PDB-6vj6: 2.55 Angstrom Resolution Crystal Structure of Peptidylprolyl Isom...

ID or keywords:

Entry

Database: PDB / ID: 6vj6

Title

2.55 Angstrom Resolution Crystal Structure of Peptidylprolyl Isomerase (PrsA) from Bacillus cereus

Components

Peptidylprolyl isomerase (PrsA)

Keywords

ISOMERASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / PrsA / foldase

Function / homology

Function and homology information

peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / protein folding / plasma membrane
Similarity search - Function

Biological species

Bacillus cereus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.553 Å

Authors

Minasov, G. / Shuvalova, L. / Dubrovska, I. / Kiryukhina, O. / Wiersum, G. / Endres, M. / Satchell, K.J.F. / Center for Structural Genomics of Infectious Diseases (CSGID)

Citation

Journal: To Be Published
Title: 2.55 Angstrom Resolution Crystal Structure of Peptidylprolyl Isomerase (PrsA) from Bacillus cereus
Authors: Minasov, G. / Shuvalova, L. / Dubrovska, I. / Kiryukhina, O. / Wiersum, G. / Endres, M. / Satchell, K.J.F. / Center for Structural Genomics of Infectious Diseases (CSGID)

History

Deposition	Jan 14, 2020	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Feb 5, 2020	Provider: repository / Type: Initial release
Revision 1.1	Oct 9, 2024	Group: Data collection / Database references / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6vj6.cif.gz	215.6 KB	Display	PDBx/mmCIF format
PDB format	pdb6vj6.ent.gz	170.4 KB	Display	PDB format
PDBx/mmJSON format	6vj6.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	6vj6_validation.pdf.gz	786.9 KB	Display	wwPDB validaton report
Full document	6vj6_full_validation.pdf.gz	790.1 KB	Display
Data in XML	6vj6_validation.xml.gz	22 KB	Display
Data in CIF	6vj6_validation.cif.gz	30.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/vj/6vj6 ftp://data.pdbj.org/pub/pdb/validation_reports/vj/6vj6	HTTPS FTP

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Related structure data

Similar structure data	6icn-d 3gob-d 3gcf-5 6icm-d 3gkq-2 4qdd-1 3gl0-d 5a0g-d 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
Other databases	TargetTrack: CSGID-IDP97038

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#261 - Sep 2021 DNA-Sequencing Nanopores similarity (1) #163 - Jul 2013 HIV Capsid similarity (1) #245 - May 2020 Spliceosomes similarity (1) #22 - Oct 2001 Photosystem I similarity (1) #262 - Oct 2021 Fifty Years of Open Access to PDB Structures similarity (1) #29 - May 2002 Penicillin-binding Proteins similarity (1) #95 - Nov 2007 Multidrug Resistance Transporters similarity (1)

PDB pages

PDBj /

wwPDB /

NCBI

Related items in Molecule of the Month

#261 - Sep 2021
DNA-Sequencing Nanopores
similarity (1)
#163 - Jul 2013
HIV Capsid
similarity (1)
#245 - May 2020
Spliceosomes
similarity (1)
#22 - Oct 2001
Photosystem I
similarity (1)
#262 - Oct 2021
Fifty Years of Open Access to PDB Structures
similarity (1)
#29 - May 2002
Penicillin-binding Proteins
similarity (1)
#95 - Nov 2007
Multidrug Resistance Transporters
similarity (1)

Deposited unit

A: Peptidylprolyl isomerase (PrsA)

B: Peptidylprolyl isomerase (PrsA)

hetero molecules

60.8 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Peptidylprolyl isomerase (PrsA)

hetero molecules

A: Peptidylprolyl isomerase (PrsA)

hetero molecules

defined by author&software
Evidence: homology
60.9 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Peptidylprolyl isomerase (PrsA)

hetero molecules

B: Peptidylprolyl isomerase (PrsA)

hetero molecules

defined by author&software
Evidence: homology
60.6 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	151.425, 70.358, 79.357
Angle α, β, γ (deg.)	90.000, 91.749, 90.000
Int Tables number	5
Space group name H-M	C121

