PDB-1w2m: Ca-substituted form of E. coli aminopeptidase P

ID or keywords:

Entry

Database: PDB / ID: 1w2m

Title

Ca-substituted form of E. coli aminopeptidase P

Components

XAA-PRO AMINOPEPTIDASE

Keywords

HYDROLASE / PROLINE-SPECIFIC PEPTIDASE / METALLOENZYME / PITA- BREAD FOLD / METALLOPROTEASE

Function / homology

Function and homology information

Xaa-Pro aminopeptidase / metalloexopeptidase activity / metalloaminopeptidase activity / aminopeptidase activity / manganese ion binding / protein homotetramerization / protein-containing complex / proteolysis / identical protein binding / cytosol
Similarity search - Function

Biological species

ESCHERICHIA COLI (E. coli)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 2.4 Å

Authors

Graham, S.C. / Bond, C.S. / Freeman, H.C. / Guss, J.M.

Citation

Journal: Biochemistry / Year: 2005
Title: Structural and Functional Implications of Metal Ion Selection in Aminopeptidase P, a Metalloprotease with a Dinuclear Metal Center.
Authors: Graham, S.C. / Bond, C.S. / Freeman, H.C. / Guss, J.M.

History

Deposition	Jul 7, 2004	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Sep 29, 2005	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.2	Dec 13, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn.ptnr2_label_seq_id / _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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	1w2m.cif.gz	534.4 KB	Display	PDBx/mmCIF format
PDB format	pdb1w2m.ent.gz	442 KB	Display	PDB format
PDBx/mmJSON format	1w2m.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	1w2m_validation.pdf.gz	464.6 KB	Display	wwPDB validaton report
Full document	1w2m_full_validation.pdf.gz	475 KB	Display
Data in XML	1w2m_validation.xml.gz	96.5 KB	Display
Data in CIF	1w2m_validation.cif.gz	134.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/w2/1w2m ftp://data.pdbj.org/pub/pdb/validation_reports/w2/1w2m	HTTPS FTP

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Related structure data

Related structure data	1w7vC 1wbqC 1wl6C 1wl9C 1wlrC 2bh3C 2bhaC 2bhbC 2bhcC 2bhdC 2bn7C 1m35S 1a16 1jaw 1n51 2bws 2bwt 2bwu 2bwv 2bww 2bwx 2bwy S: Starting model for refinement C: citing same article (ref.)
Similar structure data	1m35-1 1m35-2 1wbq-1 1wbq-2 1n51-1 2bh3-1 2bwv-1 1w7v-2 1w7v-1 1n51-3 2bha-1 1wl6-1 2bwy-1 1wl9-1 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

Related structure data

S: Starting model for refinement

C: citing same article (ref.)

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#70 - Oct 2005 Designer Proteins similarity (1)

Deposited unit

A: XAA-PRO AMINOPEPTIDASE

B: XAA-PRO AMINOPEPTIDASE

C: XAA-PRO AMINOPEPTIDASE

D: XAA-PRO AMINOPEPTIDASE

E: XAA-PRO AMINOPEPTIDASE

F: XAA-PRO AMINOPEPTIDASE

hetero molecules

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

1

A: XAA-PRO AMINOPEPTIDASE

B: XAA-PRO AMINOPEPTIDASE

C: XAA-PRO AMINOPEPTIDASE

D: XAA-PRO AMINOPEPTIDASE

hetero molecules

defined by author&software
200 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

E: XAA-PRO AMINOPEPTIDASE

F: XAA-PRO AMINOPEPTIDASE

hetero molecules

E: XAA-PRO AMINOPEPTIDASE

F: XAA-PRO AMINOPEPTIDASE

hetero molecules

defined by author&software
200 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	208.359, 312.688, 160.198
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	20
Space group name H-M	C222₁

