PDB-6vj2: 3.10 Angstrom Resolution Crystal Structure of Foldase Protein (Pr...

ID or keywords:

Entry

Database: PDB / ID: 6vj2

Title

3.10 Angstrom Resolution Crystal Structure of Foldase Protein (PrsA) from Lactococcus lactis

Components

Foldase

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

Lactococcus lactis subsp. lactis (lactic acid bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 3.1 Å

Authors

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

Citation

Journal: To Be Published
Title: 3.10 Angstrom Resolution Crystal Structure of Foldase Protein (PrsA) from Lactococcus lactis
Authors: Minasov, G. / Shuvalova, L. / Kiryukhina, O. / 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

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6vj2.cif.gz	428.5 KB	Display	PDBx/mmCIF format
PDB format	pdb6vj2.ent.gz	370 KB	Display	PDB format
PDBx/mmJSON format	6vj2.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/vj/6vj2 ftp://data.pdbj.org/pub/pdb/validation_reports/vj/6vj2	HTTPS FTP

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Related structure data

Similar structure data	4bsn-d 6uip-d 2c47-d 1h3g-d 6kid-d 5v3g-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-IDP97054

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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: Foldase

B: Foldase

C: Foldase

D: Foldase

127 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Foldase

C: Foldase

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

2

B: Foldase

D: Foldase

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

Unit cell

Length a, b, c (Å)	81.513, 117.609, 149.310
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	A
2	1	B
1	2	A
2	2	C
1	3	A
2	3	D
1	4	B
2	4	C
1	5	B
2	5	D
1	6	C
2	6	D

NCS domain segments:

Dom-ID	Ens-ID	Auth asym-ID	Auth seq-ID
1	1	A	31 - 299
2	1	B	31 - 299
1	2	A	32 - 299
2	2	C	32 - 299
1	3	A	32 - 300
2	3	D	32 - 300
1	4	B	32 - 299
2	4	C	32 - 299
1	5	B	32 - 299
2	5	D	32 - 299
1	6	C	32 - 299
2	6	D	32 - 299

NCS ensembles :

ID
1
2
3
4
5
6

#1: Protein	Foldase / / PrsA Mass: 31635.309 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lactococcus lactis subsp. lactis (strain IL1403) (lactic acid bacteria) Strain: IL1403 / Gene: prsA, pmpA, LL1725, L164604 / Variant: lactis Il1403 / Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): DE3 / Variant (production host): magic / References: UniProt: Q9CEV9, peptidylprolyl isomerase
#2: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 88 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.8 Å³/Da / Density % sol: 56.1 %
Crystal grow	Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: Protein: 6.4 mg/ml, 0.01M Tris HCl (pH 8.3); Reservoir (PEGs II screen, B6): 0.1M HEPES (pH 7.5), 20% (w/v) PEG 1500

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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: Aug 16, 2018 / 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: 3.1→30 Å / Num. obs: 26817 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 4.9 % / B_iso Wilson estimate: 66.4 Å² / R_merge(I) obs: 0.122 / R_pim(I) all: 0.061 / R_rim(I) all: 0.137 / R_sym value: 0.122 / Χ²: 1.099 / Net I/σ(I): 13.7
Reflection shell	Resolution: 3.1→3.15 Å / Redundancy: 5 % / R_merge(I) obs: 0.776 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 1306 / CC_1/2: 0.787 / CC star: 0.939 / R_pim(I) all: 0.381 / R_rim(I) all: 0.867 / R_sym value: 0.776 / Χ²: 0.996 / % possible all: 100

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0258	refinement
PDB_EXTRACT	3.25	data extraction
HKL-3000		data reduction
HKL-3000		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

SAD / Resolution: 3.1→29.4 Å / Cor.coef. F_o:F_c: 0.939 / Cor.coef. F_o:F_c free: 0.923 / SU B: 52.217 / SU ML: 0.42 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.531
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2897	1307	4.9 %	RANDOM
R_work	0.2337	-	-	-
obs	0.2364	25380	99.77 %	-

Solvent computation

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

Displacement parameters

B_iso max: 182.38 Å² / B_iso mean: 72.399 Å² / B_iso min: 22.39 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	2.58 Å²	0 Å²	0 Å²
2-	-	-2.27 Å²	0 Å²
3-	-	-	-0.32 Å²

Refinement step

Cycle: final / Resolution: 3.1→29.4 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8456	0	0	88	8544
B_iso mean	-	-	-	46.4	-
Num. residues	-	-	-	-	1080