#1: Protein	Peptidylprolyl isomerase (PrsA) / Foldase protein PrsA 4 Mass: 30007.086 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus cereus (strain ATCC 14579 / DSM 31 / JCM 2152 / NBRC 15305 / NCIMB 9373 / NRRL B-3711) (bacteria) Strain: ATCC 14579 / DSM 31 / JCM 2152 / NBRC 15305 / NCIMB 9373 / NRRL B-3711 Gene: prsA4, BC_2862 / Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 / Variant (production host): (DE3)magic / References: UniProt: Q81CB1, peptidylprolyl isomerase
#2: Chemical	ChemComp-2NV / 3,6,9,12,15-pentaoxaoctadecan-17-amine / Jeffamine ED-2001 Mass: 279.373 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₃H₂₉NO₅
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 157 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N
Has protein modification	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 3.6 Å³/Da / Density % sol: 66.2 %
Crystal grow	Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7 Details: Protein: 8.3 mg/ml, 0.01M Tris pH 8.3; Reservior (Screen JCSG+, G1): 0.1M HEPES pH 7.0, 30% v/v Jeffamine ED-2001 pH 7.0

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
Detector	Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 14, 2019 / Details: C(111)
Radiation	Monochromator: Be / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97856 Å / Relative weight: 1
Reflection	Resolution: 2.55→30 Å / Num. obs: 27237 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 5 % / B_iso Wilson estimate: 56.3 Å² / R_merge(I) obs: 0.084 / R_pim(I) all: 0.044 / R_rim(I) all: 0.095 / R_sym value: 0.084 / Χ²: 1.108 / Net I/σ(I): 18.1
Reflection shell	Resolution: 2.55→2.59 Å / Redundancy: 5.1 % / R_merge(I) obs: 0.787 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 1368 / CC_1/2: 0.831 / CC star: 0.953 / R_pim(I) all: 0.394 / R_rim(I) all: 0.883 / R_sym value: 0.787 / Χ²: 1 / % possible all: 100

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0258	refinement
HKL-3000		data reduction
HKL-3000		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

SAD / Resolution: 2.553→29.73 Å / Cor.coef. F_o:F_c: 0.953 / Cor.coef. F_o:F_c free: 0.94 / SU B: 25.586 / SU ML: 0.259 / Cross valid method: FREE R-VALUE / ESU R: 0.412 / ESU R Free: 0.265
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2474	1382	5.075 %
R_work	0.2174	-	-
all	0.219	-	-
obs	-	27229	99.645 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å

Displacement parameters

B_iso mean: 77.617 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-5.799 Å²	0 Å²	-1.495 Å²
2-	-	-7.05 Å²	0 Å²
3-	-	-	12.917 Å²

Refinement step

Cycle: LAST / Resolution: 2.553→29.73 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4180	0	50	157	4387

