PDB-5ibz: Crystal structure of a novel cyclase (pfam04199).

ID or keywords:

Entry

Database: PDB / ID: 5ibz

Title

Crystal structure of a novel cyclase (pfam04199).

Components

Uncharacterized protein

Keywords

LYASE / cyclase / pfam04199 / Uncultured organism clone MGS0169

Function / homology

Kynurenine formamidase/cyclase-like / Kynurenine formamidase superfamily / Putative cyclase / arylformamidase activity / L-tryptophan catabolic process to kynurenine / TRIETHYLENE GLYCOL / ACETYLPHOSPHATE / Cyclase

Function and homology information

Biological species

uncultured organism (environmental samples)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.611 Å

Authors

Nocek, B. / Skarina, T. / Brown, G. / Joachimiak, A. / Savchenko, A. / Yakunin, A.

Citation

Journal: To Be Published
Title: Crystal structure of a novel cyclase (pfam04199).
Authors: Nocek, B. / Skarina, T. / Brown, G. / Joachimiak, A. / Savchenko, A. / Yakunin, A.

History

Deposition	Feb 22, 2016	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 9, 2017	Provider: repository / Type: Initial release
Revision 1.1	Nov 13, 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

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	5ibz.cif.gz	695.1 KB	Display	PDBx/mmCIF format
PDB format	pdb5ibz.ent.gz	585.4 KB	Display	PDB format
PDBx/mmJSON format	5ibz.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	5ibz_validation.pdf.gz	479.4 KB	Display	wwPDB validaton report
Full document	5ibz_full_validation.pdf.gz	489.1 KB	Display
Data in XML	5ibz_validation.xml.gz	60.8 KB	Display
Data in CIF	5ibz_validation.cif.gz	94.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ib/5ibz ftp://data.pdbj.org/pub/pdb/validation_reports/ib/5ibz	HTTPS FTP

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Related structure data

Similar structure data	1bvp-1 3t91-1 1bvp-2 3t9q-1 6qrq-1 22456 2jc9-1 1ht8-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

Deposited unit

A: Uncharacterized protein

B: Uncharacterized protein

C: Uncharacterized protein

D: Uncharacterized protein

hetero molecules

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	64.508, 120.618, 148.822
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Uncharacterized protein Mass: 35173.172 Da / Num. of mol.: 4 / Fragment: UNP residues 19-341 Source method: isolated from a genetically manipulated source Source: (gene. exp.) uncultured organism (environmental samples) Production host: Escherichia coli (E. coli) / References: UniProt: A0A0G3FEK2
#2: Chemical	ChemComp-UVW / ACETYLPHOSPHATE Mass: 140.032 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂H₅O₅P
#3: Chemical	ChemComp-PGE / TRIETHYLENE GLYCOL Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₆H₁₄O₄
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1616 / Source method: isolated from a natural source / Formula: H₂O
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: 2.07 Å³/Da / Density % sol: 40.54 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / Details: 2KMME 30%, Tris pH 8 0.1M, NH4Acet 0.2M

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 3, 2015
Radiation	Monochromator: Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9794 Å / Relative weight: 1
Reflection	Resolution: 1.611→38.814 Å / Num. obs: 150117 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Redundancy: 5.9 % / R_merge(I) obs: 0.083 / Net I/σ(I): 17
Reflection shell	Resolution: 1.611→1.64 Å / Redundancy: 4.9 % / R_merge(I) obs: 0.484 / Mean I/σ(I) obs: 2.8 / % possible all: 98.5

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Processing

Software

Name	Version	Classification
PHENIX	dev_1888	refinement
HKL-3000		data reduction
HKL-3000		data scaling
HKL-3000		phasing

Refinement

Method to determine structure:

SAD / Resolution: 1.611→38.814 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 14.51 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1614	7523	5.02 %
R_work	0.1328	-	-
obs	0.1342	149872	99.78 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 1.611→38.814 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9269	0	42	1616	10927

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009	9736
X-RAY DIFFRACTION	f_angle_d	1.331	13334
X-RAY DIFFRACTION	f_dihedral_angle_d	12.871	3526
X-RAY DIFFRACTION	f_chiral_restr	0.05	1445
X-RAY DIFFRACTION	f_plane_restr	0.007	1758