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.004	0.013	8613
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.018	7934
X-RAY DIFFRACTION	r_angle_refined_deg	1.241	1.66	11606
X-RAY DIFFRACTION	r_angle_other_deg	0.327	1.586	18629
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	1.425	5	1082
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	21.586	26.306	379
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	7.371	15	1591
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	13.201	15	8
X-RAY DIFFRACTION	r_chiral_restr	0.053	0.2	1217
X-RAY DIFFRACTION	r_gen_planes_refined	0.054	0.02	9462
X-RAY DIFFRACTION	r_gen_planes_other	0.052	0.02	1582

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-ID	Dom-ID	Auth asym-ID	Number	Rms dev position (Å)
1	1	A	8150	0.1
1	2	B	8150	0.1
2	1	A	8047	0.11
2	2	C	8047	0.11
3	1	A	8152	0.1
3	2	D	8152	0.1
4	1	B	8131	0.1
4	2	C	8131	0.1
5	1	B	8132	0.1
5	2	D	8132	0.1
6	1	C	8148	0.1
6	2	D	8148	0.1

LS refinement shell

Resolution: 3.1→3.18 Å / R_factor R_free error: 0 / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.39	102	-
R_work	0.35	1842	-
all	-	1944	-
obs	-	-	99.95 %

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	2.5332	-0.5461	-1.5688	1.9857	0.6153	2.7725	0.2055	0.0841	0.3445	-0.0963	0.1175	0.0024	-0.107	0.0784	-0.323	0.1141	0.0143	-0.0546	0.1812	0.075	0.206	19.4461	81.122	71.8553
2	2.1975	0.7217	-0.4411	2.4219	-0.3856	0.1251	-0.0121	0.1442	0.2411	0.0531	0.0928	0.0893	0.0112	-0.0147	-0.0807	0.1175	0.0277	-0.0178	0.2571	-0.0295	0.1099	10.3795	59.4765	87.2214
3	3.2881	-3.4828	-1.288	7.004	-1.1949	2.5153	0.0461	0.0125	-0.0152	-0.3182	-0.0953	0.0238	0.1782	0.0689	0.0492	0.0382	-0.0453	-0.0239	0.2055	0.0243	0.147	-1.3189	38.9194	94.8397
4	5.171	3.7297	-3.8593	3.2173	-1.7007	5.2644	-0.1731	0.1851	-0.1404	-0.1514	-0.0284	0	0.1394	-0.3885	0.2015	0.0797	0.0955	0.0356	0.2181	0.1067	0.3776	-3.4166	64.9468	87.3415
5	3.4894	1.2604	-2.1832	1.681	-0.485	7.2317	-0.1061	0.0155	-0.0128	-0.3121	0.0965	0.208	-0.0355	-0.6601	0.0096	0.1073	0.0639	-0.0624	0.3444	0.1245	0.2065	8.6046	79.6137	66.3715
6	2.9116	-3.3544	3.0264	5.0848	-1.4283	6.7569	0.4647	-0.1873	-0.3331	-0.2994	0.2378	0.1451	1.0033	-0.0978	-0.7025	0.2643	-0.0017	0.0163	0.1194	0.0024	0.259	24.0008	29.8107	67.8343
7	1.6538	0.4108	2.2436	0.2614	0.0642	4.64	0.0206	0.1974	-0.1436	0.0534	0.146	-0.0721	-0.0588	0.0475	-0.1666	0.2651	0.0157	-0.0264	0.2171	-0.1237	0.2318	20.3857	40.0358	73.3874
8	2.0804	0.6536	0.6115	1.7706	0.7155	0.3591	0.1243	0.1465	-0.1065	0.0227	-0.0607	-0.0633	0.0268	0.0209	-0.0635	0.1068	0.0123	0.0054	0.2558	0.006	0.1319	31.3558	64.0035	88.6314
9	4.4929	-0.8336	1.8621	5.8089	-0.0828	0.7856	-0.0202	0.1264	-0.0605	-0.3751	0.0474	0.1336	-0.0256	0.0755	-0.0272	0.0256	-0.0051	-0.0009	0.2991	0.0367	0.2251	42.1492	79.3714	92.7247
