PDB-2pef: Crystal Structure of a Thermophilic Serpin, Tengpin, in the Laten...

ID or keywords:

Entry

Database: PDB / ID: 2pef

Title

Crystal Structure of a Thermophilic Serpin, Tengpin, in the Latent State

Components

Serine protease inhibitor

Keywords

Protease Inhibitor / serpin

Function / homology

Function and homology information

serine-type endopeptidase inhibitor activity / extracellular space
Similarity search - Function

Biological species

Thermoanaerobacter tengcongensis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.6 Å

Authors

Zhang, Q.W. / Buckle, A.M. / Whisstock, J.C.

Citation

Journal: Embo Rep. / Year: 2007
Title: The N terminus of the serpin, tengpin, functions to trap the metastable native state.
Authors: Zhang, Q. / Buckle, A.M. / Law, R.H. / Pearce, M.C. / Cabrita, L.D. / Lloyd, G.J. / Irving, J.A. / Smith, A.I. / Ruzyla, K. / Rossjohn, J. / Bottomley, S.P. / Whisstock, J.C.

History

Deposition	Apr 3, 2007	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jun 19, 2007	Provider: repository / Type: Initial release
Revision 1.1	May 1, 2008	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Advisory / Source and taxonomy / Version format compliance
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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Download

PDBx/mmCIF format	2pef.cif.gz	99.1 KB	Display	PDBx/mmCIF format
PDB format	pdb2pef.ent.gz	73.9 KB	Display	PDB format
PDBx/mmJSON format	2pef.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	2pef_validation.pdf.gz	424.3 KB	Display	wwPDB validaton report
Full document	2pef_full_validation.pdf.gz	430.2 KB	Display
Data in XML	2pef_validation.xml.gz	19.8 KB	Display
Data in CIF	2pef_validation.cif.gz	30.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/pe/2pef ftp://data.pdbj.org/pub/pdb/validation_reports/pe/2pef	HTTPS FTP

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Related structure data

Related structure data	2peeC 1sngS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	6ly2-1 3ndf-d 4roa-d 2oay-d 4rsq-2 7ahp-d 4rsq-10 5ci2-d 3q03-2 5cdz-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

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#53 - May 2004 Serpins similarity (10)

Deposited unit

A: Serine protease inhibitor

42.2 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author

Unit cell

Length a, b, c (Å)	44.762, 44.907, 159.233
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Serine protease inhibitor Mass: 42246.031 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermoanaerobacter tengcongensis (bacteria) Strain: MB4 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8R9P5
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 484 / 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: 1.89 Å³/Da / Density % sol: 35.04 %
Crystal grow	Temperature: 294 K / pH: 7.5 Details: 28% PEG 400, 0.1 M Na Hepes, 0.2 M Calcium Chloride, VAPOR DIFFUSION, HANGING DROP, temperature 294K, pH 7.5

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 1
Detector	Type: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 24, 2004
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.6→79 Å / Num. obs: 42797 / % possible obs: 98.4 % / Observed criterion σ(I): 3 / Redundancy: 5.4 % / R_merge(I) obs: 0.076 / Net I/σ(I): 20.1
Reflection shell	Resolution: 1.6→1.66 Å / Redundancy: 1.6 % / R_merge(I) obs: 0.351 / Mean I/σ(I) obs: 1.6 / % possible all: 98.1

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Phasing

Phasing MR	R rigid body: 0.269 / Cor.coef. F_o:F_c: 0.849 / Cor.coef. Io to Ic: 0.838

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Processing

Software

Name	Version	Classification
AMoRE		phasing
REFMAC		refinement
PDB_EXTRACT	2	data extraction
DENZO		data reduction
SCALEPACK		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1SNG, THERMOPIN

1sng

Resolution: 1.6→79 Å / Cor.coef. F_o:F_c: 0.934 / Cor.coef. F_o:F_c free: 0.897 / SU B: 5.747 / SU ML: 0.104 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.119 / ESU R Free: 0.119 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.253	2138	5 %	RANDOM
R_work	0.206	-	-	-
obs	0.208	40547	98.5 %	-

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: 17.58 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.08 Å²	0 Å²	0 Å²
2-	-	0.23 Å²	0 Å²
3-	-	-	-0.16 Å²

Refinement step

Cycle: LAST / Resolution: 1.6→79 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2841	0	0	484	3325

