PDB-4avr: Crystal structure of the hypothetical protein Pa4485 from Pseudom...

ID or keywords:

Entry

Database: PDB / ID: 4avr

Title

Crystal structure of the hypothetical protein Pa4485 from Pseudomonas aeruginosa

Components

PA4485

Keywords

UNKNOWN FUNCTION / GRAM-NEGATIVE BACTERIA / INFECTIOUS DISEASE / STRUCTURE-BASED INHIBITOR DESIGN

Function / homology

Function and homology information

Lyases; Carbon-oxygen lyases; Acting on polysaccharides / lytic endotransglycosylase activity / peptidoglycan metabolic process / cell wall organization / lyase activity
Similarity search - Function

Biological species

PSEUDOMONAS AERUGINOSA PA01 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.08 Å

Authors

McMahon, S.A. / Moynie, L. / Liu, H. / Duthie, F. / Alphey, M.S. / Naismith, J.H.

Citation

Journal: Acta Crystallogr.,Sect.F / Year: 2013
Title: The Aeropath Project Targeting Pseudomonas Aeruginosa: Crystallographic Studies for Assessment of Potential Targets in Early-Stage Drug Discovery.
Authors: Moynie, L. / Schnell, R. / Mcmahon, S.A. / Sandalova, T. / Boulkerou, W.A. / Schmidberger, J.W. / Alphey, M.S. / Cukier, C. / Duthie, F. / Kopec, J. / Liu, H. / Jacewicz, A. / Hunter, W.N. / ...

History

Deposition	May 29, 2012	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jan 9, 2013	Provider: repository / Type: Initial release
Revision 1.1	Jan 23, 2013	Group: Database references
Revision 1.2	May 8, 2024	Group: Data collection / Database references / Other Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

Remark 700

SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ...

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	4avr.cif.gz	92.3 KB	Display	PDBx/mmCIF format
PDB format	pdb4avr.ent.gz	73.2 KB	Display	PDB format
PDBx/mmJSON format	4avr.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	4avr_validation.pdf.gz	414.6 KB	Display	wwPDB validaton report
Full document	4avr_full_validation.pdf.gz	414.6 KB	Display
Data in XML	4avr_validation.xml.gz	11.2 KB	Display
Data in CIF	4avr_validation.cif.gz	16 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/av/4avr ftp://data.pdbj.org/pub/pdb/validation_reports/av/4avr	HTTPS FTP

-
Related structure data

Related structure data	2xu8C 4avfC 4avyC 4b79C 4b7cC 4b7xC 4b9aC 4b9eC 4es6C 4etrC 4exaC 4exbC C: citing same article (ref.)
Similar structure data	3fi5-2 6usi-d 6us0-d 6l81-2 5yvk-d 1d2w-d 1c6m-d 1g0m-d 6unt-d 127l-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

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: PA4485

B: PA4485

21 kDa, 2 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)	33.978, 39.020, 41.870
Angle α, β, γ (deg.)	102.80, 103.48, 115.54
Int Tables number	1
Space group name H-M	P1

#1: Protein	PA4485 Mass: 10487.896 Da / Num. of mol.: 2 / Fragment: RESIDUES 32-125 Source method: isolated from a genetically manipulated source Source: (gene. exp.) PSEUDOMONAS AERUGINOSA PA01 (bacteria) / Plasmid: PEHISTEV / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): C43 / References: UniProt: Q9HVT6
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 204 / Source method: isolated from a natural source / Formula: H₂O
Sequence details	RESIDUES 1 - 30 OMITTED FROM FINAL CONSTRUCT AS PROPOSED TO BE SIGNAL PEPTIDE

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.2 Å³/Da / Density % sol: 44.5 % / Description: NONE
Crystal grow	pH: 5.5 / Details: 25% PEG 3350, 0.2M NACL AND 0.1M BIS-TRIS PH 5.5

