PDB-3cpx: Crystal structure of putative M42 glutamyl aminopeptidase (YP_676...

ID or keywords:

Entry

Database: PDB / ID: 3cpx

Title

Crystal structure of putative M42 glutamyl aminopeptidase (YP_676701.1) from Cytophaga hutchinsonii ATCC 33406 at 2.39 A resolution

Components

Aminopeptidase, M42 family

Keywords

HYDROLASE / YP_676701.1 / Putative M42 Glutamyl Aminopeptidase / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2

Function / homology

Function and homology information

aminopeptidase activity / metal ion binding
Similarity search - Function

Biological species

Cytophaga hutchinsonii ATCC 33406 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.39 Å

Authors

Joint Center for Structural Genomics (JCSG)

Citation

Journal: To be published
Title: Crystal structure of putative M42 glutamyl aminopeptidase (YP_676701.1) from Cytophaga hutchinsonii ATCC 33406 at 2.39 A resolution
Authors: Joint Center for Structural Genomics (JCSG)

History

Deposition	Apr 1, 2008	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 29, 2008	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.2	Oct 25, 2017	Group: Author supporting evidence / Refinement description / Category: pdbx_struct_assembly_auth_evidence / software / Item: _software.classification / _software.name
Revision 1.3	Jul 24, 2019	Group: Data collection / Derived calculations / Refinement description Category: software / struct_conn Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4	Feb 1, 2023	Group: Database references / Derived calculations Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5	Nov 20, 2024	Group: Data collection / Refinement description / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim Item: _pdbx_entry_details.has_protein_modification / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	3cpx.cif.gz	206 KB	Display	PDBx/mmCIF format
PDB format	pdb3cpx.ent.gz	163.5 KB	Display	PDB format
PDBx/mmJSON format	3cpx.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	3cpx_validation.pdf.gz	475.1 KB	Display	wwPDB validaton report
Full document	3cpx_full_validation.pdf.gz	510.3 KB	Display
Data in XML	3cpx_validation.xml.gz	41.7 KB	Display
Data in CIF	3cpx_validation.cif.gz	58.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/cp/3cpx ftp://data.pdbj.org/pub/pdb/validation_reports/cp/3cpx	HTTPS FTP

-
Related structure data

Similar structure data	3eh2-1 6kg3-1 6b9l-d 5ip3-d 5dtl-1 5dtl-2 4pbq-d 1dzx-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
Other databases	TargetDB: 375102

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Aminopeptidase, M42 family

B: Aminopeptidase, M42 family

C: Aminopeptidase, M42 family

hetero molecules

112 kDa, 3 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)	83.840, 83.840, 682.310
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	178
Space group name H-M	P6₁22

Noncrystallographic symmetry (NCS)

