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- PDB-4n02: Type 2 IDI from S. pneumoniae -

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Open data

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Basic information

Entry

Database: PDB / ID: 4n02

Title

Type 2 IDI from S. pneumoniae

Components

Isopentenyl-diphosphate delta-isomerase

Keywords

ISOMERASE / TIM Barrel

Function / homology

Function and homology information

isopentenyl-diphosphate Delta-isomerase / isopentenyl-diphosphate delta-isomerase activity / isoprenoid biosynthetic process / NADPH binding / FMN binding / oxidoreductase activity / magnesium ion binding / cytoplasm
Similarity search - Function

Biological species

Streptococcus pneumoniae (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.4 Å

Authors

de Ruyck, J. / Schubert, H.L. / Poulter, C.D.

Citation

Journal: Chembiochem / Year: 2014
Title: Determination of Kinetics and the Crystal Structure of a Novel Type 2 Isopentenyl Diphosphate: Dimethylallyl Diphosphate Isomerase from Streptococcus pneumoniae.
Authors: de Ruyck, J. / Janczak, M.W. / Neti, S.S. / Rothman, S.C. / Schubert, H.L. / Cornish, R.M. / Matagne, A. / Wouters, J. / Poulter, C.D.

History

Deposition	Sep 30, 2013	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jul 2, 2014	Provider: repository / Type: Initial release
Revision 1.1	Jul 16, 2014	Group: Database references
Revision 1.2	Feb 28, 2024	Group: Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewer	Molecule: MolmilJmol/JSmol

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Downloads & links

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Download

PDBx/mmCIF format	4n02.cif.gz	163.7 KB	Display	PDBx/mmCIF format
PDB format	pdb4n02.ent.gz	129.4 KB	Display	PDB format
PDBx/mmJSON format	4n02.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4n02_validation.pdf.gz	796.1 KB	Display	wwPDB validaton report
Full document	4n02_full_validation.pdf.gz	796.1 KB	Display
Data in XML	4n02_validation.xml.gz	17.8 KB	Display
Data in CIF	4n02_validation.cif.gz	27.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/n0/4n02 ftp://data.pdbj.org/pub/pdb/validation_reports/n0/4n02	HTTPS FTP

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Related structure data

Similar structure data	2zry-d 2zrw-d 3b03-d 3b04-d 3b06-d 2rdu-1 2zrx-d 2zrz-d 3b05-d 2zrv-d 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

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#201 - Sep 2016 Isoprene Synthase similarity (4)

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Assembly

Deposited unit

A: Isopentenyl-diphosphate delta-isomerase

hetero molecules

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

1

A: Isopentenyl-diphosphate delta-isomerase

hetero molecules

A: Isopentenyl-diphosphate delta-isomerase

hetero molecules

A: Isopentenyl-diphosphate delta-isomerase

hetero molecules

A: Isopentenyl-diphosphate delta-isomerase

hetero molecules

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

Unit cell

Length a, b, c (Å)	131.329, 131.329, 59.412
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	79
Space group name H-M	I4

Components on special symmetry positions

ID	Model	Components
1	1	A-819- HOH

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Components

#1: Protein	Isopentenyl-diphosphate delta-isomerase / IPP isomerase / Isopentenyl pyrophosphate isomerase Mass: 39918.371 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Streptococcus pneumoniae (bacteria) / Strain: CGSP14 References: UniProt: B2ILS5, isopentenyl-diphosphate Delta-isomerase
#2: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO₄
#3: Chemical	ChemComp-FNR / 1-DEOXY-1-(7,8-DIMETHYL-2,4-DIOXO-3,4-DIHYDRO-2H-BENZO[G]PTERIDIN-1-ID-10(5H)-YL)-5-O-PHOSPHONATO-D-RIBITOL / TWO ELECTRON REDUCED FLAVIN MONONUCLEOTIDE Mass: 458.360 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₇H₂₃N₄O₉P
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 369 / Source method: isolated from a natural source / Formula: H₂O

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Experimental details

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 3.21 Å³/Da / Density % sol: 61.67 %