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.006	0.022	2951
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	0.999	1.961	4025
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.091	5	385
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	35.556	26.24	125
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	11.854	15	510
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	13.638	15	2
X-RAY DIFFRACTION	r_chiral_restr	0.072	0.2	477
X-RAY DIFFRACTION	r_gen_planes_refined	0.003	0.02	2197
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined	0.178	0.2	1467
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined	0.3	0.2	2095
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.099	0.2	408
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	0.155	0.2	57
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.089	0.2	64
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	0.799	3	1913
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	1.281	5	3021
X-RAY DIFFRACTION	r_scbond_it	2.202	7	1183
X-RAY DIFFRACTION	r_scangle_it	3.036	10	993
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 1.6→1.64 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.265	145	-
R_work	0.228	2774	-
obs	-	-	93.62 %

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	1.1197	0.0195	0.4838	6.1787	0.8444	1.0246	0.0066	-0.1175	-0.0119	0.0146	0.0377	0.1184	-0.0195	-0.0689	-0.0443	-0.0009	-0.0324	0.0001	0.0505	0.0159	0.0096	1.425	22.2	27.837
2	1.7093	-0.9716	0.4551	1.1313	-0.3213	0.9677	-0.0313	0.0577	-0.1374	-0.0036	0.0229	0.0333	0.1775	-0.0133	0.0084	0.0458	-0.0182	0.0024	0.0027	0.0035	-0.0003	8.139	14.538	18.171
3	2.4287	0.8444	1.1792	1.8652	0.3522	2.1579	-0.0769	-0.0427	0.1326	0.0098	0.0092	0.1839	-0.0321	-0.3435	0.0677	-0.0328	-0.0011	-0.0014	0.06	0.0177	0.0101	-4.266	27.422	19.542
4	7.8423	-0.882	1.1353	1.7148	-0.4104	1.9246	-0.0108	-0.0071	0.2532	0.0196	-0.0286	0.044	-0.0455	0.0166	0.0394	0.0266	-0.0079	-0.0172	0.0139	0.0026	0.0197	18.231	30.688	25.931
5	7.1711	-1.104	8.005	1.3138	0.4611	17.8617	0.0461	0.1417	0.0476	-0.2746	-0.1204	0.0737	-0.3552	-0.7395	0.0743	0.0511	-0.0063	-0.0239	0.0501	0.0292	-0.0198	6.929	29.134	3.013
6	15.4452	2.2124	9.3158	6.7943	2.9691	17.351	0.1256	0.2531	0.0642	-0.1279	-0.2702	-0.2881	-0.4774	0.0309	0.1447	0.0137	-0.0183	-0.0054	0.0061	0.0476	-0.0271	-0.688	36.107	6.773
7	1.8348	-1.2089	-0.7555	1.5918	0.7626	4.2085	0.1216	0.2115	0.1274	-0.1861	-0.0673	-0.0779	-0.1137	-0.1135	-0.0544	0.0264	-0.0332	-0.0104	0.0057	0.0285	0.0021	10.461	29.339	3.595
8	4.7201	-2.3458	3.2377	4.532	-5.6341	8.6878	0.1705	0.0986	-0.0821	-0.0571	-0.1816	0.0436	0.2587	0.4094	0.0111	-0.0018	-0.0118	0.013	0.0576	0.0052	-0.011	19.999	23.212	9.699
9	13.585	-6.1019	4.5026	7.2345	-2.0063	6.3307	0.7303	0.3096	-0.9143	-0.7637	-0.2951	0.7491	0.4727	0.0103	-0.4352	0.1124	-0.0881	-0.0897	0.025	0.0028	-0.0605	8.273	18.918	-1.344
10	1.7846	-0.331	1.8132	0.4757	-0.5936	2.2449	-0.0752	0.1216	-0.0098	-0.0468	0.0475	-0.0441	-0.132	0.1655	0.0277	0.0354	0.0006	0.0101	0.0276	-0.0163	0.0091	22.455	20.623	23.719
11	10.8571	14.736	13.8464	20.9428	17.6726	18.9919	0.5066	0.1074	-1.1408	0.2699	0.4205	-1.3201	0.727	-0.063	-0.927	-0.0796	-0.012	0.0299	-0.0285	-0.0969	0.1695	30.905	-1.993	25.583
12	4.0743	-0.0892	-2.0281	1.1726	0.2812	1.7805	0.0255	0.1977	-0.2626	-0.1045	-0.0433	-0.123	0.0248	-0.1159	0.0177	0.0503	0.0028	-0.0139	0.0104	-0.0126	0.0585	25.852	8.499	35.353
13	17.5539	7.1552	3.3025	12.5769	4.1145	1.4146	-0.1352	-0.2036	0.5423	0.3056	-0.2486	0.7587	0.1162	-0.3937	0.3838	0.0354	-0.0288	0.0111	0.0181	-0.007	0.0589	9.694	4.622	41.154
14	0.5816	0.6587	0.0183	2.3025	0.1294	0.0082	0.0022	0.0002	-0.0141	0.0022	0.0102	0.0712	0.0171	-0.0182	-0.0124	0.0272	-0.0056	-0.0121	0.0067	0.0045	0.0125	14.089	10.288	33.244
15	1.0886	-0.3327	1.1189	0.448	-0.3768	1.1536	-0.077	-0.2664	-0.0796	0.0508	0.0839	0.0571	-0.0464	-0.1391	-0.0069	0.0232	-0.0104	-0.0058	0.0234	0.0006	0.0204	14.119	12.779	38.415
16	6.6461	3.5131	4.5546	7.1317	-0.2521	4.881	0.1878	0.3717	0.1117	-0.1478	0.1059	0.122	0.0794	0.449	-0.2937	0.0778	0.0166	-0.0089	0.0522	-0.0135	0.0491	21.738	9.564	19.285
17	1.6029	-0.8155	-0.0171	1.3726	0.2103	1.0036	0.0801	0.2096	-0.1229	-0.0899	-0.0831	0.2172	0.1465	-0.2662	0.003	0.035	-0.0703	-0.0397	0.0743	-0.0076	-0.0061	-3.695	17.613	8.533
18	6.0602	-0.9699	4.2264	0.5704	-0.765	4.1343	-0.0164	0.3565	-0.0889	-0.1605	0.0482	0.0755	0.0119	0.1291	-0.0317	0.056	-0.0239	-0.0246	0.0242	0.0004	0.0171	11.705	17.08	12.657
19	5.7729	2.9022	-5.6728	6.8348	-4.3755	14.1277	0.0873	0.1909	-0.073	-0.0428	0.1939	-0.0467	0.3781	-0.0654	-0.2812	0.0208	0.016	0.0259	0.0286	0.0046	0.0515	21.392	-2.374	24.42
20	1.1358	0.4172	-0.1279	2.4503	0.397	0.9833	-0.0053	-0.0147	-0.0085	-0.1084	-0.0015	-0.0335	0.0015	-0.0025	0.0068	0.0244	-0.0101	-0.0045	0.0221	0.0064	0.0248	14.608	13.313	27.821