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.005	0.013	4292
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.018	4102
X-RAY DIFFRACTION	r_angle_refined_deg	1.452	1.666	5717
X-RAY DIFFRACTION	r_angle_other_deg	0.384	1.618	9674
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	1.828	5	516
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	19.598	26.744	215
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	8.763	15	884
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	8.272	15	6
X-RAY DIFFRACTION	r_chiral_restr	0.07	0.2	541
X-RAY DIFFRACTION	r_gen_planes_refined	0.054	0.02	4632
X-RAY DIFFRACTION	r_gen_planes_other	0.054	0.02	718
X-RAY DIFFRACTION	r_nbd_refined	0.219	0.2	876
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.174	0.2	3498
X-RAY DIFFRACTION	r_nbtor_refined	0.169	0.2	2018
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.092	0.2	1573
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.163	0.2	158
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.151	0.2	34
X-RAY DIFFRACTION	r_nbd_other	0.185	0.2	118
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.204	0.2	26
X-RAY DIFFRACTION	r_mcbond_it	4.163	5.392	2067
X-RAY DIFFRACTION	r_mcbond_other	4.163	5.39	2066
X-RAY DIFFRACTION	r_mcangle_it	6.322	8.09	2582
X-RAY DIFFRACTION	r_mcangle_other	6.321	8.092	2583
X-RAY DIFFRACTION	r_scbond_it	4.761	5.995	2225
X-RAY DIFFRACTION	r_scbond_other	4.76	5.996	2226
X-RAY DIFFRACTION	r_scangle_it	7.583	8.75	3135
X-RAY DIFFRACTION	r_scangle_other	7.582	8.752	3136
X-RAY DIFFRACTION	r_lrange_it	10.751	64.254	4660
X-RAY DIFFRACTION	r_lrange_other	10.748	64.089	4642
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.123	0.05	7566

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
2.553-2.619	0.435	87	0.376	1855	0.379	1973	0.619	0.616	98.4288	0.36
2.619-2.69	0.369	94	0.348	1862	0.349	1958	0.658	0.675	99.8979	0.332
2.69-2.768	0.353	82	0.328	1797	0.329	1879	0.66	0.71	100	0.307
2.768-2.852	0.353	66	0.293	1777	0.295	1843	0.771	0.818	100	0.276
2.852-2.945	0.281	97	0.281	1681	0.281	1780	0.858	0.871	99.8876	0.266
2.945-3.047	0.277	96	0.265	1633	0.266	1730	0.817	0.882	99.9422	0.252
3.047-3.161	0.303	83	0.243	1573	0.246	1657	0.872	0.909	99.9397	0.236
3.161-3.288	0.309	86	0.244	1509	0.247	1595	0.863	0.913	100	0.237
3.288-3.433	0.298	89	0.243	1470	0.246	1559	0.892	0.92	100	0.241
3.433-3.598	0.273	75	0.207	1382	0.21	1458	0.914	0.938	99.9314	0.209
3.598-3.789	0.203	81	0.191	1352	0.192	1433	0.946	0.945	100	0.195
3.789-4.015	0.245	69	0.171	1236	0.174	1306	0.921	0.955	99.9234	0.179
4.015-4.287	0.214	58	0.17	1192	0.172	1250	0.938	0.949	100	0.184
4.287-4.622	0.22	62	0.172	1124	0.175	1186	0.952	0.958	100	0.192
4.622-5.051	0.231	64	0.207	1022	0.208	1086	0.94	0.948	100	0.243
5.051-5.627	0.265	53	0.248	931	0.249	985	0.925	0.912	99.8985	0.283
5.627-6.459	0.27	28	0.228	851	0.229	881	0.907	0.929	99.773	0.254
6.459-7.819	0.214	46	0.177	696	0.179	745	0.941	0.951	99.5973	0.217
7.819-10.694	0.179	42	0.162	554	0.163	601	0.961	0.967	99.1681	0.181
10.694-29.73	0.154	24	0.201	350	0.198	384	0.973	0.967	97.3958	0.229