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Details: MIRRORS
Radiation	Monochromator: SI(311) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9763 Å / Relative weight: 1
Reflection	Resolution: 1.08→50 Å / Num. obs: 65937 / % possible obs: 92.1 % / Observed criterion σ(I): 2 / Redundancy: 4.1 % / R_merge(I) obs: 0.06 / Net I/σ(I): 38.7
Reflection shell	Resolution: 1.08→1.1 Å / Redundancy: 3.6 % / R_merge(I) obs: 0.17 / Mean I/σ(I) obs: 9.1 / % possible all: 88.8

-
Processing

Software

Name	Version	Classification
REFMAC	5.6.0117	refinement
xia2		data reduction
xia2		data scaling
SHELX		phasing

Refinement

Method to determine structure:

SAD
Starting model: NONE

Resolution: 1.08→37.87 Å / Cor.coef. F_o:F_c: 0.969 / Cor.coef. F_o:F_c free: 0.954 / SU B: 0.661 / SU ML: 0.016 / Cross valid method: THROUGHOUT / ESU R: 0.03 / ESU R Free: 0.032 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.17747	3501	5 %	RANDOM
R_work	0.14873	-	-	-
obs	0.15015	65937	91.98 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK

Displacement parameters

B_iso mean: 14.625 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.1 Å²	-0.27 Å²	0.26 Å²
2-	-	-0.09 Å²	-0.22 Å²
3-	-	-	-0.21 Å²

Refinement step

Cycle: LAST / Resolution: 1.08→37.87 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1447	0	0	204	1651

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.009	0.019	1476
X-RAY DIFFRACTION	r_bond_other_d	0.003	0.02	1090
X-RAY DIFFRACTION	r_angle_refined_deg	1.531	1.957	1986
X-RAY DIFFRACTION	r_angle_other_deg	1.357	3	2573
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.36	5	188
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	22.952	19.167	72
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	11.986	15	250
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	18.127	15	32
X-RAY DIFFRACTION	r_chiral_restr	0.098	0.2	214
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.021	1689
X-RAY DIFFRACTION	r_gen_planes_other	0.005	0.02	360
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined
X-RAY DIFFRACTION	r_long_range_B_other
X-RAY DIFFRACTION	r_rigid_bond_restr	10.058	3	2566
X-RAY DIFFRACTION	r_sphericity_free	22.173	5	62
X-RAY DIFFRACTION	r_sphericity_bonded	9.609	5	2687

LS refinement shell

Resolution: 1.079→1.107 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.186	245	-
R_work	0.155	4649	-
obs	-	-	87.24 %