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	51 - 73	1 - 23
2	X-RAY DIFFRACTION	2	A	A	74 - 95	24 - 45
3	X-RAY DIFFRACTION	3	A	A	96 - 127	46 - 77
4	X-RAY DIFFRACTION	4	A	A	128 - 139	78 - 89
5	X-RAY DIFFRACTION	5	A	A	140 - 152	90 - 102
6	X-RAY DIFFRACTION	6	A	A	153 - 162	103 - 112
7	X-RAY DIFFRACTION	7	A	A	163 - 184	113 - 134
8	X-RAY DIFFRACTION	8	A	A	185 - 196	135 - 146
9	X-RAY DIFFRACTION	9	A	A	197 - 208	147 - 158
10	X-RAY DIFFRACTION	10	A	A	209 - 226	159 - 176
11	X-RAY DIFFRACTION	11	A	A	227 - 241	177 - 191
12	X-RAY DIFFRACTION	12	A	A	242 - 255	192 - 205
13	X-RAY DIFFRACTION	13	A	A	256 - 261	206 - 211
14	X-RAY DIFFRACTION	14	A	A	262 - 292	212 - 242
15	X-RAY DIFFRACTION	15	A	A	293 - 315	243 - 265
16	X-RAY DIFFRACTION	16	A	A	316 - 319	266 - 269
17	X-RAY DIFFRACTION	17	A	A	320 - 352	270 - 302
18	X-RAY DIFFRACTION	18	A	A	353 - 384	303 - 334
19	X-RAY DIFFRACTION	19	A	A	392 - 399	342 - 349
20	X-RAY DIFFRACTION	20	A	A	400 - 423	350 - 373

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