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
3	1	C
4	1	D
5	1	E
6	1	F

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	SER	SER	ARG	ARG	5	A	A	1 - 10	1 - 10
2	1	SER	SER	ARG	ARG	5	B	B	1 - 10	1 - 10
3	1	SER	SER	ARG	ARG	5	C	C	1 - 10	1 - 10
4	1	SER	SER	ARG	ARG	5	D	D	1 - 10	1 - 10
5	1	SER	SER	ARG	ARG	5	E	E	1 - 10	1 - 10
6	1	SER	SER	ARG	ARG	5	F	F	1 - 10	1 - 10
1	2	ARG	ARG	ALA	ALA	2	A	A	11 - 37	11 - 37
2	2	ARG	ARG	ALA	ALA	2	B	B	11 - 37	11 - 37
3	2	ARG	ARG	ALA	ALA	2	C	C	11 - 37	11 - 37
4	2	ARG	ARG	ALA	ALA	2	D	D	11 - 37	11 - 37
5	2	ARG	ARG	ALA	ALA	2	E	E	11 - 37	11 - 37
6	2	ARG	ARG	ALA	ALA	2	F	F	11 - 37	11 - 37
1	3	ASP	ASP	ASP	ASP	5	A	A	38	38
2	3	ASP	ASP	ASP	ASP	5	B	B	38	38
3	3	ASP	ASP	ASP	ASP	5	C	C	38	38
4	3	ASP	ASP	ASP	ASP	5	D	D	38	38
5	3	ASP	ASP	ASP	ASP	5	E	E	38	38
6	3	ASP	ASP	ASP	ASP	5	F	F	38	38
1	4	SER	SER	ASP	ASP	2	A	A	39 - 68	39 - 68
2	4	SER	SER	ASP	ASP	2	B	B	39 - 68	39 - 68
3	4	SER	SER	ASP	ASP	2	C	C	39 - 68	39 - 68
4	4	SER	SER	ASP	ASP	2	D	D	39 - 68	39 - 68
5	4	SER	SER	ASP	ASP	2	E	E	39 - 68	39 - 68
6	4	SER	SER	ASP	ASP	2	F	F	39 - 68	39 - 68
1	5	ASP	ASP	ASP	ASP	5	A	A	69	69
2	5	ASP	ASP	ASP	ASP	5	B	B	69	69
3	5	ASP	ASP	ASP	ASP	5	C	C	69	69
4	5	ASP	ASP	ASP	ASP	5	D	D	69	69
5	5	ASP	ASP	ASP	ASP	5	E	E	69	69
6	5	ASP	ASP	ASP	ASP	5	F	F	69	69
1	6	THR	THR	PRO	PRO	2	A	A	70 - 99	70 - 99
2	6	THR	THR	PRO	PRO	2	B	B	70 - 99	70 - 99
3	6	THR	THR	PRO	PRO	2	C	C	70 - 99	70 - 99
4	6	THR	THR	PRO	PRO	2	D	D	70 - 99	70 - 99
5	6	THR	THR	PRO	PRO	2	E	E	70 - 99	70 - 99
6	6	THR	THR	PRO	PRO	2	F	F	70 - 99	70 - 99
1	7	GLU	GLU	LYS	LYS	5	A	A	100 - 101	100 - 101
2	7	GLU	GLU	LYS	LYS	5	B	B	100 - 101	100 - 101
3	7	GLU	GLU	LYS	LYS	5	C	C	100 - 101	100 - 101
4	7	GLU	GLU	LYS	LYS	5	D	D	100 - 101	100 - 101
5	7	GLU	GLU	LYS	LYS	5	E	E	100 - 101	100 - 101
6	7	GLU	GLU	LYS	LYS	5	F	F	100 - 101	100 - 101
1	8	LEU	LEU	ASP	ASP	2	A	A	102 - 105	102 - 105
2	8	LEU	LEU	ASP	ASP	2	B	B	102 - 105	102 - 105
3	8	LEU	LEU	ASP	ASP	2	C	C	102 - 105	102 - 105
4	8	LEU	LEU	ASP	ASP	2	D	D	102 - 105	102 - 105
5	8	LEU	LEU	ASP	ASP	2	E	E	102 - 105	102 - 105
6	8	LEU	LEU	ASP	ASP	2	F	F	102 - 105	102 - 105
1	9	ARG	ARG	ARG	ARG	5	A	A	106	106
2	9	ARG	ARG	ARG	ARG	5	B	B	106	106
3	9	ARG	ARG	ARG	ARG	5	C	C	106	106
4	9	ARG	ARG	ARG	ARG	5	D	D	106	106
5	9	ARG	ARG	ARG	ARG	5	E	E	106	106
6	9	ARG	ARG	ARG	ARG	5	F	F	106	106
1	10	ALA	ALA	ASN	ASN	2	A	A	107 - 142	107 - 142
2	10	ALA	ALA	ASN	ASN	2	B	B	107 - 142	107 - 142
3	10	ALA	ALA	ASN	ASN	2	C	C	107 - 142	107 - 142
4	10	ALA	ALA	ASN	ASN	2	D	D	107 - 142	107 - 142
5	10	ALA	ALA	ASN	ASN	2	E	E	107 - 142	107 - 142
6	10	ALA	ALA	ASN	ASN	2	F	F	107 - 142	107 - 142
1	11	SER	SER	SER	SER	2	A	A	143	143