NCS domain:
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	Refine code	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	ASN	ASN	GLY	GLY	2	A	A	-5 - 0	14 - 19
2	1	ASN	ASN	GLY	GLY	2	B	B	-5 - 0	14 - 19
3	1	ASN	ASN	GLY	GLY	2	C	C	-5 - 0	14 - 19
4	2	MSE	MSE	MSE	MSE	5	A	A	1	20
5	2	MSE	MSE	MSE	MSE	5	B	B	1	20
6	2	MSE	MSE	MSE	MSE	5	C	C	1	20
7	3	GLN	GLN	SER	SER	2	A	A	2 - 36	21 - 55
8	3	GLN	GLN	SER	SER	2	B	B	2 - 36	21 - 55
9	3	GLN	GLN	SER	SER	2	C	C	2 - 36	21 - 55
10	4	TYR	TYR	TYR	TYR	5	A	A	37	56
11	4	TYR	TYR	TYR	TYR	5	B	B	37	56
12	4	TYR	TYR	TYR	TYR	5	C	C	37	56
13	5	GLN	GLN	ALA	ALA	1	A	A	38 - 43	57 - 62
14	5	GLN	GLN	ALA	ALA	1	B	B	38 - 43	57 - 62
15	5	GLN	GLN	ALA	ALA	1	C	C	38 - 43	57 - 62
16	6	ASP	ASP	ASN	ASN	6	A	A	44 - 45	63 - 64
17	6	ASP	ASP	ASN	ASN	6	B	B	44 - 45	63 - 64
18	6	ASP	ASP	ASN	ASN	6	C	C	44 - 45	63 - 64
19	7	ASP	ASP	ARG	ARG	1	A	A	46 - 119	65 - 138
20	7	ASP	ASP	ARG	ARG	1	B	B	46 - 119	65 - 138
21	7	ASP	ASP	ARG	ARG	1	C	C	46 - 119	65 - 138
22	8	LEU	LEU	PRO	PRO	2	A	A	120 - 143	139 - 162
23	8	LEU	LEU	PRO	PRO	2	B	B	120 - 143	139 - 162
24	8	LEU	LEU	PRO	PRO	2	C	C	120 - 143	139 - 162
25	9	TYR	TYR	TYR	TYR	5	A	A	144	163
26	9	TYR	TYR	TYR	TYR	5	B	B	144	163
27	9	TYR	TYR	TYR	TYR	5	C	C	144	163
28	10	LEU	LEU	PHE	PHE	2	A	A	145 - 190	164 - 209
29	10	LEU	LEU	PHE	PHE	2	B	B	145 - 190	164 - 209
30	10	LEU	LEU	PHE	PHE	2	C	C	145 - 190	164 - 209
31	11	HIS	HIS	HIS	HIS	5	A	A	191	210
32	11	HIS	HIS	HIS	HIS	5	B	B	191	210
33	11	HIS	HIS	HIS	HIS	5	C	C	191	210
34	12	VAL	VAL	ASN	ASN	1	A	A	192 - 229	211 - 248
35	12	VAL	VAL	ASN	ASN	1	B	B	192 - 229	211 - 248
36	12	VAL	VAL	ASN	ASN	1	C	C	192 - 229	211 - 248
37	13	ARG	ARG	GLU	GLU	5	A	A	230 - 233	249 - 252
38	13	ARG	ARG	GLU	GLU	5	B	B	230 - 233	249 - 252
39	13	ARG	ARG	GLU	GLU	5	C	C	230 - 233	249 - 252
40	14	LEU	LEU	LEU	LEU	2	A	A	234 - 302	253 - 321
41	14	LEU	LEU	LEU	LEU	2	B	B	234 - 302	253 - 321
42	14	LEU	LEU	LEU	LEU	2	C	C	234 - 302	253 - 321

Details

SIZE-EXCLUSION CHROMATOGRAPHY SUPPORTS THE ASSIGNMENT OF A TRIMER AS A SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION.

#1: Protein	Aminopeptidase, M42 family Mass: 37006.590 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Cytophaga hutchinsonii ATCC 33406 (bacteria) Species: Cytophaga hutchinsonii / Strain: NCIMB 9469 / Gene: YP_676701.1, frvX, CHU_0067 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q11Z05, UniProt: A0A6N4SM89*PLUS
#2: Chemical	ChemComp-FE / FE (III) ION Mass: 55.845 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Fe
#3: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 322 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y
Sequence details	THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG.

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 3.12 Å³/Da / Density % sol: 60.55 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6 Details: NANODROP, 1.0M LiCl, 10.0% PEG 6000, 0.1M MES pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K

-
Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

SSRL

/ Beamline: BL11-1 / Wavelength: 0.97859 Å

Detector

Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Feb 1, 2008 / Details: Flat mirror (vertical focusing)

Radiation

Monochromator: Single crystal Si(111) bent (horizontal focusing)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.97859 Å / Relative weight: 1

Reflection

Resolution: 2.39→29.656 Å / Num. obs: 52024 / % possible obs: 88.6 % / Observed criterion σ(I): -3 / Redundancy: 7.98 % / B_iso Wilson estimate: 58.48 Å² / R_merge(I) obs: 0.055 / Net I/σ(I): 16.87

Reflection shell

Diffraction-ID: 1

Resolution (Å)	R_merge(I) obs	Mean I/σ(I) obs	Num. measured obs	Num. unique obs	% possible all	R_sym value
2.39-2.6	0.616	2.27	52703	16895	73.5
2.6-3	0.248	6.3	101186	24886	86.3	0.285
3-4	0.063	19.8	135459	29190	94.1	0.071
4-6	0.038	34.8	89069	15929	99.8	0.042
6-10	0.033	37.2	29063	5172	99	0.036
10-29.656	0.029	40.9	7878	1389	94.9	0.032

-
Phasing

Phasing	Method: SAD

-
Processing

Software

Name	Version	Classification
REFMAC	5.4.0067	refinement
PHENIX		refinement
SHELX		phasing
MolProbity	3beta29	model building
XSCALE		data scaling
PDB_EXTRACT	3.004	data extraction
MAR345	CCD	data collection
XDS		data reduction
SOLVE		phasing
PHENIX		phasing
SHELXD		phasing

Refinement

Method to determine structure:

SAD / Resolution: 2.39→29.656 Å / Cor.coef. F_o:F_c: 0.957 / Cor.coef. F_o:F_c free: 0.939 / SU B: 12.494 / SU ML: 0.15 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.308 / ESU R Free: 0.224
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN ...

