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

ID or keywords:

Entry

Database: PDB / ID: 2pi8

Title

Crystal structure of E. coli MltA with bound chitohexaose

Components

Membrane-bound lytic murein transglycosylase A

Keywords

HYDROLASE / double-psi beta-barrel / protein-sugar complex / lytic transglycosylase

Function / homology

Function and homology information

: / lytic transglycosylase activity / peptidoglycan turnover / hydrolase activity, hydrolyzing O-glycosyl compounds / peptidoglycan catabolic process / cell wall organization / cell outer membrane / outer membrane-bounded periplasmic space
Similarity search - Function

Biological species

Escherichia coli (E. coli)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MAD / Resolution: 2.25 Å

Authors

van 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.

History

Deposition	Apr 13, 2007	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 8, 2007	Provider: repository / Type: Initial release
Revision 1.1	Nov 19, 2007	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Source and taxonomy / Version format compliance
Revision 1.3	Jun 13, 2012	Group: Other
Revision 1.4	Oct 18, 2017	Group: Refinement description / Category: software
Revision 1.5	Mar 14, 2018	Group: Data collection / Database references / Category: diffrn_source / struct_ref_seq_dif Item: _diffrn_source.pdbx_synchrotron_site / _struct_ref_seq_dif.details
Revision 2.0	Jul 29, 2020	Group: 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

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	2pi8.cif.gz	274.6 KB	Display	PDBx/mmCIF format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/pi/2pi8 ftp://data.pdbj.org/pub/pdb/validation_reports/pi/2pi8	HTTPS FTP

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Related structure data

Related structure data	2picC 2pjjC 2ae0 C: citing same article (ref.)
Similar structure data	3ja5-d 2hig-1 2xgj-1 3f2d-d 6t1t-d 6t1u-d 5o1p-1 4b3g-d Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#261 - Sep 2021 DNA-Sequencing Nanopores similarity (1) #22 - Oct 2001 Photosystem I similarity (1) #262 - Oct 2021 Fifty Years of Open Access to PDB Structures similarity (1) #29 - May 2002 Penicillin-binding Proteins similarity (1) #95 - Nov 2007 Multidrug Resistance Transporters similarity (1)

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

160 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author

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 number	144
Space group name H-M	P3₁

Noncrystallographic symmetry (NCS)

NCS oper:

ID	Code	Matrix	Vector
1	given	(1), (1), (1)
2	given	(-0.9999, -0.0112, 0.0031), (0.0108, -0.7932, 0.6089), (-0.0044, 0.6089, 0.7932)	174.4428, -1.514, 0.7045

#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- ...

Type: oligosaccharide

/ Mass: 1237.172 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source

Descriptor	Type	Program
DGlcpNAcb1-4DGlcpNAcb1-4DGlcpNAcb1-4DGlcpNAcb1-4DGlcpNAcb1-4DGlcpNAcb1-ROH	Glycam Condensed Sequence	GMML 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-f1	WURCS	PDB2Glycan 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]{}}}}}}	LINUCS	PDB-CARE

#3: Chemical

ChemComp-PO4 / PHOSPHATE ION /

Phosphate

Mass: 94.971 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: PO₄

#4: Water

ChemComp-HOH / water /

Water

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

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.89 Å³/Da / Density % sol: 57.51 %
Crystal grow	Temperature: 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

ID	Mean temperature (K)	Crystal-ID
1	100	1
2	100	1
3		1

Diffraction source

Source	Site	Beamline	ID	Wavelength (Å)
SYNCHROTRON	ESRF	ID14-1	1	0.934
SYNCHROTRON	EMBL/DESY, HAMBURG	BW7A	2	0.9792, 0.9794, 0.9393

Detector

Type	ID	Detector
ADSC QUANTUM 4	1	CCD
MAR CCD 165 mm	2	CCD

Radiation

ID	Protocol	Monochromatic (M) / Laue (L)	Scattering type	Wavelength-ID
1	SINGLE WAVELENGTH	M	x-ray	1
2	MAD	M	x-ray	1

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	0.934	1
2	0.9792	1
3	0.9794	1
4	0.9393	1

Reflection

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

ID	Av σ(I) over netI	Number	R_merge(I) obs	Χ²	Num. obs
1	16.7	584170	0.058	0.97	59614
2	15.3	346275	0.049	0.95	59705
3	17.5	341552	0.047	0.93	59754

Diffraction reflection shell

Highest resolution (Å)	Lowest resolution (Å)	% possible obs (%)	ID	R_merge(I) obs	Chi squared
5.31	15	100	1	0.045	1.053
4.25	5.31	100	1	0.037	1.032
3.72	4.25	100	1	0.04	0.994
3.39	3.72	100	1	0.052	0.93
3.14	3.39	100	1	0.066	0.968
2.96	3.14	100	1	0.094	0.953
2.81	2.96	100	1	0.124	0.943
2.69	2.81	99.9	1	0.172	0.942
2.59	2.69	99.9	1	0.229	0.93
2.5	2.59	99.9	1	0.306	0.941
5.31	15	100	2	0.025	1.044
4.25	5.31	100	2	0.027	0.938
3.72	4.25	100	2	0.033	1.057
3.39	3.72	100	2	0.047	0.971
3.14	3.39	100	2	0.064	0.955
2.96	3.14	100	2	0.096	0.831
2.81	2.96	100	2	0.131	0.907
2.69	2.81	99.9	2	0.187	0.944
2.59	2.69	99.9	2	0.254	0.949
2.5	2.59	99.9	2	0.343	0.95
5.31	15	100	3	0.035	0.903
4.25	5.31	100	3	0.029	0.939
3.72	4.25	100	3	0.032	0.947
3.39	3.72	100	3	0.043	1.017
3.14	3.39	100	3	0.056	0.927
2.96	3.14	100	3	0.08	0.924
2.81	2.96	100	3	0.108	0.933
2.69	2.81	99.9	3	0.148	0.913
2.59	2.69	99.9	3	0.199	0.904
2.5	2.59	100	3	0.264	0.921