2	11	SER	SER	SER	SER	2	B	B	143	143
3	11	SER	SER	SER	SER	2	C	C	143	143
4	11	SER	SER	SER	SER	2	D	D	143	143
5	11	SER	SER	SER	SER	2	E	E	143	143
6	11	SER	SER	SER	SER	2	F	F	143	143
1	12	ALA	ALA	ARG	ARG	2	A	A	144 - 149	144 - 149
2	12	ALA	ALA	ARG	ARG	2	B	B	144 - 149	144 - 149
3	12	ALA	ALA	ARG	ARG	2	C	C	144 - 149	144 - 149
4	12	ALA	ALA	ARG	ARG	2	D	D	144 - 149	144 - 149
5	12	ALA	ALA	ARG	ARG	2	E	E	144 - 149	144 - 149
6	12	ALA	ALA	ARG	ARG	2	F	F	144 - 149	144 - 149
1	13	LYS	LYS	ARG	ARG	5	A	A	150 - 153	150 - 153
2	13	LYS	LYS	ARG	ARG	5	B	B	150 - 153	150 - 153
3	13	LYS	LYS	ARG	ARG	5	C	C	150 - 153	150 - 153
4	13	LYS	LYS	ARG	ARG	5	D	D	150 - 153	150 - 153
5	13	LYS	LYS	ARG	ARG	5	E	E	150 - 153	150 - 153
6	13	LYS	LYS	ARG	ARG	5	F	F	150 - 153	150 - 153
1	14	GLN	GLN	GLY	GLY	2	A	A	154 - 188	154 - 188
2	14	GLN	GLN	GLY	GLY	2	B	B	154 - 188	154 - 188
3	14	GLN	GLN	GLY	GLY	2	C	C	154 - 188	154 - 188
4	14	GLN	GLN	GLY	GLY	2	D	D	154 - 188	154 - 188
5	14	GLN	GLN	GLY	GLY	2	E	E	154 - 188	154 - 188
6	14	GLN	GLN	GLY	GLY	2	F	F	154 - 188	154 - 188
1	15	GLU	GLU	GLU	GLU	5	A	A	189	189
2	15	GLU	GLU	GLU	GLU	5	B	B	189	189
3	15	GLU	GLU	GLU	GLU	5	C	C	189	189
4	15	GLU	GLU	GLU	GLU	5	D	D	189	189
5	15	GLU	GLU	GLU	GLU	5	E	E	189	189
6	15	GLU	GLU	GLU	GLU	5	F	F	189	189
1	16	ILE	ILE	MET	MET	2	A	A	190 - 251	190 - 251
2	16	ILE	ILE	MET	MET	2	B	B	190 - 251	190 - 251
3	16	ILE	ILE	MET	MET	2	C	C	190 - 251	190 - 251
4	16	ILE	ILE	MET	MET	2	D	D	190 - 251	190 - 251
5	16	ILE	ILE	MET	MET	2	E	E	190 - 251	190 - 251
6	16	ILE	ILE	MET	MET	2	F	F	190 - 251	190 - 251
1	17	ARG	ARG	ARG	ARG	5	A	A	252	252
2	17	ARG	ARG	ARG	ARG	5	B	B	252	252
3	17	ARG	ARG	ARG	ARG	5	C	C	252	252
4	17	ARG	ARG	ARG	ARG	5	D	D	252	252
5	17	ARG	ARG	ARG	ARG	5	E	E	252	252
6	17	ARG	ARG	ARG	ARG	5	F	F	252	252
1	18	ASP	ASP	GLY	GLY	2	A	A	253 - 280	253 - 280
2	18	ASP	ASP	GLY	GLY	2	B	B	253 - 280	253 - 280
3	18	ASP	ASP	GLY	GLY	2	C	C	253 - 280	253 - 280
4	18	ASP	ASP	GLY	GLY	2	D	D	253 - 280	253 - 280
5	18	ASP	ASP	GLY	GLY	2	E	E	253 - 280	253 - 280
6	18	ASP	ASP	GLY	GLY	2	F	F	253 - 280	253 - 280
1	19	LYS	LYS	THR	THR	5	A	A	281 - 283	281 - 283
2	19	LYS	LYS	THR	THR	5	B	B	281 - 283	281 - 283
3	19	LYS	LYS	THR	THR	5	C	C	281 - 283	281 - 283
4	19	LYS	LYS	THR	THR	5	D	D	281 - 283	281 - 283
5	19	LYS	LYS	THR	THR	5	E	E	281 - 283	281 - 283
6	19	LYS	LYS	THR	THR	5	F	F	281 - 283	281 - 283
1	20	ALA	ALA	LEU	LEU	2	A	A	285 - 297	285 - 297
2	20	ALA	ALA	LEU	LEU	2	B	B	285 - 297	285 - 297
3	20	ALA	ALA	LEU	LEU	2	C	C	285 - 297	285 - 297
4	20	ALA	ALA	LEU	LEU	2	D	D	285 - 297	285 - 297
5	20	ALA	ALA	LEU	LEU	2	E	E	285 - 297	285 - 297
6	20	ALA	ALA	LEU	LEU	2	F	F	285 - 297	285 - 297
