PDB-8b2e: Muramidase from Kionochaeta sp natural catalytic core

ID or keywords:

Entry

Database: PDB / ID: 8b2e

Title

Muramidase from Kionochaeta sp natural catalytic core

Components

Muramidase

Keywords

HYDROLASE / SH3-like / muramidase / peptidoglycan / cell wall binding domain

Function / homology

:

Function and homology information

Biological species

Kionochaeta sp. (fungus)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.1 Å

Authors

Moroz, O.V. / Blagova, E. / Lebedev, A.A. / Skov, L.K. / Pache, R.A. / Schnorr, K.M. / Kiemer, L. / Nymand-Grarup, S. / Ming, L. / Ye, L. ...

Funding support

1items

Citation

Journal: Acta Crystallogr D Struct Biol / Year: 2023
Title: Module walking using an SH3-like cell-wall-binding domain leads to a new GH184 family of muramidases.
Authors: Moroz, O.V. / Blagova, E. / Lebedev, A.A. / Skov, L.K. / Pache, R.A. / Schnorr, K.M. / Kiemer, L. / Friis, E.P. / Nymand-Grarup, S. / Ming, L. / Ye, L. / Klausen, M. / Cohn, M.T. / Schmidt, ...

History

Deposition	Sep 13, 2022	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jul 19, 2023	Provider: repository / Type: Initial release
Revision 1.1	Aug 9, 2023	Group: Data collection / Database references / Category: citation / diffrn_source Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _diffrn_source.pdbx_synchrotron_site

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8b2e.cif.gz	94.4 KB	Display	PDBx/mmCIF format
PDB format	pdb8b2e.ent.gz	56.5 KB	Display	PDB format
PDBx/mmJSON format	8b2e.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8b2e_validation.pdf.gz	400.9 KB	Display	wwPDB validaton report
Full document	8b2e_full_validation.pdf.gz	400.8 KB	Display
Data in XML	8b2e_validation.xml.gz	9.5 KB	Display
Data in CIF	8b2e_validation.cif.gz	13.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/b2/8b2e ftp://data.pdbj.org/pub/pdb/validation_reports/b2/8b2e	HTTPS FTP

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Related structure data

Related structure data	8b2fC 8b2gC 8b2hC 8b2sC C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Muramidase

hetero molecules

15.4 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	61.521, 61.521, 85.188
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	152
Space group name H-M	P3₁21

#1: Protein	Muramidase Mass: 15152.332 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Kionochaeta sp. (fungus) / Production host: Aspergillus oryzae (mold)
#2: Chemical	ChemComp-CD / CADMIUM ION Mass: 112.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cd
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 210 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 3.07 Å³/Da / Density % sol: 59.95 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.9 M sodium acetate, Hepes pH 7.5, 40 mM CdCl2

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

Diamond

/ Beamline: I03 / Wavelength: 0.976 Å

Detector

Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 15, 2017

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.976 Å / Relative weight: 1

Reflection

Resolution: 1.1→53.28 Å / Num. obs: 71381 / % possible obs: 94.1 % / Redundancy: 9.4 % / CC_1/2: 0.999 / R_merge(I) obs: 0.044 / R_pim(I) all: 0.021 / R_rim(I) all: 0.049 / Χ²: 0.91 / Net I/σ(I): 22.7

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. unique obs	CC_1/2	R_pim(I) all	R_rim(I) all	Χ²	% possible all
6.02-53.28	8.1	0.039	54.4	551	0.998	0.019	0.043	1.31	99.9
1.1-1.12	6.4	0.676	2.1	2466	0.726	0.369	0.775	0.81	66.4

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Processing

Software

Name	Version	Classification
XDS		data reduction
xia2		data reduction
Aimless		data scaling
CRANK2		phasing
REFMAC	5.8.0352	refinement

Refinement

Method to determine structure:

SAD / Resolution: 1.1→53.279 Å / Cor.coef. F_o:F_c: 0.983 / Cor.coef. F_o:F_c free: 0.981 / WR_factor R_free: 0.124 / WR_factor R_work: 0.111 / SU B: 0.514 / SU ML: 0.011 / Average fsc free: 0.9898 / Average fsc work: 0.9914 / Cross valid method: THROUGHOUT / ESU R: 0.019 / ESU R Free: 0.019
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.1239	3492	4.893 %
R_work	0.1128	67870	-
all	0.113	-	-
obs	-	71362	93.719 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 13.631 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.322 Å²	0.161 Å²	0 Å²
2-	-	0.322 Å²	-0 Å²
3-	-	-	-1.044 Å²