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.6112-1.6296	0.2194	253	0.191	4435	X-RAY DIFFRACTION	95
1.6296-1.6487	0.1975	224	0.181	4725	X-RAY DIFFRACTION	100
1.6487-1.6688	0.2242	282	0.1783	4635	X-RAY DIFFRACTION	100
1.6688-1.69	0.2226	206	0.1751	4767	X-RAY DIFFRACTION	100
1.69-1.7122	0.2247	251	0.1611	4714	X-RAY DIFFRACTION	100
1.7122-1.7357	0.1908	269	0.1582	4648	X-RAY DIFFRACTION	100
1.7357-1.7605	0.2146	236	0.1507	4743	X-RAY DIFFRACTION	100
1.7605-1.7867	0.1909	261	0.1465	4679	X-RAY DIFFRACTION	100
1.7867-1.8146	0.173	258	0.1387	4703	X-RAY DIFFRACTION	100
1.8146-1.8444	0.1735	229	0.1379	4763	X-RAY DIFFRACTION	100
1.8444-1.8762	0.1747	225	0.1338	4748	X-RAY DIFFRACTION	100
1.8762-1.9103	0.1576	273	0.1336	4709	X-RAY DIFFRACTION	100
1.9103-1.9471	0.1588	265	0.1293	4698	X-RAY DIFFRACTION	100
1.9471-1.9868	0.1534	253	0.1239	4701	X-RAY DIFFRACTION	100
1.9868-2.03	0.1542	282	0.1186	4721	X-RAY DIFFRACTION	100
2.03-2.0772	0.157	233	0.1213	4772	X-RAY DIFFRACTION	100
2.0772-2.1292	0.16	232	0.1216	4712	X-RAY DIFFRACTION	100
2.1292-2.1867	0.1372	240	0.1172	4729	X-RAY DIFFRACTION	100
2.1867-2.2511	0.14	273	0.1155	4744	X-RAY DIFFRACTION	100
2.2511-2.3237	0.162	231	0.1168	4801	X-RAY DIFFRACTION	100
2.3237-2.4068	0.136	245	0.1162	4718	X-RAY DIFFRACTION	100
2.4068-2.5031	0.1514	255	0.1168	4749	X-RAY DIFFRACTION	100
2.5031-2.617	0.1473	266	0.1197	4764	X-RAY DIFFRACTION	100
2.617-2.7549	0.1471	245	0.1192	4781	X-RAY DIFFRACTION	100
2.7549-2.9275	0.1615	257	0.1253	4807	X-RAY DIFFRACTION	100
2.9275-3.1534	0.1622	239	0.1271	4786	X-RAY DIFFRACTION	100
3.1534-3.4706	0.1395	270	0.1287	4790	X-RAY DIFFRACTION	100
3.4706-3.9724	0.1526	255	0.1282	4853	X-RAY DIFFRACTION	100
3.9724-5.0031	0.1461	269	0.1263	4897	X-RAY DIFFRACTION	100
5.0031-38.8257	0.1956	246	0.1798	5057	X-RAY DIFFRACTION	99

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	0.7695	0.0875	-0.0041	0.3947	-0.119	0.696	-0.0097	0.0138	-0.0369	0.0013	0.0096	-0.0503	0.0014	0.0976	-0.0003	0.1046	-0.0003	-0.0025	0.0648	-0.0142	0.0999	74.2771	10.0441	86.8638
2	5.4749	-0.5236	0.0648	0.6791	-1.2604	2.4356	-0.0407	0.0039	0.4107	0.1837	0.0018	-0.0231	-0.2428	-0.2336	0.028	0.1491	0.0046	0.0004	0.1496	-0.0063	0.1661	45.1352	21.6329	109.6504
3	0.3589	-0.0158	-0.1307	0.2323	0.0392	0.5565	-0.0174	-0.0076	-0.0398	-0.017	0.0172	0.0063	0.0664	0.0125	0.0025	0.0923	-0.0006	-0.0015	0.0876	0.0043	0.0934	73.5036	3.1524	91.3425
4	1.0109	0.1809	0.1124	0.8885	0.3552	0.6974	0.0035	-0.0321	-0.0852	-0.0173	-0.0043	-0.0057	0.0783	-0.0088	0.0032	0.0835	-0.0085	0.0074	0.0734	0.0103	0.0705	70.8202	5.0332	88.0173
5	0.9298	-0.1907	-0.3507	0.1869	0.0116	1.0214	0.0125	0.068	-0.0236	-0.003	-0.0009	0.0197	-0.004	-0.0433	-0.0277	0.0893	0.006	-0.0104	0.0419	-0.0038	0.0995	62.9371	12.816	130.2489
6	0.4347	-0.0452	-0.0786	0.4361	-0.1201	0.4958	-0.0069	0.0102	-0.0597	0.0093	-0.0001	0.0275	0.0558	-0.037	0.0074	0.0817	-0.0034	0.0049	0.0877	-0.0045	0.0882	56.443	2.8211	133.0768
7	0.8664	0.0989	0.2476	0.2072	0.0134	0.601	0.0122	-0.0669	-0.022	-0.0159	0.0039	0.0089	0.003	-0.002	-0.0286	0.1145	-0.0015	0.0009	0.0617	-0.0019	0.0973	62.7193	17.9686	94.1967
8	0.1881	-0.1277	0.0329	0.4176	-0.1799	0.4294	-0.0024	-0.0177	0.0168	-0.0073	0.0149	0.0071	-0.0482	-0.031	-0.0092	0.0956	-0.0017	-0.0114	0.0978	-0.0012	0.0946	52.4185	29.4316	93.4806
9	0.9296	0.151	-0.229	0.9375	-0.3845	0.6432	0.0404	-0.016	0.071	-0.0344	-0.0209	0.0233	-0.0544	-0.0109	-0.0145	0.0939	-0.0073	-0.0113	0.0824	-0.0054	0.076	55.0227	27.7066	89.0401
10	0.8231	-0.016	0.3195	0.2081	-0.1181	0.8166	0.0122	0.0596	-0.0225	0.0014	-0.0078	-0.0009	0.004	0.0212	-0.0132	0.0986	0.0074	0.0046	0.0598	-0.0085	0.1021	65.9314	17.6342	129.7796
11	0.3318	0.0443	0.0057	0.4821	0.1455	0.5645	-0.0004	-0.0073	0.0467	0.0209	-0.0045	-0.0219	-0.0678	0.0338	0.0043	0.0831	-0.0025	-0.0103	0.0859	0.0034	0.0883	74.9089	28.3638	132.0223

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 28 through 90 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 91 through 118 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 119 through 258 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 259 through 341 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 28 through 118 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 119 through 341 )
7	X-RAY DIFFRACTION	7	chain 'C' and (resid 34 through 118 )
8	X-RAY DIFFRACTION	8	chain 'C' and (resid 119 through 257 )
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 258 through 341 )
10	X-RAY DIFFRACTION	10	chain 'D' and (resid 34 through 118 )
11	X-RAY DIFFRACTION	11	chain 'D' and (resid 119 through 341 )

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