PDB-2y0f: STRUCTURE OF GCPE (IspG) FROM THERMUS THERMOPHILUS HB27

ID or keywords:

Entry

Database: PDB / ID: 2y0f

Title

STRUCTURE OF GCPE (IspG) FROM THERMUS THERMOPHILUS HB27

Components

4-HYDROXY-3-METHYLBUT-2-EN-1-YL DIPHOSPHATE SYNTHASE

Keywords

OXIDOREDUCTASE / ISOPRENOID BIOSYNTHESIS /

NON-MEVALONATE PATHWAY

Function / homology

Function and homology information

(E)-4-hydroxy-3-methylbut-2-enyl-diphosphate synthase (flavodoxin) /

4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase activity / isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway / terpenoid biosynthetic process / 4 iron, 4 sulfur cluster binding / iron ion binding
Similarity search - Function

Biological species

THERMUS THERMOPHILUS (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MAD / Resolution: 2.5 Å

Authors

Rekittke, I. / Nonaka, T. / Wiesner, J. / Demmer, U. / Warkentin, E. / Jomaa, H. / Ermler, U.

Citation

Journal: FEBS Lett. / Year: 2011
Title: Structure of the E-1-Hydroxy-2-Methyl-But-2-Enyl-4-Diphosphate Synthase (Gcpe) from Thermus Thermophilus.
Authors: Rekittke, I. / Nonaka, T. / Wiesner, J. / Demmer, U. / Warkentin, E. / Jomaa, H. / Ermler, U.

History

Deposition	Dec 2, 2010	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jan 26, 2011	Provider: repository / Type: Initial release
Revision 1.1	May 8, 2011	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Version format compliance
Revision 1.3	Nov 20, 2019	Group: Derived calculations / Other Category: pdbx_database_status / pdbx_struct_conn_angle / struct_conn Item: _pdbx_database_status.status_code_sf

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	2y0f.cif.gz	618.7 KB	Display	PDBx/mmCIF format
PDB format	pdb2y0f.ent.gz	535.1 KB	Display	PDB format
PDBx/mmJSON format	2y0f.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/y0/2y0f ftp://data.pdbj.org/pub/pdb/validation_reports/y0/2y0f	HTTPS FTP

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Related structure data

Similar structure data	4gs7-d 2qg4-3 5kxe-d 3nyw-d 5css-d 5tcy-d 5hgi-1 2y0c-1 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

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: 4-HYDROXY-3-METHYLBUT-2-EN-1-YL DIPHOSPHATE SYNTHASE

B: 4-HYDROXY-3-METHYLBUT-2-EN-1-YL DIPHOSPHATE SYNTHASE

C: 4-HYDROXY-3-METHYLBUT-2-EN-1-YL DIPHOSPHATE SYNTHASE

D: 4-HYDROXY-3-METHYLBUT-2-EN-1-YL DIPHOSPHATE SYNTHASE

hetero molecules

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

1

C: 4-HYDROXY-3-METHYLBUT-2-EN-1-YL DIPHOSPHATE SYNTHASE

D: 4-HYDROXY-3-METHYLBUT-2-EN-1-YL DIPHOSPHATE SYNTHASE

hetero molecules

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

2

A: 4-HYDROXY-3-METHYLBUT-2-EN-1-YL DIPHOSPHATE SYNTHASE

B: 4-HYDROXY-3-METHYLBUT-2-EN-1-YL DIPHOSPHATE SYNTHASE

hetero molecules

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

Unit cell

Length a, b, c (Å)	84.500, 130.970, 101.260
Angle α, β, γ (deg.)	90.00, 102.10, 90.00
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
3	1	C
4	1	D

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Refine code	Auth asym-ID	Auth seq-ID
1	1	1	6	A	4 - 64
2	1	1	6	B	4 - 64
3	1	1	6	C	4 - 64
4	1	1	6	D	4 - 64
1	2	1	6	A	67 - 96
2	2	1	6	B	67 - 96
3	2	1	6	C	67 - 96
4	2	1	6	D	67 - 96
1	3	1	6	A	98 - 101
2	3	1	6	B	98 - 101
3	3	1	6	C	98 - 101
4	3	1	6	D	98 - 101
1	4	1	6	A	103 - 232
2	4	1	6	B	103 - 232
3	4	1	6	C	103 - 232
4	4	1	6	D	103 - 232
1	5	1	6	A	234 - 267
2	5	1	6	B	234 - 267
3	5	1	6	C	234 - 267
4	5	1	6	D	234 - 267
1	6	1	6	A	270 - 285
2	6	1	6	B	270 - 285
3	6	1	6	C	270 - 285
4	6	1	6	D	270 - 285
1	7	1	6	A	294 - 404
2	7	1	6	B	294 - 404
3	7	1	6	C	294 - 404
4	7	1	6	D	294 - 404
1	8	1	6	A	501
2	8	1	6	B	501
3	8	1	6	C	501
4	8	1	6	D	501