Refinement step

Cycle: LAST / Resolution: 1.1→53.279 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1044	0	2	210	1256

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.012	0.012	1092
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	1001
X-RAY DIFFRACTION	r_angle_refined_deg	1.664	1.636	1488
X-RAY DIFFRACTION	r_angle_other_deg	0.59	1.561	2337
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.08	5	148
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	3.604	5	5
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.483	10	174
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	20.471	10	43
X-RAY DIFFRACTION	r_chiral_restr	0.097	0.2	169
X-RAY DIFFRACTION	r_gen_planes_refined	0.009	0.02	1274
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	206
X-RAY DIFFRACTION	r_nbd_refined	0.272	0.2	254
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.169	0.2	909
X-RAY DIFFRACTION	r_nbtor_refined	0.179	0.2	568
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.071	0.2	559
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.26	0.2	105
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.087	0.2	3
X-RAY DIFFRACTION	r_nbd_other	0.148	0.2	17
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.452	0.2	16
X-RAY DIFFRACTION	r_mcbond_it	1.084	1.299	577
X-RAY DIFFRACTION	r_mcbond_other	1.084	1.299	577
X-RAY DIFFRACTION	r_mcangle_it	1.252	1.963	724
X-RAY DIFFRACTION	r_mcangle_other	1.251	1.964	725
X-RAY DIFFRACTION	r_scbond_it	2.353	1.622	515
X-RAY DIFFRACTION	r_scbond_other	2.35	1.622	516
X-RAY DIFFRACTION	r_scangle_it	2.883	2.341	762
X-RAY DIFFRACTION	r_scangle_other	2.881	2.342	763
X-RAY DIFFRACTION	r_lrange_it	4.062	25.182	1349
X-RAY DIFFRACTION	r_lrange_other	3.465	19.25	1283
X-RAY DIFFRACTION	r_rigid_bond_restr	4.513	3	2093

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
1.1-1.129	0.245	169	0.246	3662	0.246	5534	0.971	0.969	69.2266	0.222
1.129-1.159	0.179	211	0.197	4442	0.196	5442	0.98	0.977	85.5017	0.169
1.159-1.193	0.155	256	0.136	4533	0.137	5281	0.987	0.988	90.6836	0.113
1.193-1.23	0.119	214	0.108	4542	0.108	5124	0.99	0.992	92.8181	0.087
1.23-1.27	0.111	221	0.095	4464	0.096	4979	0.992	0.994	94.0952	0.074
1.27-1.315	0.113	241	0.084	4349	0.086	4843	0.992	0.995	94.776	0.068
1.315-1.364	0.11	204	0.081	4300	0.082	4688	0.991	0.996	96.0751	0.067
1.364-1.42	0.117	190	0.077	4103	0.078	4471	0.991	0.996	96.0188	0.066
1.42-1.483	0.099	217	0.075	3979	0.076	4306	0.993	0.996	97.4454	0.066
1.483-1.555	0.1	172	0.072	3822	0.073	4090	0.995	0.997	97.6528	0.066
1.555-1.639	0.089	211	0.068	3659	0.07	3958	0.995	0.997	97.7767	0.064
1.639-1.739	0.086	184	0.076	3458	0.077	3711	0.996	0.997	98.1407	0.074
1.739-1.859	0.093	169	0.083	3296	0.084	3514	0.995	0.996	98.6056	0.084
1.859-2.007	0.112	176	0.093	3059	0.094	3273	0.993	0.995	98.839	0.098
2.007-2.199	0.111	177	0.098	2837	0.099	3046	0.993	0.995	98.9494	0.108
2.199-2.458	0.116	133	0.102	2580	0.102	2730	0.992	0.994	99.3773	0.118
2.458-2.837	0.141	119	0.116	2316	0.117	2447	0.989	0.992	99.5096	0.139
2.837-3.472	0.143	97	0.141	1982	0.141	2084	0.986	0.987	99.7601	0.176
3.472-4.9	0.105	71	0.138	1572	0.136	1647	0.994	0.99	99.7571	0.185
4.9-53.279	0.23	60	0.222	914	0.223	976	0.965	0.972	99.7951	0.302

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