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.223	2650	5.1 %	RANDOM
R_work	0.187	-	-	-
obs	0.189	51910	89.28 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 35.947 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	3.4 Å²	1.7 Å²	0 Å²
2-	-	3.4 Å²	0 Å²
3-	-	-	-5.1 Å²

Refinement step

Cycle: LAST / Resolution: 2.39→29.656 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7333	0	55	322	7710

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.016	0.022	7581
X-RAY DIFFRACTION	r_bond_other_d	0.006	0.02	5069
X-RAY DIFFRACTION	r_angle_refined_deg	1.818	1.948	10293
X-RAY DIFFRACTION	r_angle_other_deg	1.589	3	12309
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	4.216	5	932
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	30.862	24.132	363
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.26	15	1203
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	12.584	15	42
X-RAY DIFFRACTION	r_chiral_restr	0.099	0.2	1105
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.021	8519
X-RAY DIFFRACTION	r_gen_planes_other	0.005	0.02	1571
X-RAY DIFFRACTION	r_mcbond_it	0.776	2	4621
X-RAY DIFFRACTION	r_mcbond_other	0.206	2	1891
X-RAY DIFFRACTION	r_mcangle_it	1.287	3	7443
X-RAY DIFFRACTION	r_scbond_it	0.915	2	2960
X-RAY DIFFRACTION	r_scangle_it	1.369	3	2847

Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	A	2521	TIGHT POSITIONAL	0.16	0.05
2	B	2521	TIGHT POSITIONAL	0.22	0.05
3	C	2521	TIGHT POSITIONAL	0.19	0.05
1	A	1379	MEDIUM POSITIONAL	0.17	0.5
2	B	1379	MEDIUM POSITIONAL	0.23	0.5
3	C	1379	MEDIUM POSITIONAL	0.2	0.5
1	A	101	LOOSE POSITIONAL	0.66	5
2	B	101	LOOSE POSITIONAL	0.46	5
3	C	101	LOOSE POSITIONAL	0.64	5
1	A	2521	TIGHT THERMAL	0.53	0.5
2	B	2521	TIGHT THERMAL	0.58	0.5
3	C	2521	TIGHT THERMAL	0.56	0.5
1	A	1379	MEDIUM THERMAL	0.51	2
2	B	1379	MEDIUM THERMAL	0.59	2
3	C	1379	MEDIUM THERMAL	0.57	2
1	A	101	LOOSE THERMAL	0.76	10
2	B	101	LOOSE THERMAL	0.9	10
3	C	101	LOOSE THERMAL	0.42	10

LS refinement shell

Resolution: 2.39→2.46 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.408	153	-
R_work	0.385	2839	-
all	-	2992	-
obs	-	-	71.89 %

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	1.175	0.0855	-0.3048	1.8133	-0.8032	3.4087	0.0093	-0.0351	-0.132	-0.2132	-0.0916	-0.3551	0.5179	0.769	0.0823	-0.0849	0.1243	0.0192	-0.1857	0.02	-0.0346	26.0615	32.6107	306.9346
2	1.4615	-0.1747	0.0495	1.2999	-0.6792	3.1489	0.1084	-0.2152	0.164	0.3093	0.0765	0.0126	-0.568	-0.216	-0.185	0.0097	0.0036	0.0982	-0.3269	0.0089	-0.0883	5.7772	51.108	329.2829
3	1.2397	0.1746	-0.5875	1.7757	0.0051	3.3617	0.0542	0.1036	0.2932	0.04	0.1625	0.0273	-0.9272	0.0938	-0.2167	0.1247	-0.073	0.0712	-0.3443	0.0917	-0.0194	14.196	64.5883	297.5316

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	0 - 302	19 - 321
2	X-RAY DIFFRACTION	2	B	B	0 - 302	19 - 321
3	X-RAY DIFFRACTION	3	C	C	0 - 302	19 - 321

-
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

-
Phasing

-
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

-Phasing

-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

-
Phasing

-
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