOPPAR:ion.param

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