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	0.1497	0.0879	-0.2963	0.1154	-0.3673	1.1735	0.0018	0.0128	0.0005	0.0068	0.0063	0.0023	-0.0177	-0.0182	-0.0081	0.0132	0.0117	-0.0053	0.0149	-0.002	0.0098	18.676	-13.818	6.467
2	0.1636	-0.1767	0.2235	4.3856	0.295	0.3739	0.004	0.0091	0.0141	0.1444	-0.0015	-0.1927	0.0223	0.0118	-0.0025	0.0165	0.0118	-0.0102	0.015	-0.0017	0.019	18.694	-16.076	23.136
3	0.0287	0.0236	-0.0214	0.1399	0.137	0.2342	0.0066	0.0011	0.008	-0.0032	0.0052	-0.0062	-0.0121	0.0064	-0.0118	0.0117	0.0105	-0.0024	0.0187	-0.0033	0.0168	18.132	-5.735	16.611
4	0.0878	0.2953	0.0272	1.4667	0.9895	1.7796	0.0006	-0.0009	0.0169	-0.0382	-0.0288	0.0623	-0.1058	-0.0822	0.0282	0.0168	0.0172	-0.0053	0.0199	-0.0023	0.014	11.147	-4.467	3.729
5	0.1508	-0.0935	-0.0795	0.2037	0.0564	0.3446	0.0031	0.0076	0.0006	-0.0138	-0.0097	0.0115	0.0023	-0.0386	0.0067	0.01	0.0113	-0.0021	0.0187	-0.0024	0.0141	13.966	-10.167	6.22
6	4.3203	-0.3422	2.3393	1.0463	-2.3994	6.0795	-0.0674	0.1048	-0.0618	-0.0209	-0.0823	-0.0801	0.0193	0.2094	0.1497	0.0165	0.0124	-0.0031	0.0256	0	0.0264	28.363	-16.229	7.768
7	0.2098	0.0587	-0.1434	0.0303	0.0223	0.3808	-0.0025	0.0061	-0.005	0.0018	-0.0062	-0.0002	0.0129	-0.0414	0.0087	0.0105	0.0098	-0.0047	0.0205	-0.002	0.0111	11.699	-15	10.397
8	0.0649	-0.0175	-0.1795	0.1795	-0.1605	0.7492	-0.0063	0.0119	0.0023	0.0125	0.0093	-0.0072	0.0069	-0.046	-0.0029	0.013	0.01	-0.0063	0.017	-0.0021	0.0091	14.721	-13.557	2.151
9	0.1168	-0.2696	-0.06	0.7339	0.012	1.538	-0.014	0.0059	-0.0108	0.036	0.0085	0.0177	0.0881	0.0853	0.0055	0.0147	0.0137	-0.0032	0.0223	-0.0004	0.016	14.955	-30.415	33.253
10	0.0946	0.0022	0.0089	0.2002	-0.1283	0.0868	-0.003	0.0043	0.0015	-0.0125	-0.0103	-0.0307	0.0107	0.0088	0.0133	0.0109	0.0127	-0.0038	0.0172	-0.0013	0.0177	24.884	-24.892	15.904
11	0.4059	-0.191	0.0498	0.2412	-0.0063	0.0081	0.0029	-0.0191	-0.0238	0.023	0.0028	-0.0187	0.0025	-0.0039	-0.0057	0.0113	0.0102	-0.0062	0.0196	0.0013	0.0158	24.335	-34.763	27.067
12	0.1613	-0.0736	-0.1342	0.0738	0.0908	0.1814	-0.0144	0.0242	-0.0154	0.0098	-0.0008	-0.003	0.0149	-0.0175	0.0152	0.0113	0.0083	-0.0022	0.0189	-0.0039	0.0155	15.92	-32.143	24.374
13	0.5857	3.8293	2.3796	25.0369	15.5592	9.6696	0.0408	0.142	-0.2375	0.2587	0.9167	-1.5402	0.1568	0.5656	-0.9574	0.1149	0.0825	-0.0903	0.1167	-0.092	0.1597	20.532	-19.576	30.512
14	0.0948	0.047	-0.1018	0.0897	-0.0472	0.1099	-0.0123	0.0045	-0.0042	-0.009	0.0056	-0.0027	0.0121	-0.0052	0.0067	0.0107	0.0107	-0.0045	0.0169	-0.0027	0.0116	13.475	-29.205	22.986

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1 - 10
2	X-RAY DIFFRACTION	2	A	11 - 16
3	X-RAY DIFFRACTION	3	A	17 - 40
4	X-RAY DIFFRACTION	4	A	41 - 45
5	X-RAY DIFFRACTION	5	A	46 - 62
6	X-RAY DIFFRACTION	6	A	63 - 67
7	X-RAY DIFFRACTION	7	A	68 - 82
8	X-RAY DIFFRACTION	8	A	83 - 94
9	X-RAY DIFFRACTION	9	B	1 - 6
10	X-RAY DIFFRACTION	10	B	7 - 32
11	X-RAY DIFFRACTION	11	B	33 - 43
12	X-RAY DIFFRACTION	12	B	44 - 62
13	X-RAY DIFFRACTION	13	B	63 - 67
14	X-RAY DIFFRACTION	14	B	68 - 94

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi