PDB-6w4n: Co-crystal structure of Pd_dinase with probe glycine-propargylgly...

ID or keywords:

Entry

Database: PDB / ID: 6w4n

Title

Co-crystal structure of Pd_dinase with probe glycine-propargylglycine-AOMK

Components

Aminopeptidase

Keywords

HYDROLASE / Diaminopeptidase

Function / homology

Function and homology information

cysteine-type aminopeptidase activity / homocysteine catabolic process / response to toxic substance / proteolysis / cytoplasm
Similarity search - Function

Biological species

Parabacteroides distasonis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.623 Å

Authors

Xu, J.H. / Solania, A. / Wolan, D.W.

Citation

Journal: To Be Published
Title: Co-crystal structure of Pd_dinase with probe glycine-propargylglycine-AOMK
Authors: Xu, J.H. / Solania, A. / Wolan, D.W.

History

Deposition	Mar 11, 2020	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 17, 2021	Provider: repository / Type: Initial release
Revision 1.1	Oct 18, 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_ncs_dom_lim Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	6w4n.cif.gz	439.3 KB	Display	PDBx/mmCIF format
PDB format	pdb6w4n.ent.gz	354.7 KB	Display	PDB format
PDBx/mmJSON format	6w4n.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	6w4n_validation.pdf.gz	1.8 MB	Display	wwPDB validaton report
Full document	6w4n_full_validation.pdf.gz	1.8 MB	Display
Data in XML	6w4n_validation.xml.gz	79 KB	Display
Data in CIF	6w4n_validation.cif.gz	108.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/w4/6w4n ftp://data.pdbj.org/pub/pdb/validation_reports/w4/6w4n	HTTPS FTP

-
Related structure data

Related structure data	3pw3S S: Starting model for refinement
Similar structure data	5wdk-d 3pw3-d 5wdl-d 5wa3-3 3134 5wa4-d 1flo-d 1m6x-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
Related items in Molecule of the Month	#142 - Oct 2011 PDB Pioneers similarity (2)

Deposited unit

A: Aminopeptidase

B: Aminopeptidase

C: Aminopeptidase

D: Aminopeptidase

E: Aminopeptidase

F: Aminopeptidase

hetero molecules

277 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	105.113, 138.613, 220.130
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	(chain A and (resid 33 through 34 or (resid 35...
2	1	(chain B and (resid 33 through 34 or (resid 35...
3	1	(chain C and (resid 33 through 34 or (resid 35...
4	1	(chain D and (resid 33 through 159 or (resid 160...
5	1	(chain E and (resid 33 through 34 or (resid 35...
6	1	(chain F and (resid 33 through 34 or (resid 35...

NCS domain segments:

Ens-ID: 1

Dom-ID	Component-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	GLY	GLY	PHE	PHE	(chain A and (resid 33 through 34 or (resid 35...	A	A	33 - 34	29 - 30
1	2	VAL	VAL	VAL	VAL	(chain A and (resid 33 through 34 or (resid 35...	A	A	35	31
1	3	GLY	GLY	LYS	LYS	(chain A and (resid 33 through 34 or (resid 35...	A	A	33 - 405	29 - 401
1	4	GLY	GLY	LYS	LYS	(chain A and (resid 33 through 34 or (resid 35...	A	A	33 - 405	29 - 401
1	5	GLY	GLY	LYS	LYS	(chain A and (resid 33 through 34 or (resid 35...	A	A	33 - 405	29 - 401
1	6	GLY	GLY	LYS	LYS	(chain A and (resid 33 through 34 or (resid 35...	A	A	33 - 405	29 - 401
2	1	GLY	GLY	PHE	PHE	(chain B and (resid 33 through 34 or (resid 35...	B	B	33 - 34	29 - 30
2	2	VAL	VAL	VAL	VAL	(chain B and (resid 33 through 34 or (resid 35...	B	B	35	31
2	3	GLY	GLY	LYS	LYS	(chain B and (resid 33 through 34 or (resid 35...	B	B	33 - 405	29 - 401
2	4	GLY	GLY	LYS	LYS	(chain B and (resid 33 through 34 or (resid 35...	B	B	33 - 405	29 - 401
2	5	GLY	GLY	LYS	LYS	(chain B and (resid 33 through 34 or (resid 35...	B	B	33 - 405	29 - 401
2	6	GLY	GLY	LYS	LYS	(chain B and (resid 33 through 34 or (resid 35...	B	B	33 - 405	29 - 401
3	1	GLY	GLY	PHE	PHE	(chain C and (resid 33 through 34 or (resid 35...	C	C	33 - 34	29 - 30
3	2	VAL	VAL	VAL	VAL	(chain C and (resid 33 through 34 or (resid 35...	C	C	35	31
3	3	GLY	GLY	ILE	ILE	(chain C and (resid 33 through 34 or (resid 35...	C	C	33 - 404	29 - 400
3	4	GLY	GLY	ILE	ILE	(chain C and (resid 33 through 34 or (resid 35...	C	C	33 - 404	29 - 400
3	5	GLY	GLY	ILE	ILE	(chain C and (resid 33 through 34 or (resid 35...	C	C	33 - 404	29 - 400
3	6	GLY	GLY	ILE	ILE	(chain C and (resid 33 through 34 or (resid 35...	C	C	33 - 404	29 - 400
4	1	GLY	GLY	GLY	GLY	(chain D and (resid 33 through 159 or (resid 160...	D	D	33 - 159	29 - 155
4	2	LYS	LYS	LYS	LYS	(chain D and (resid 33 through 159 or (resid 160...	D	D	160	156
4	3	GLY	GLY	LYS	LYS	(chain D and (resid 33 through 159 or (resid 160...	D	D	33 - 405	29 - 401
4	4	GLY	GLY	LYS	LYS	(chain D and (resid 33 through 159 or (resid 160...	D	D	33 - 405	29 - 401
4	5	GLY	GLY	LYS	LYS	(chain D and (resid 33 through 159 or (resid 160...	D	D	33 - 405	29 - 401
4	6	GLY	GLY	LYS	LYS	(chain D and (resid 33 through 159 or (resid 160...	D	D	33 - 405	29 - 401
5	1	GLY	GLY	PHE	PHE	(chain E and (resid 33 through 34 or (resid 35...	E	E	33 - 34	29 - 30
5	2	VAL	VAL	VAL	VAL	(chain E and (resid 33 through 34 or (resid 35...	E	E	35	31
5	3	GLY	GLY	LYS	LYS	(chain E and (resid 33 through 34 or (resid 35...	E	E	33 - 405	29 - 401
5	4	GLY	GLY	LYS	LYS	(chain E and (resid 33 through 34 or (resid 35...	E	E	33 - 405	29 - 401
5	5	GLY	GLY	LYS	LYS	(chain E and (resid 33 through 34 or (resid 35...	E	E	33 - 405	29 - 401
5	6	GLY	GLY	LYS	LYS	(chain E and (resid 33 through 34 or (resid 35...	E	E	33 - 405	29 - 401
6	1	GLY	GLY	PHE	PHE	(chain F and (resid 33 through 34 or (resid 35...	F	F	33 - 34	29 - 30
6	2	VAL	VAL	VAL	VAL	(chain F and (resid 33 through 34 or (resid 35...	F	F	35	31
6	3	GLY	GLY	LYS	LYS	(chain F and (resid 33 through 34 or (resid 35...	F	F	33 - 405	29 - 401
6	4	GLY	GLY	LYS	LYS	(chain F and (resid 33 through 34 or (resid 35...	F	F	33 - 405	29 - 401
6	5	GLY	GLY	LYS	LYS	(chain F and (resid 33 through 34 or (resid 35...	F	F	33 - 405	29 - 401
6	6	GLY	GLY	LYS	LYS	(chain F and (resid 33 through 34 or (resid 35...	F	F	33 - 405	29 - 401

#1: Protein	Aminopeptidase Mass: 45895.367 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Parabacteroides distasonis (bacteria) Gene: DW188_02780, DW692_01025, DW700_01025, DW808_17970, DW814_08450, DW867_06285, DW984_01045, DW998_13650, DWW19_04025, DWY54_02375, DWZ58_02465, DXD05_07510 Production host: Escherichia coli (E. coli) / References: UniProt: A0A395YY96
#2: Chemical	ChemComp-SWJ / 2-azanyl-~{N}-[(3~{S})-2-oxidanylidenehex-5-yn-3-yl]ethanamide Mass: 168.193 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₈H₁₂N₂O₂ / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-K / POTASSIUM ION Mass: 39.098 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: K
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 561 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.91 Å³/Da / Density % sol: 57.76 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2 M K/Na Tartrate, 15% PEG3350, 1 mM ZnCl2

-
Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

SSRL

/ Beamline: BL12-2 / Wavelength: 0.97946 Å

Detector

Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 12, 2019

Radiation

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

Radiation wavelength

Wavelength: 0.97946 Å / Relative weight: 1

Reflection

Resolution: 2.62→50 Å / Num. obs: 96251 / % possible obs: 99.4 % / Redundancy: 7.3 % / B_iso Wilson estimate: 39.96 Å² / R_merge(I) obs: 0.124 / R_pim(I) all: 0.048 / R_rim(I) all: 0.133 / Χ²: 0.906 / Net I/σ(I): 5.5 / Num. measured all: 707012