1	21	GLU	GLU	ARG	ARG	5	A	A	298 - 305	298 - 305
2	21	GLU	GLU	ARG	ARG	5	B	B	298 - 305	298 - 305
3	21	GLU	GLU	ARG	ARG	5	C	C	298 - 305	298 - 305
4	21	GLU	GLU	ARG	ARG	5	D	D	298 - 305	298 - 305
5	21	GLU	GLU	ARG	ARG	5	E	E	298 - 305	298 - 305
6	21	GLU	GLU	ARG	ARG	5	F	F	298 - 305	298 - 305
1	22	PRO	PRO	VAL	VAL	2	A	A	306 - 326	306 - 326
2	22	PRO	PRO	VAL	VAL	2	B	B	306 - 326	306 - 326
3	22	PRO	PRO	VAL	VAL	2	C	C	306 - 326	306 - 326
4	22	PRO	PRO	VAL	VAL	2	D	D	306 - 326	306 - 326
5	22	PRO	PRO	VAL	VAL	2	E	E	306 - 326	306 - 326
6	22	PRO	PRO	VAL	VAL	2	F	F	306 - 326	306 - 326
1	23	LYS	LYS	LYS	LYS	5	A	A	327	327
2	23	LYS	LYS	LYS	LYS	5	B	B	327	327
3	23	LYS	LYS	LYS	LYS	5	C	C	327	327
4	23	LYS	LYS	LYS	LYS	5	D	D	327	327
5	23	LYS	LYS	LYS	LYS	5	E	E	327	327
6	23	LYS	LYS	LYS	LYS	5	F	F	327	327
1	24	LEU	LEU	ALA	ALA	2	A	A	328 - 340	328 - 340
2	24	LEU	LEU	ALA	ALA	2	B	B	328 - 340	328 - 340
3	24	LEU	LEU	ALA	ALA	2	C	C	328 - 340	328 - 340
4	24	LEU	LEU	ALA	ALA	2	D	D	328 - 340	328 - 340
5	24	LEU	LEU	ALA	ALA	2	E	E	328 - 340	328 - 340
6	24	LEU	LEU	ALA	ALA	2	F	F	328 - 340	328 - 340
1	25	GLN	GLN	GLN	GLN	5	A	A	341	341
2	25	GLN	GLN	GLN	GLN	5	B	B	341	341
3	25	GLN	GLN	GLN	GLN	5	C	C	341	341
4	25	GLN	GLN	GLN	GLN	5	D	D	341	341
5	25	GLN	GLN	GLN	GLN	5	E	E	341	341
6	25	GLN	GLN	GLN	GLN	5	F	F	341	341
1	26	ASN	ASN	ALA	ALA	2	A	A	342 - 392	342 - 392
2	26	ASN	ASN	ALA	ALA	2	B	B	342 - 392	342 - 392
3	26	ASN	ASN	ALA	ALA	2	C	C	342 - 392	342 - 392
4	26	ASN	ASN	ALA	ALA	2	D	D	342 - 392	342 - 392
5	26	ASN	ASN	ALA	ALA	2	E	E	342 - 392	342 - 392
6	26	ASN	ASN	ALA	ALA	2	F	F	342 - 392	342 - 392
1	27	GLU	GLU	GLU	GLU	5	A	A	393 - 396	393 - 396
2	27	GLU	GLU	GLU	GLU	5	B	B	393 - 396	393 - 396
3	27	GLU	GLU	GLU	GLU	5	C	C	393 - 396	393 - 396
4	27	GLU	GLU	GLU	GLU	5	D	D	393 - 396	393 - 396
5	27	GLU	GLU	GLU	GLU	5	E	E	393 - 396	393 - 396
6	27	GLU	GLU	GLU	GLU	5	F	F	393 - 396	393 - 396
1	28	GLN	GLN	PRO	PRO	2	A	A	397 - 427	397 - 427
2	28	GLN	GLN	PRO	PRO	2	B	B	397 - 427	397 - 427
3	28	GLN	GLN	PRO	PRO	2	C	C	397 - 427	397 - 427
4	28	GLN	GLN	PRO	PRO	2	D	D	397 - 427	397 - 427
5	28	GLN	GLN	PRO	PRO	2	E	E	397 - 427	397 - 427
6	28	GLN	GLN	PRO	PRO	2	F	F	397 - 427	397 - 427
1	29	GLU	GLU	GLU	GLU	5	A	A	428	428
2	29	GLU	GLU	GLU	GLU	5	B	B	428	428
3	29	GLU	GLU	GLU	GLU	5	C	C	428	428
4	29	GLU	GLU	GLU	GLU	5	D	D	428	428
5	29	GLU	GLU	GLU	GLU	5	E	E	428	428
6	29	GLU	GLU	GLU	GLU	5	F	F	428	428
1	30	GLU	GLU	MET	MET	2	A	A	429 - 434	429 - 434
2	30	GLU	GLU	MET	MET	2	B	B	429 - 434	429 - 434
3	30	GLU	GLU	MET	MET	2	C	C	429 - 434	429 - 434
4	30	GLU	GLU	MET	MET	2	D	D	429 - 434	429 - 434
5	30	GLU	GLU	MET	MET	2	E	E	429 - 434	429 - 434
6	30	GLU	GLU	MET	MET	2	F	F	429 - 434	429 - 434