10	1.9857	2.1712	1.7816	2.5081	2.3291	3.5119	-0.2708	0.316	-0.226	-0.303	0.3215	-0.3121	-0.1824	0.4247	-0.0506	0.1126	0.0775	-0.0233	0.2767	-0.1091	0.3571	38.8743	48.2128	78.1133
11	9.6895	-0.6222	-1.2355	1.663	-1.0889	1.0103	0.0227	0.8356	0.0788	0.1285	-0.0216	-0.1	-0.1205	-0.1184	-0.0011	0.1564	-0.0603	0.0545	0.2323	-0.0737	0.2832	32.478	78.819	57.3721
12	1.8431	0.7015	1.0509	0.8884	0.815	1.1517	0.1273	-0.0276	0.2953	-0.0802	0.117	-0.2267	0.0835	-0.2815	-0.2443	0.209	-0.1449	0.0886	0.5806	0.0638	0.4655	28.498	66.4726	44.6934
13	1.6251	0.1666	-0.603	1.8278	-0.0204	0.3547	0.0982	-0.1962	-0.2192	0.0052	0.0437	-0.009	-0.0029	0.0184	-0.1419	0.0735	0.0348	-0.0791	0.2377	0.0693	0.4109	29.3973	32.7796	30.48
14	0.6143	-1.9284	-0.5527	6.1346	1.7791	0.5223	-0.1102	-0.0324	-0.0381	0.4082	-0.0093	0.2801	0.1357	-0.0402	0.1195	0.0795	-0.1023	0.0863	0.2106	-0.1899	0.3473	42.211	52.166	40.1582
15	5.636	-0.6203	1.7582	0.1315	-0.422	4.5668	-0.298	-0.8367	-0.2849	0.0067	0.0889	-0.1579	0.4422	0.6272	0.2091	0.2065	0.1274	0.0212	0.3702	-0.0333	0.6314	42.2695	69.4949	59.797
16	5.6302	-1.1241	4.2457	1.6194	-0.791	3.2047	0.107	0.5473	-0.3426	-0.2946	0.1383	0.4851	0.056	0.4309	-0.2453	0.2761	-0.1585	0.0186	0.2577	0.0388	0.231	6.7137	39.7011	53.9834
17	3.2125	-1.7195	-1.9704	1.6141	-0.0407	2.9611	0.0503	0.2264	-0.0185	-0.2249	-0.2341	-0.1369	0.3391	0.0035	0.1838	0.2562	-0.1868	-0.104	0.5436	0.0893	0.1707	20.1793	50.3344	40.3985
18	1.3259	-0.5094	0.2058	0.9598	-0.2328	0.4221	0.1048	-0.5637	0.1983	-0.3084	0.0947	0.1759	0.228	-0.0458	-0.1994	0.2275	-0.022	-0.1032	0.358	-0.0538	0.3163	7.3027	67.7622	36.6855
19	2.8343	1.8342	1.4416	2.0664	0.457	3.6594	0.2453	-0.1396	0.29	0.0728	-0.1064	-0.2021	0.0368	0.0569	-0.1388	0.1268	0.0249	0.0646	0.1789	0.0087	0.3303	14.4173	84.0909	29.0812
20	2.4377	-1.823	0.9268	4.7497	-4.1509	3.8867	-0.2695	-0.2531	0.1369	0.3619	0.4901	0.1723	-0.25	-0.4254	-0.2206	0.2809	-0.1601	-0.0878	0.2362	0.0786	0.2588	-2.2304	56.0983	46.9106

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	31 - 82
2	X-RAY DIFFRACTION	2	A	83 - 174
3	X-RAY DIFFRACTION	3	A	175 - 243
4	X-RAY DIFFRACTION	4	A	244 - 277
5	X-RAY DIFFRACTION	5	A	278 - 301
6	X-RAY DIFFRACTION	6	B	31 - 44
7	X-RAY DIFFRACTION	7	B	45 - 82
8	X-RAY DIFFRACTION	8	B	83 - 184
9	X-RAY DIFFRACTION	9	B	185 - 244
10	X-RAY DIFFRACTION	10	B	245 - 300
11	X-RAY DIFFRACTION	11	C	32 - 58
12	X-RAY DIFFRACTION	12	C	59 - 134
13	X-RAY DIFFRACTION	13	C	135 - 249
14	X-RAY DIFFRACTION	14	C	250 - 277
15	X-RAY DIFFRACTION	15	C	278 - 300
16	X-RAY DIFFRACTION	16	D	32 - 79
17	X-RAY DIFFRACTION	17	D	80 - 112
18	X-RAY DIFFRACTION	18	D	113 - 173
19	X-RAY DIFFRACTION	19	D	174 - 246
20	X-RAY DIFFRACTION	20	D	247 - 301

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