PDB-2qf5: High resolution structure of the major periplasmic domain from th...

ID or keywords:

Entry

Database: PDB / ID: 2qf5

Title

High resolution structure of the major periplasmic domain from the cell shape-determining filament MreC (monoclinic form)

Components

Cell shape determining protein MreC

Keywords

STRUCTURAL PROTEIN / filament a-lytic protease fold

Function / homology

Function and homology information

regulation of cell shape / plasma membrane
Similarity search - Function

Biological species

Streptococcus pneumoniae (bacteria)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 2.23 Å

Authors

Lovering, A.L. / Strynadka, N.C.J.

Citation

Journal: J.Mol.Biol. / Year: 2007
Title: High-resolution Structure of the Major Periplasmic Domain from the Cell Shape-determining Filament MreC.
Authors: Lovering, A.L. / Strynadka, N.C.

History

Deposition	Jun 26, 2007	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 7, 2007	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.2	Oct 18, 2017	Group: Refinement description / Category: software
Revision 1.3	Aug 30, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	2qf5.cif.gz	44.8 KB	Display	PDBx/mmCIF format
PDB format	pdb2qf5.ent.gz	30.6 KB	Display	PDB format
PDBx/mmJSON format	2qf5.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	2qf5_validation.pdf.gz	424.6 KB	Display	wwPDB validaton report
Full document	2qf5_full_validation.pdf.gz	426.7 KB	Display
Data in XML	2qf5_validation.xml.gz	8.7 KB	Display
Data in CIF	2qf5_validation.cif.gz	11.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/qf/2qf5 ftp://data.pdbj.org/pub/pdb/validation_reports/qf/2qf5	HTTPS FTP

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Related structure data

Related structure data	2qf4SC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	1ryl-1 5vbp-2 5dw2-d 2qf4-2 6btz-1 6lcy-d 6q2u-d 2lha-d 5ml2-d 5u2e-1 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

Deposited unit

A: Cell shape determining protein MreC

18.2 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)	81.998, 48.283, 48.429
Angle α, β, γ (deg.)	90.000, 115.320, 90.000
Int Tables number	5
Space group name H-M	C121

#1: Protein	Cell shape determining protein MreC Mass: 18227.457 Da / Num. of mol.: 1 / Fragment: Major Periplasmic Domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Strain: R6 / Gene: mreC / Plasmid: pET41 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q8DMY2
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 74 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

Cell shape determining protein MreC

Mass: 18227.457 Da / Num. of mol.: 1 / Fragment: Major Periplasmic Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Streptococcus pneumoniae (bacteria) / Strain: R6 / Gene: mreC / Plasmid: pET41 / Species (production host): Escherichia coli / Production host:

Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q8DMY2

#2: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 74 / 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: 2.38 Å³/Da / Density % sol: 48.25 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: 0.1M Sodium acetate pH 4.6, 0.2M Ammonium sulfate, 12.5% PEG 4000, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å

Detector

Type: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Jun 15, 2006

Radiation

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

Radiation wavelength

Wavelength: 1.5418 Å / Relative weight: 1

Reflection

Resolution: 2.23→23.83 Å / Num. obs: 7873 / % possible obs: 90.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.2 % / R_merge(I) obs: 0.03 / R_sym value: 0.03 / Net I/σ(I): 18.3

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. measured all	Num. unique all	R_sym value	% possible all
2.23-2.33	5.1	0.123	6	4945	966	0.123	76.4
2.33-2.47	5.2	0.085	8.9	5809	1108	0.085	93.7
2.47-2.64	5.3	0.066	11.3	5685	1075	0.066	94.1
2.64-2.85	5.2	0.046	15.5	5174	991	0.046	94.5
2.85-3.12	5.3	0.033	20.2	4776	905	0.033	95.4
3.12-3.49	5.2	0.025	26.1	4429	846	0.025	95.4
3.49-4.03	5.3	0.022	28.7	3027	572	0.022	73.8
4.03-4.94	5.2	0.019	29.9	3326	634	0.019	96.6
4.94-6.99	5.2	0.023	23.8	2592	500	0.023	96.6
6.99-23.83	4.9	0.023	23.7	1363	276	0.023	95

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Processing

Software

Name	Version	Classification
SCALA		data scaling
REFMAC		refinement
PDB_EXTRACT	2	data extraction
MOSFLM		data reduction
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB entry 2QF4

2qf4

Resolution: 2.23→23.83 Å / Cor.coef. F_o:F_c: 0.945 / Cor.coef. F_o:F_c free: 0.886 / SU B: 11.789 / SU ML: 0.158 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.313 / ESU R Free: 0.253 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.268	365	4.6 %	RANDOM
R_work	0.194	-	-	-
obs	0.197	7870	92.72 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 20.21 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	2.9 Å²	0 Å²	-1.19 Å²
2-	-	-1.76 Å²	0 Å²
3-	-	-	-2.16 Å²

Refinement step

Cycle: LAST / Resolution: 2.23→23.83 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1161	0	0	74	1235

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.012	0.022	1170
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	734
X-RAY DIFFRACTION	r_angle_refined_deg	1.376	1.957	1587
X-RAY DIFFRACTION	r_angle_other_deg	0.882	3	1831
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.329	5	156
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	38.843	27.111	45
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.396	15	208
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	22.352	15	3
X-RAY DIFFRACTION	r_chiral_restr	0.075	0.2	201
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.02	1304
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	190
X-RAY DIFFRACTION	r_nbd_refined	0.195	0.2	170
X-RAY DIFFRACTION	r_nbd_other	0.19	0.2	773
X-RAY DIFFRACTION	r_nbtor_refined	0.163	0.2	536
X-RAY DIFFRACTION	r_nbtor_other	0.086	0.2	684
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.155	0.2	67
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.145	0.2	13
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.254	0.2	18
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.195	0.2	10
X-RAY DIFFRACTION	r_mcbond_it	0.688	1.5	1001
X-RAY DIFFRACTION	r_mcbond_other	0.124	1.5	327
X-RAY DIFFRACTION	r_mcangle_it	0.867	2	1257
X-RAY DIFFRACTION	r_scbond_it	1.541	3	431
X-RAY DIFFRACTION	r_scangle_it	2.393	4.5	330

LS refinement shell

Resolution: 2.23→2.29 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.225	24	-
R_work	0.226	536	-
obs	-	560	91.21 %

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	23.2698	-8.7235	27.7671	23.6101	-17.6032	52.0674	0.4178	0.7015	-0.7978	-0.3398	0.0462	1.3097	0.2266	-1.0167	-0.464	-0.0477	-0.0079	0.1396	0.1195	-0.0302	0.0384	-2.9988	0.5315	21.2704
2	3.6536	-2.297	0.5862	6.6563	-0.4888	6.3579	0.143	0.4013	-0.0198	-0.1976	-0.1348	-0.5321	0.2105	0.582	-0.0082	-0.04	0.017	-0.0578	-0.0972	0.0044	-0.0575	13.8816	-11.1727	21.2351
3	6.849	2.9712	-7.003	9.4749	-15.6268	36.3135	-0.2493	0.1338	-0.5355	-0.4555	0.7656	0.7835	0.8116	-1.0738	-0.5163	-0.153	0.0215	-0.0027	0.077	0.0259	0.079	-2.7817	-9.2103	21.4098
4	1.3404	-0.0522	-1.1022	2.2309	2.0035	3.182	0.1052	-0.0585	-0.2041	0.0318	0.0617	-0.1284	0.003	-0.0918	-0.1669	-0.0135	0.0147	-0.0579	-0.0633	0.0426	-0.0569	6.6279	-4.1757	17.3073
5	0.3114	-0.6048	0.981	2.5516	-0.5141	4.4959	-0.0666	0.2348	-0.2909	-0.0869	0.0373	-0.2355	0.4105	-0.1283	0.0292	-0.0408	0.0143	0.0169	-0.0494	-0.0398	-0.0243	10.098	-9.0972	15.3559
6	3.6648	0.2314	1.0859	2.5071	-0.9668	3.7835	-0.0853	0.3545	0.0151	-0.471	0.1056	-0.1378	-0.0796	0.2958	-0.0203	-0.0238	-0.0377	0.049	-0.0712	-0.0174	-0.1301	11.3757	5.0659	3.5417
7	11.6022	0.1511	7.3899	5.8571	-1.6869	10.3829	0.0198	-0.1878	-0.2321	0.1715	0.0671	-0.2151	-0.0709	-0.0852	-0.087	-0.0023	0.0156	-0.0235	-0.1825	-0.0226	-0.0946	9.2215	-0.0255	21.1263

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	X-RAY DIFFRACTION	1	A	A	110 - 115	5 - 10
2	X-RAY DIFFRACTION	2	A	A	116 - 135	11 - 30
3	X-RAY DIFFRACTION	3	A	A	136 - 143	31 - 38
4	X-RAY DIFFRACTION	4	A	A	144 - 160	39 - 55
5	X-RAY DIFFRACTION	5	A	A	161 - 174	56 - 69
6	X-RAY DIFFRACTION	6	A	A	175 - 258	70 - 153
7	X-RAY DIFFRACTION	7	A	A	259 - 272	154 - 167

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