#1: Protein	XAA-PRO AMINOPEPTIDASE / X-PRO AMINOPEPTIDASE / AMINOPEPTIDASE P II / APP-II / AMINOACYLPROLINE AMINOPEPTIDASE Mass: 49760.062 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Gene: PEPP / Plasmid: PPL670 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): AN1459 / References: UniProt: P15034, Xaa-Pro aminopeptidase
#2: Chemical	ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL Mass: 60.095 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C₃H₈O / Comment: alkaloid*YM
#3: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#4: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1072 / Source method: isolated from a natural source / Formula: H₂O
Compound details	CATALYSES THE RELEASE OF ANY N-TERMINAL AMINO ACID, INCLUDING PROLINE, THAT IS LINKED WITH PROLINE, ...CATALYSES THE RELEASE OF ANY N-TERMINAL AMINO ACID, INCLUDING PROLINE, THAT IS LINKED WITH PROLINE, EVEN FROM A DIPEPTIDE OR TRIPEPTIDE.

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 4.4 Å³/Da / Density % sol: 71.7 %
Crystal grow	pH: 8.2 Details: 25% PEG 4K, 0.1 MM EDTA, 0.1 M TRIS (PH 8.2), 0.2 M NA ACETATE CRYSTALS SOAKED IN 30% ISOPROPANOL PLUS 5 MM CACL2 FOR 10 MIN PRIOR TO FREEZING