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	7.5092	1.6192	-1.8096	1.0345	-0.4586	0.4928	-0.0668	0.1423	-0.3215	-0.0495	0.0308	-0.0752	0.0004	-0.027	0.0361	0.3128	-0.0091	0.0161	0.3434	0.0123	0.0505	0.2461	17.6905	39.7055
2	0.1493	0.1518	0.2243	0.5578	-1.1137	5.0835	-0.101	0.0509	0.1241	0.0014	0.1072	0.1898	-0.4465	0.1489	-0.0062	0.3306	-0.0367	-0.0023	0.2854	0.0073	0.2881	14.7515	31.8305	58.2535
3	5.7523	4.2417	-3.1778	3.2647	-2.0745	2.4053	-0.1556	-0.2591	-0.0407	0.0074	-0.1792	0.0918	0.2443	-0.0404	0.3348	0.462	-0.0246	-0.0008	0.5009	-0.0452	0.1655	21.9391	34.473	42.6865
4	3.6307	-1.5609	0.5908	5.9103	-0.6465	0.129	0.2374	-0.0072	-0.381	-0.1826	-0.1977	-0.0757	0.0321	-0.0107	-0.0397	0.2704	0.022	-0.0141	0.246	0.0076	0.0525	25.5645	70.143	28.7848
5	7.5185	5.7969	0.6111	7.0408	0.759	0.098	-0.2798	0.0205	0.6113	-0.4407	0.2018	0.6054	-0.0165	0.0921	0.0779	0.3964	0.0199	-0.0162	0.3479	0.0627	0.065	27.3953	42.2599	36.8353
6	4.3078	-1.9505	-0.9077	1.8128	1.7778	4.7744	0.0858	1.0446	0.2914	-0.4016	-0.0858	-0.1161	-0.0313	-0.3884	-0.0001	0.5358	-0.1091	0.0239	0.6971	0.0844	0.0218	8.253	20.6974	25.4652
7	4.7803	-0.635	1.0922	0.9991	0.0115	0.5012	0.0781	0.0359	0.0942	0.0412	-0.1079	-0.0411	0.0247	0.0342	0.0298	0.4005	0.0199	0.0357	0.3847	0.0648	0.0154	6.203	23.7236	-3.9536
8	2.434	1.135	-1.4118	4.3923	-2.4849	1.7784	-0.0523	0.1773	-0.0461	-0.1253	0.289	0.1922	0.1051	-0.2589	-0.2367	0.3442	-0.024	-0.0487	0.404	0.0103	0.346	7.6533	8.7337	-18.2622
9	2.9195	-1.422	0.8572	2.3614	-0.7508	1.8456	-0.2265	0.1861	-0.0138	-0.0859	-0.0197	-0.3703	-0.248	-0.3493	0.2463	0.4419	0.0123	0.0083	0.4598	0.0087	0.1195	23.719	9.1702	-1.8937
10	5.323	2.2132	0.1119	7.2137	-0.176	0.1102	0.1576	-0.054	0.1202	0.3789	-0.1589	-0.5612	0.0224	-0.1545	0.0012	0.2431	-0.0258	-0.029	0.2601	0.0429	0.0733	26.4169	-25.3341	10.9594
11	5.1603	-4.5216	-0.3071	4.1858	-0.0543	0.5131	-0.1028	-0.0968	-0.3442	0.1829	0.118	0.2812	-0.0971	-0.0484	-0.0152	0.1793	-0.0408	0.0061	0.1747	0.0286	0.2504	28.9956	2.2766	3.7756
12	3.5635	-2.042	0.334	2.635	0.4754	0.7778	-0.1746	-0.2733	0.0019	0.3289	0.1013	0.1485	-0.0814	-0.1154	0.0733	0.3134	-0.0085	0.0226	0.3092	0.0366	0.1549	9.5028	24.7118	14.1241

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	ALL	A	23 - 68
2	X-RAY DIFFRACTION	2	ALL	A	69 - 95
3	X-RAY DIFFRACTION	3	ALL	A	96 - 133
4	X-RAY DIFFRACTION	4	ALL	A	134 - 223
5	X-RAY DIFFRACTION	5	ALL	A	224 - 261
6	X-RAY DIFFRACTION	6	ALL	A	262 - 280
7	X-RAY DIFFRACTION	7	ALL	B	23 - 82
8	X-RAY DIFFRACTION	8	ALL	B	83 - 98
9	X-RAY DIFFRACTION	9	ALL	B	99 - 133
10	X-RAY DIFFRACTION	10	ALL	B	134 - 222
11	X-RAY DIFFRACTION	11	ALL	B	223 - 262
12	X-RAY DIFFRACTION	12	ALL	B	263 - 280

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