Reflection twin

Type: hemihedral / Operator: &STRIP%twin_oper / Fraction: 0.5

Reflection

Resolution: 2.15→40 Å / Num. all: 278139 / Num. obs: 93064 / % possible obs: 99.1 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / R_merge(I) obs: 0.092 / Χ²: 1.049 / Net I/σ(I): 8.7

Reflection shell

Resolution (Å)	R_merge(I) obs	Num. unique all	Χ²	Diffraction-ID	% possible all
2.15-2.23	0.692	8561	0.987	1,2	91.6
2.23-2.32	0.68	9408	1.022	1,2	99.7
2.32-2.42	0.518	9341	1.079	1,2	100
2.42-2.55	0.39	9389	1.092	1,2	100
2.55-2.71	0.269	9390	1.156	1,2	100
2.71-2.92	0.172	9409	1.126	1,2	100
2.92-3.21	0.11	9395	1.05	1,2	100
3.21-3.68	0.07	9361	0.985	1,2	100
3.68-4.63	0.054	9412	0.936	1,2	100
4.63-40	0.059	9398	1.037	1,2	99.9

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Phasing

Phasing

Method:

MAD

Phasing set

ID
1
2
3

Phasing MAD set

Clust-ID	Expt-ID	Set-ID	Wavelength (Å)	F double prime refined	F prime refined
1	3 wavelength	1	0.9807	4.15	-8.02
1	3 wavelength	2	0.981	1.69	-8.74
1	3 wavelength	3	0.9733	3.05	-4.81

Phasing MAD set site

ID	Atom type symbol	B iso	Fract x	Fract y	Fract z	Occupancy
1	Se	60	0.083	0.894	0.002	0.904
2	Se	54.69	0.903	0.001	0.132	0.625
3	Se	60	0.252	0.773	0.002	0.88
4	Se	58.598	0.237	0.669	0.257	0.614
5	Se	60	0.08	0.186	0.054	0.88
6	Se	60	0.113	0.142	0.263	0.805
7	Se	60	0.301	0.527	0.127	0.729
8	Se	57.737	0.032	0.142	0.126	0.678
9	Se	18.967	0.555	0.416	0.098	0.259
10	Se	60	0.253	0.479	0.054	0.868
11	Se	51.428	0.225	0.527	0.262	0.656
12	Se	56.07	0.431	0.668	0.133	0.61
13	Se	51.503	0.098	1	0.257	0.567
14	Se	60	0.152	0.704	0.264	0.505
15	Se	38.031	0.863	0.414	0.291	0.339
16	Se	45.444	0.79	0.257	0.078	0.392

Phasing dm

FOM : 0.81 / FOM acentric: 0.81 / FOM centric: 0 / Reflection: 38228 / Reflection acentric: 38228 / Reflection centric: 0

Phasing dm shell

Resolution (Å)	FOM	FOM acentric	Reflection	Reflection acentric
8.3-14.992	0.94	0.94	1365	1365
5.2-8.3	0.9	0.9	5140	5140
4.1-5.2	0.93	0.93	6420	6420
3.6-4.1	0.9	0.9	6520	6520
3.1-3.6	0.78	0.78	11605	11605
2.9-3.1	0.57	0.57	7178	7178

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
SOLVE	2.05	phasing
RESOLVE	2.05	phasing
CNS		refinement
PDB_EXTRACT	2	data extraction
ProDC		data collection

Refinement

Method 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

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.226	5887	7.2 %	thin resolution shells
R_work	0.182	-	-	-
all	0.184	82094	-	-
obs	0.184	82094	100 %	-

Solvent computation

B_sol: 29.404 Å²

Displacement parameters

B_iso mean: 37.25 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.504 Å²	-1.707 Å²	0 Å²
2-	-	-0.504 Å²	0 Å²
3-	-	-	1.008 Å²

Refine analyze

	Free	Obs
Luzzati coordinate error	0.3 Å	0.25 Å
Luzzati d res low	-	5 Å

Refinement step

Cycle: LAST / Resolution: 2.25→36 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10475	0	370	198	11043

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target
X-RAY DIFFRACTION	c_bond_d	0.005
X-RAY DIFFRACTION	c_angle_deg	1
X-RAY DIFFRACTION	c_dihedral_angle_d	23
X-RAY DIFFRACTION	c_improper_angle_d	0.8
X-RAY DIFFRACTION	c_mcbond_it	1.107	1.5
X-RAY DIFFRACTION	c_mcangle_it	1.896	2
X-RAY DIFFRACTION	c_scbond_it	1.476	2
X-RAY DIFFRACTION	c_scangle_it	2.263	2.5

LS refinement shell

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

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection obs
2.25-2.35	0.323	537	0.29	9657	10194
2.35-2.48	0.281	919	0.27	9397	10316
2.48-2.63	0.258	482	0.258	9775	10257
2.63-2.83	0.254	852	0.218	9418	10270
2.83-3.12	0.254	961	0.2	9294	10255
3.12-3.57	0.235	676	0.177	9583	10259
3.57-4.5	0.182	722	0.138	9571	10293
4.5-36	0.204	738	0.153	9512	10250

Xplor file

Refine-ID	Serial no	Param file
X-RAY DIFFRACTION	1	CNS_TOPPAR:protein.param
X-RAY DIFFRACTION	2	param_peptidogl_sugars.dat
X-RAY DIFFRACTION	3	CNS_TOPPAR:water.param
X-RAY DIFFRACTION	4	CNS_TOPPAR:ion.param

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