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Data collection

Diffraction	Mean temperature: 113 K
Diffraction source	Source: ROTATING ANODE / Type: RIGAKU RU200 H / Wavelength: 1.5418
Detector	Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Jun 17, 1999 / Details: YALE MIRRORS
Radiation	Monochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.5418 Å / Relative weight: 1
Reflection	Resolution: 2.4→30 Å / Num. obs: 192310 / % possible obs: 94.5 % / Observed criterion σ(I): -3 / Redundancy: 2.1 % / B_iso Wilson estimate: 40.59 Å² / R_merge(I) obs: 0.04 / Net I/σ(I): 19.6
Reflection shell	Resolution: 2.4→2.48 Å / Redundancy: 1.6 % / R_merge(I) obs: 0.16 / Mean I/σ(I) obs: 4.5 / % possible all: 86

-
Processing

Software

Name	Version	Classification
REFMAC	5.1.24	refinement
DENZO		data reduction
SCALEPACK		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1M35

1m35

Resolution: 2.4→182.57 Å / Cor.coef. F_o:F_c: 0.951 / Cor.coef. F_o:F_c free: 0.936 / SU B: 4.667 / SU ML: 0.11 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.211 / ESU R Free: 0.173 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. SUFFICIENT ELECTRON DENSITY WAS NOT PRESENT TO ALLOW THE MODELLING OF C-TERMINAL RESIDUES A440, B438, B439, B440,C440 AND E440 OR THE ...

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2	9688	5 %	RANDOM
R_work	0.175	-	-	-
obs	0.176	182590	94.8 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 26.12 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.58 Å²	0 Å²	0 Å²
2-	-	-0.67 Å²	0 Å²
3-	-	-	1.25 Å²

Refinement step

Cycle: LAST / Resolution: 2.4→182.57 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	20931	0	60	1072	22063

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.013	0.021	21399
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.02	19479
X-RAY DIFFRACTION	r_angle_refined_deg	1.254	1.951	28972
X-RAY DIFFRACTION	r_angle_other_deg	0.833	3	45074
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.867	5	2628
X-RAY DIFFRACTION	r_dihedral_angle_2_deg
X-RAY DIFFRACTION	r_dihedral_angle_3_deg
X-RAY DIFFRACTION	r_dihedral_angle_4_deg
X-RAY DIFFRACTION	r_chiral_restr	0.073	0.2	3156
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	24073
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	4472
X-RAY DIFFRACTION	r_nbd_refined	0.2	0.2	4150
X-RAY DIFFRACTION	r_nbd_other	0.235	0.2	22322
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other	0.086	0.2	12808
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.15	0.2	1081
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	0.176	0.2	26
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.295	0.2	160
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.156	0.2	41
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	0.529	1.5	13069
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	1.077	2	21048
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	1.753	3	8330
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	3.097	4.5	7924
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
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