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique obs	CC_1/2	R_pim(I) all	R_rim(I) all	Χ²	% possible all
2.62-2.67	7.5	0.764	4728	0.724	0.293	0.82	0.933	99.6
2.67-2.71	7.5	0.667	4773	0.789	0.255	0.715	0.91	99.9
2.71-2.77	7.5	0.569	4782	0.839	0.219	0.611	0.915	99.9
2.77-2.82	7.5	0.528	4771	0.862	0.203	0.566	0.909	99.9
2.82-2.88	7.4	0.451	4779	0.9	0.174	0.484	0.91	99.9
2.88-2.95	7.3	0.39	4802	0.927	0.152	0.419	0.894	99.8
2.95-3.02	7.1	0.348	4758	0.935	0.138	0.375	0.91	99.7
3.02-3.11	6.7	0.272	4712	0.951	0.111	0.295	0.91	97.9
3.11-3.2	7.7	0.242	4798	0.97	0.092	0.26	0.92	99.9
3.2-3.3	7.6	0.191	4806	0.982	0.073	0.205	0.932	99.9
3.3-3.42	7.6	0.157	4792	0.987	0.06	0.169	0.919	99.8
3.42-3.56	7.3	0.128	4832	0.991	0.05	0.138	0.939	99.8
3.56-3.72	7.1	0.11	4792	0.992	0.044	0.119	0.951	99.9
3.72-3.91	7	0.091	4752	0.994	0.036	0.098	0.949	98.1
3.91-4.16	7.6	0.078	4845	0.996	0.03	0.084	0.946	99.6
4.16-4.48	7.5	0.068	4857	0.997	0.026	0.073	0.952	99.8
4.48-4.93	7.1	0.06	4835	0.997	0.024	0.064	0.942	99.1
4.93-5.64	7.5	0.061	4829	0.997	0.024	0.066	0.963	98.4
5.64-7.11	7.3	0.062	4956	0.997	0.024	0.067	0.98	99.9
7.11-50	7	0.04	5052	0.999	0.016	0.043	0.429	97.5

-
Processing

Software

Name	Version	Classification
PHENIX	1.12_2829	refinement
HKL-2000		data scaling
PDB_EXTRACT	3.25	data extraction
HKL-2000		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3pw3

3pw3

Resolution: 2.623→49.143 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 22.85 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2291	4831	5.02 %
R_work	0.2075	91316	-
obs	0.2086	96147	99.31 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso max: 112.37 Å² / B_iso mean: 47.4049 Å² / B_iso min: 14.54 Å²

Refinement step

Cycle: final / Resolution: 2.623→49.143 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	16733	0	84	561	17378
B_iso mean	-	-	53.53	37.94	-
Num. residues	-	-	-	-	2124

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.005	17272
X-RAY DIFFRACTION	f_angle_d	0.8	23423
X-RAY DIFFRACTION	f_chiral_restr	0.046	2468
X-RAY DIFFRACTION	f_plane_restr	0.004	3026
X-RAY DIFFRACTION	f_dihedral_angle_d	5.165	11328

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Number	Refine-ID	Rms	Type
1	1	A	9585	X-RAY DIFFRACTION	11.179	TORSIONAL
1	2	B	9585	X-RAY DIFFRACTION	11.179	TORSIONAL
1	3	C	9585	X-RAY DIFFRACTION	11.179	TORSIONAL
1	4	D	9585	X-RAY DIFFRACTION	11.179	TORSIONAL
1	5	E	9585	X-RAY DIFFRACTION	11.179	TORSIONAL
1	6	F	9585	X-RAY DIFFRACTION	11.179	TORSIONAL

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	% reflection obs (%)
2.6233-2.6531	0.3278	142	0.2845	2949	98
2.6531-2.6843	0.3361	142	0.2692	3003	99
2.6843-2.7171	0.3063	160	0.2661	3040	100
2.7171-2.7514	0.2907	167	0.2584	3020	100
2.7514-2.7876	0.3019	147	0.2538	3024	100
2.7876-2.8258	0.2644	161	0.2506	3035	100
2.8258-2.8662	0.2909	155	0.2538	3036	100
2.8662-2.909	0.2865	165	0.2559	3020	100
2.909-2.9544	0.269	141	0.2563	3076	100
2.9544-3.0029	0.2682	162	0.2647	3030	100
3.0029-3.0546	0.3378	190	0.2628	2947	98
3.0546-3.1102	0.2554	167	0.2537	2968	98
3.1102-3.17	0.2622	174	0.2402	3038	100
3.17-3.2347	0.2572	186	0.2404	3003	100
3.2347-3.305	0.268	164	0.2321	3050	100
3.305-3.3818	0.2588	139	0.2266	3080	100
3.3818-3.4664	0.2483	158	0.2281	3024	100
3.4664-3.5601	0.2446	164	0.2156	3061	100
3.5601-3.6648	0.2159	155	0.2052	3054	100
3.6648-3.7831	0.2015	160	0.1857	2979	97
3.7831-3.9182	0.2093	182	0.1835	3011	100
3.9182-4.075	0.1958	169	0.1848	3071	100
4.075-4.2604	0.1937	151	0.1666	3068	100
4.2604-4.4849	0.1945	153	0.1681	3088	100
4.4849-4.7656	0.1839	165	0.1617	3088	100
4.7656-5.1332	0.1968	152	0.1639	3003	97
5.1332-5.6491	0.1928	174	0.1758	3080	100
5.6491-6.465	0.2222	171	0.1988	3128	100
6.465-8.1393	0.1794	153	0.1937	3108	98
8.1393-49.143	0.1928	162	0.1899	3234	98

-
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://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