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 0.911
Detector	Type: ADSC QUANTUM 315r / Detector: CCD
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.911 Å / Relative weight: 1
Reflection	Resolution: 1.4→32 Å / Num. obs: 98844 / B_iso Wilson estimate: 13.9 Å²

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Processing

Software

Name: PHENIX / Version: (phenix.refine: 1.7.3_928) / Classification: refinement

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.4→32 Å / SU ML: 0.17 / σ(F): 1.35 / Phase error: 14.38 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.159	3940	3.99 %
R_work	0.139	-	-
obs	0.14	98841	99.8 %
all	-	98841	-

Solvent computation

Shrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 48.78 Å² / k_sol: 0.39 e/Å³

Displacement parameters

B_iso mean: 18 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.8842 Å²	-0 Å²	0 Å²
2-	-	-1.8842 Å²	-0 Å²
3-	-	-	3.7685 Å²

Refinement step

Cycle: LAST / Resolution: 1.4→32 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2616	0	46	369	3031

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.005	2820
X-RAY DIFFRACTION	f_angle_d	1.015	3845
X-RAY DIFFRACTION	f_dihedral_angle_d	13.658	1103
X-RAY DIFFRACTION	f_chiral_restr	0.071	429
X-RAY DIFFRACTION	f_plane_restr	0.005	492

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 (%)
1.4023-1.4195	0.2929	148	0.2733	3298	X-RAY DIFFRACTION	98
1.4195-1.4374	0.2863	123	0.2622	3394	X-RAY DIFFRACTION	100
1.4374-1.4563	0.3202	142	0.2411	3406	X-RAY DIFFRACTION	100
1.4563-1.4763	0.2355	151	0.21	3380	X-RAY DIFFRACTION	100
1.4763-1.4974	0.2356	127	0.1977	3376	X-RAY DIFFRACTION	100
1.4974-1.5197	0.2325	145	0.1821	3347	X-RAY DIFFRACTION	100
1.5197-1.5435	0.1969	150	0.1683	3335	X-RAY DIFFRACTION	100
1.5435-1.5688	0.2028	132	0.1515	3433	X-RAY DIFFRACTION	100
1.5688-1.5958	0.1693	144	0.1435	3360	X-RAY DIFFRACTION	100
1.5958-1.6248	0.1774	133	0.1321	3417	X-RAY DIFFRACTION	100
1.6248-1.6561	0.1856	140	0.1349	3361	X-RAY DIFFRACTION	100
1.6561-1.6899	0.1783	147	0.1268	3364	X-RAY DIFFRACTION	100
1.6899-1.7266	0.1338	156	0.1116	3338	X-RAY DIFFRACTION	100
1.7266-1.7668	0.1252	149	0.1099	3393	X-RAY DIFFRACTION	100
1.7668-1.811	0.1452	142	0.1052	3401	X-RAY DIFFRACTION	100
1.811-1.8599	0.1334	162	0.1047	3363	X-RAY DIFFRACTION	100
1.8599-1.9147	0.1705	146	0.109	3388	X-RAY DIFFRACTION	100
1.9147-1.9765	0.1337	125	0.1144	3396	X-RAY DIFFRACTION	100
1.9765-2.0471	0.1456	129	0.114	3404	X-RAY DIFFRACTION	100
2.0471-2.129	0.1238	136	0.1187	3386	X-RAY DIFFRACTION	100
2.129-2.2259	0.1386	138	0.1117	3412	X-RAY DIFFRACTION	100
2.2259-2.3432	0.1496	122	0.1152	3400	X-RAY DIFFRACTION	100
2.3432-2.49	0.1368	148	0.1234	3427	X-RAY DIFFRACTION	100
2.49-2.6822	0.1607	158	0.1381	3382	X-RAY DIFFRACTION	100
2.6822-2.9519	0.1445	151	0.1456	3406	X-RAY DIFFRACTION	100
2.9519-3.3787	0.1624	136	0.1426	3422	X-RAY DIFFRACTION	100
3.3787-4.2554	0.1331	145	0.1307	3444	X-RAY DIFFRACTION	100
4.2554-32.8412	0.1683	115	0.1704	3468	X-RAY DIFFRACTION	98

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