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	2312	tight positional	0.04	0.05
2	B	2312	tight positional	0.05	0.05
3	C	2312	tight positional	0.05	0.05
4	D	2312	tight positional	0.04	0.05
5	E	2312	tight positional	0.04	0.05
6	F	2312	tight positional	0.04	0.05
1	A	3898	medium positional	0.18	0.5
2	B	3898	medium positional	0.23	0.5
3	C	3898	medium positional	0.19	0.5
4	D	3898	medium positional	0.17	0.5
5	E	3898	medium positional	0.19	0.5
6	F	3898	medium positional	0.18	0.5
1	A	421	loose positional	1.28	5
2	B	421	loose positional	1.03	5
3	C	421	loose positional	1.02	5
4	D	421	loose positional	0.77	5
5	E	421	loose positional	1.04	5
6	F	421	loose positional	1.15	5
1	A	2312	tight thermal	0.07	0.5
2	B	2312	tight thermal	0.07	0.5
3	C	2312	tight thermal	0.08	0.5
4	D	2312	tight thermal	0.08	0.5
5	E	2312	tight thermal	0.09	0.5
6	F	2312	tight thermal	0.08	0.5
1	A	3898	medium thermal	0.38	2
2	B	3898	medium thermal	0.35	2
3	C	3898	medium thermal	0.38	2
4	D	3898	medium thermal	0.37	2
5	E	3898	medium thermal	0.43	2
6	F	3898	medium thermal	0.41	2
1	A	421	loose thermal	1.96	10
2	B	421	loose thermal	1.57	10
3	C	421	loose thermal	1.53	10
4	D	421	loose thermal	1.7	10
5	E	421	loose thermal	2.81	10
6	F	421	loose thermal	2.09	10

LS refinement shell

Resolution: 2.4→2.46 Å / Total num. of bins used: 20 /

	R_factor	Num. reflection
R_free	0.265	619
R_work	0.218	12247

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	1.05	0.0338	0.0597	0.3214	0.0401	0.4454	-0.1105	0.0192	-0.0214	-0.0632	0.0478	0.0067	-0.0074	-0.0127	0.0628	0.0689	-0.0708	-0.0385	0.1252	0.0064	0.0607	32.625	67.52	6.972
2	1.414	0.1004	0.1622	0.3914	0.0693	0.6025	-0.0857	0.0823	-0.1269	-0.098	0.0926	-0.0913	0.0338	0.0737	-0.0069	0.0743	-0.0693	0.0556	0.1338	-0.035	0.0836	86.961	77.478	10.059
3	1.0134	0.3395	-0.3936	0.7419	0.0285	0.6979	0.0037	-0.1129	-0.0159	-0.0499	0.04	-0.1065	-0.0101	0.0793	-0.0437	0.0442	-0.0575	-0.0027	0.0983	-0.0284	0.0434	80.069	90.549	37.607
4	0.5686	0.3647	0.2131	0.4748	0.0843	0.5724	0.0033	-0.088	0.0181	-0.0166	-0.0169	0.0218	0.0479	-0.0615	0.0136	0.082	-0.0785	-0.0168	0.1312	0.0239	0.0583	34.71	59.146	36.969
5	0.4901	-0.188	-0.0719	0.5039	-0.0163	0.4816	0.0054	0.0201	0.0228	0.0258	-0.068	0.0031	-0.0141	-0.0243	0.0626	0.0542	-0.0043	0.0027	0.0351	-0.0064	0.0433	98.445	183.831	13.634
6	0.2878	-0.2956	-0.0258	1.2068	0.4168	0.2308	-0.0037	0.0037	-0.006	0.2495	-0.0298	0.0838	0.0659	0.0004	0.0335	0.1434	0.0224	0.0347	0.0323	0.0198	0.0248	109.919	129.687	15.503

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1 - 439
2	X-RAY DIFFRACTION	2	B	1 - 438
3	X-RAY DIFFRACTION	3	C	1 - 439
4	X-RAY DIFFRACTION	4	D	1 - 440
5	X-RAY DIFFRACTION	5	E	1 - 439
6	X-RAY DIFFRACTION	6	F	1 - 440

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