NCS oper:

ID	Code	Matrix	Vector
1	given	(-0.1066, -0.5795, 0.808), (-0.5993, -0.6109, -0.5173), (0.7934, -0.5394, -0.2822)	7.074, -33.46, -33.17
2	given	(0.2518, 0.536, -0.8058), (0.5443, -0.7669, -0.3401), (-0.8002, -0.3529, -0.4848)	64.76, -63.5, 58.72
3	given	(-0.9876, -0.04444, 0.1507), (0.1261, 0.3476, 0.9291), (-0.09366, 0.9366, -0.3376)	75.15, -21.9, 81.24

#1: Protein	4-HYDROXY-3-METHYLBUT-2-EN-1-YL DIPHOSPHATE SYNTHASE / / 1-HYDROXY-2-METHYL-2-(E)-BUTENYL 4-DIPHOSPHATE SYNTHASE / GCPE Mass: 44281.094 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) THERMUS THERMOPHILUS (bacteria) / Strain: HB27 / Plasmid: PQETTGCPE / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): TOP10 / References: UniProt: Q72H18, EC: 1.17.7.1
#2: Chemical	ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster Mass: 351.640 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe₄S₄
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 135 / 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: 3.1 Å³/Da / Density % sol: 60 % / Description: NONE
Crystal grow	pH: 7.5 Details: PROTEIN SOLUTION 30MM TRIS-HCL PH7.5, 0.15M NACL, 12MG/ML PROTEIN. RESERVOIR/PRECIPITANT 47% MPD, 2% TERT-BUTANOL

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1
Detector	Type: MARRESEARCH / Detector: CCD / Date: Apr 27, 2009 / Details: MIRROR
Radiation	Monochromator: SI (1 1 1) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.5→50 Å / Num. obs: 71563 / % possible obs: 96 % / Observed criterion σ(I): -3 / Redundancy: 3.6 % / R_merge(I) obs: 0.07 / Net I/σ(I): 11.8
Reflection shell	Resolution: 2.5→2.6 Å / Redundancy: 2.4 % / R_merge(I) obs: 0.47 / Mean I/σ(I) obs: 2.2 / % possible all: 86.6

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Processing

Software

Name	Version	Classification
XDS		data reduction
XSCALE		data scaling
SHELXD		phasing
SHARP		phasing
REFMAC	5.6.0093	refinement

Refinement

Method to determine structure:

MAD
Starting model: NONE

Resolution: 2.5→20 Å / Cor.coef. F_o:F_c: 0.96 / Cor.coef. F_o:F_c free: 0.929 / SU B: 22.564 / SU ML: 0.234 / Cross valid method: THROUGHOUT / ESU R: 0.413 / ESU R Free: 0.288 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.263	3609	5 %	RANDOM
R_work	0.199	-	-	-
obs	0.202	67936	96.1 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 89.2 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.39 Å²	0 Å²	2.7 Å²
2-	-	1.24 Å²	0 Å²
3-	-	-	-1.5 Å²

Refinement step

Cycle: LAST / Resolution: 2.5→20 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	12078	0	32	135	12245

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.018	0.022	12347
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.809	1.998	16766
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.9	5	1574
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	37.342	22.788	495
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	21.14	15	2139
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	19.391	15	122
X-RAY DIFFRACTION	r_chiral_restr	0.117	0.2	1937
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.021	9196
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
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
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
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
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined
X-RAY DIFFRACTION	r_long_range_B_other
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Ens-ID: 1 / Number: 2868 / Refine-ID: X-RAY DIFFRACTION

Dom-ID	Auth asym-ID	Type	Rms dev position (Å)	Weight position
1	A	loose positional	0.97	5
2	B	loose positional	0.69	5
3	C	loose positional	0.66	5
4	D	loose positional	0.93	5
1	A	loose thermal	5.05	10
2	B	loose thermal	4.81	10
3	C	loose thermal	5.44	10
4	D	loose thermal	5.54	10

LS refinement shell

Resolution: 2.5→2.56 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.482	201	-
R_work	0.39	4135	-
obs	-	-	80.77 %

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	2.752	1.2979	0.3492	5.9103	-1.0087	3.5816	-0.1571	0.1976	0.7194	-0.2792	0.0802	0.608	-0.4081	-0.2713	0.0769	0.1913	0.1079	-0.0978	0.1825	0.0033	0.2904	31.7772	-5.7023	10.9683
2	5.4431	-0.1013	2.7045	7.1343	0.4138	4.0825	-0.2343	0.3993	-0.277	-0.6319	0.0425	1.582	0.3103	-0.6531	0.1919	0.3786	-0.0766	-0.1216	0.4566	-0.1492	0.4961	16.241	-53.4698	-10.4336
3	4.3879	-2.2919	0.0051	6.0204	-0.411	10.0152	-0.4438	-0.4762	-0.8001	0.1955	0.0794	-0.9695	2.156	2.3865	0.3644	0.8657	0.5404	-0.0331	0.7003	0.2014	0.7749	60.164	-46.9354	31.2813
4	2.0628	0.4452	0.9205	4.473	0.59	8.466	0.2446	-0.5337	0.4144	0.7377	-0.2114	0.8229	0.0363	0.6588	-0.0332	0.6992	-0.1859	0.0835	0.4588	-0.06	0.6114	48.5483	-9.241	69.7419
5	2.087	1.1565	-0.1087	3.2188	0.8448	2.3356	-0.1411	0.2824	0.1595	-0.3412	0.0536	0.0673	-0.1229	-0.1848	0.0875	0.0875	0.0278	-0.0248	0.1609	0.0387	0.088	39.0662	-20.274	8.1472
6	1.5508	0.567	-0.6864	2.9929	0.9956	3.399	-0.01	0.0754	-0.1476	0.0872	-0.0824	0.6065	0.4618	-0.3117	0.0925	0.2018	-0.0438	-0.0102	0.263	-0.0713	0.2165	21.3306	-48.4768	6.8978
7	3.3164	0.8748	-0.4645	3.1152	0.715	2.4619	0.1379	-0.3476	-0.2328	0.2712	-0.1033	-0.6117	0.5652	0.704	-0.0346	0.2192	0.1393	-0.125	0.3036	0.0939	0.2938	56.91	-28.9361	30.6106
8	5.2589	2.3204	1.2648	1.6741	1.6877	3.2069	0.0803	-0.455	0.8506	0.3838	-0.3032	0.2549	-0.0254	-0.1383	0.2229	0.6901	-0.0655	-0.1129	0.2525	0.0394	0.3993	38.2892	-16.7546	55.3667
9	3.8969	-1.5532	-0.4759	11.3227	-0.4434	4.5193	-0.1792	0.1024	0.036	0.3251	-0.1641	1.231	0.2259	-1.1074	0.3433	0.124	-0.0426	0.135	0.6922	-0.1486	0.2996	6.0342	-33.4473	29.6234
10	7.392	3.0267	3.4823	4.8086	3.4677	8.5896	-0.3402	1.0255	-0.2787	-1.0631	0.4348	-0.499	-0.1015	0.2481	-0.0946	0.5768	-0.0942	0.3068	0.4542	-0.08	0.2085	49.3358	-32.4158	-18.7867
11	7.5192	-2.7652	0.4569	7.8271	1.7145	4.7943	0.473	-0.3216	-0.781	0.543	-0.3303	-0.0065	1.0966	-0.26	-0.1427	0.7247	-0.1961	0.0386	0.2896	0.0253	0.1508	24.7323	-44.7999	51.1571
12	10.5434	2.3658	1.1599	6.3331	0.77	11.4081	0.3102	-1.8034	1.8836	0.857	-0.641	-0.42	-0.4817	0.7345	0.3308	0.1601	-0.1037	-0.1356	0.6823	-0.2443	0.9331	75.1035	-5.4029	39.844

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	4 - 122
2	X-RAY DIFFRACTION	2	B	4 - 122
3	X-RAY DIFFRACTION	3	C	4 - 122
4	X-RAY DIFFRACTION	4	D	4 - 122
5	X-RAY DIFFRACTION	5	A	123 - 289
6	X-RAY DIFFRACTION	6	B	124 - 289
7	X-RAY DIFFRACTION	7	C	125 - 289
8	X-RAY DIFFRACTION	8	D	124 - 289
9	X-RAY DIFFRACTION	9	A	290 - 501
10	X-RAY DIFFRACTION	10	B	290 - 501
11	X-RAY DIFFRACTION	11	C	290 - 501
12	X-RAY DIFFRACTION	12	D	290 - 501

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