PDB-8pru: Engineered form of T thermophiles AHIR

ID or keywords:

Entry

Database: PDB / ID: 8pru

Title

Engineered form of T thermophiles AHIR

Components

Ketol-acid reductoisomerase (NADP(+))

Keywords

OXIDOREDUCTASE / Protein-engineering / Ketol-acid reductoisomerase / Thermostable protein

Function / homology

Function and homology information

ketol-acid reductoisomerase (NADP+) / ketol-acid reductoisomerase activity / L-valine biosynthetic process / isoleucine biosynthetic process / NADP binding / magnesium ion binding / cytosol
Similarity search - Function

Biological species

Thermus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2 Å

Authors

Roberts, M. / Powell, A. / Lewis, C. / Sinclair, J.

Funding support

United Kingdom, 1items

Citation

Journal: To Be Published
Title: Engineered form of T thermophiles AHIR
Authors: Roberts, M. / Powell, A. / Lewis, C. / Sinclair, J.

History

Deposition	Jul 12, 2023	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Sep 25, 2024	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	8pru.cif.gz	707.6 KB	Display	PDBx/mmCIF format
PDB format	pdb8pru.ent.gz	573.9 KB	Display	PDB format
PDBx/mmJSON format	8pru.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	8pru_validation.pdf.gz	517.8 KB	Display	wwPDB validaton report
Full document	8pru_full_validation.pdf.gz	565.6 KB	Display
Data in XML	8pru_validation.xml.gz	75.2 KB	Display
Data in CIF	8pru_validation.cif.gz	96.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/pr/8pru ftp://data.pdbj.org/pub/pdb/validation_reports/pr/8pru	HTTPS FTP

-
Related structure data

Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#228 - Dec 2018 Directed Evolution of Enzymes similarity (10) #111 - Mar 2009 Hydrogenase similarity (1) #127 - Jul 2010 Crystallins similarity (1)

Deposited unit

A: Ketol-acid reductoisomerase (NADP(+))

B: Ketol-acid reductoisomerase (NADP(+))

C: Ketol-acid reductoisomerase (NADP(+))

D: Ketol-acid reductoisomerase (NADP(+))

E: Ketol-acid reductoisomerase (NADP(+))

F: Ketol-acid reductoisomerase (NADP(+))

hetero molecules

228 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Ketol-acid reductoisomerase (NADP(+))

hetero molecules

A: Ketol-acid reductoisomerase (NADP(+))

hetero molecules

defined by author&software
Evidence: gel filtration, Widely observed assembly for this class of enzyme, which has tetrahedral symmetry, with intimate dimers formed around the particle 2-fold axes
76 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Ketol-acid reductoisomerase (NADP(+))

F: Ketol-acid reductoisomerase (NADP(+))

hetero molecules

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

3

C: Ketol-acid reductoisomerase (NADP(+))

hetero molecules

C: Ketol-acid reductoisomerase (NADP(+))

hetero molecules

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

4

D: Ketol-acid reductoisomerase (NADP(+))

E: Ketol-acid reductoisomerase (NADP(+))

hetero molecules

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

Unit cell

Length a, b, c (Å)	136.030, 142.720, 126.130
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	18
Space group name H-M	P2₁2₁2

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: MET / End label comp-ID: MET / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 1 - 340 / Label seq-ID: 5 - 344

NCS ensembles :

ID	Details
1	Local NCS retraints between domains: 1 2
2	Local NCS retraints between domains: 3 4
3	Local NCS retraints between domains: 5 6
4	Local NCS retraints between domains: 7 8
5	Local NCS retraints between domains: 9 10
6	Local NCS retraints between domains: 11 12
7	Local NCS retraints between domains: 13 14
8	Local NCS retraints between domains: 15 16
9	Local NCS retraints between domains: 17 18
10	Local NCS retraints between domains: 19 20
11	Local NCS retraints between domains: 21 22
12	Local NCS retraints between domains: 23 24
13	Local NCS retraints between domains: 25 26
14	Local NCS retraints between domains: 27 28
15	Local NCS retraints between domains: 29 30

#1: Protein	Ketol-acid reductoisomerase (NADP(+)) / KARI / Acetohydroxy-acid isomeroreductase / AHIR / Alpha-keto-beta-hydroxylacyl reductoisomerase / ...KARI / Acetohydroxy-acid isomeroreductase / AHIR / Alpha-keto-beta-hydroxylacyl reductoisomerase / Ketol-acid reductoisomerase type 1 / Ketol-acid reductoisomerase type I Mass: 37969.254 Da / Num. of mol.: 6 Mutation: N-terminal MGMT expression artefact, insert of sequence PGHLVRSEYQKGSG between residues 131 and 132 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus (bacteria) / Gene: ilvC, TT_C0850 / Production host: Escherichia coli (E. coli) References: UniProt: Q72JC8, ketol-acid reductoisomerase (NADP+)
#2: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#3: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO₄
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 251 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.69 Å³/Da / Density % sol: 54.23 %
Crystal grow	Temperature: 294 K / Method: vapor diffusion, hanging drop / Details: PEG 4000

-
Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 14, 2012
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9795 Å / Relative weight: 1
Reflection	Resolution: 1.89→63.06 Å / Num. obs: 184696 / % possible obs: 94.7 % / Redundancy: 4 % / CC_1/2: 0.993 / R_merge(I) obs: 0.154 / R_pim(I) all: 0.085 / R_rim(I) all: 0.177 / Net I/σ(I): 5.6
Reflection shell	Resolution: 1.89→1.92 Å / Redundancy: 3.9 % / R_merge(I) obs: 1.122 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 9269 / CC_1/2: 0.679 / R_pim(I) all: 0.637 / R_rim(I) all: 1.298 / % possible all: 96.8

-
Processing

Software

Name	Version	Classification
REFMAC	5.8.0411	refinement
MOSFLM		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2→63.06 Å / Cor.coef. F_o:F_c: 0.926 / Cor.coef. F_o:F_c free: 0.905 / SU B: 7.796 / SU ML: 0.2 / Cross valid method: FREE R-VALUE / ESU R: 0.211 / ESU R Free: 0.184
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2884	8715	5.399 %
R_work	0.2589	152718	-
all	0.26	-	-
obs	-	161433	97.45 %

Solvent computation

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

Displacement parameters

B_iso mean: 46.788 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.829 Å²	0 Å²	0 Å²
2-	-	0.781 Å²	-0 Å²
3-	-	-	-1.611 Å²

Refinement step

Cycle: LAST / Resolution: 2→63.06 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	14460	0	25	251	14736

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.012	14758
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	14256
X-RAY DIFFRACTION	r_angle_refined_deg	1.449	1.645	19932
X-RAY DIFFRACTION	r_angle_other_deg	0.481	1.571	32724
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.578	5	1854
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	16.468	5	126
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.875	10	2526
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	15.437	10	672
X-RAY DIFFRACTION	r_chiral_restr	0.065	0.2	2182
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	17478
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	3402
X-RAY DIFFRACTION	r_nbd_refined	0.23	0.2	3063
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.191	0.2	12595
X-RAY DIFFRACTION	r_nbtor_refined	0.184	0.2	7230
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.079	0.2	8212
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.152	0.2	356
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.002	0.2	1
X-RAY DIFFRACTION	r_metal_ion_refined	0.231	0.2	1
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.146	0.2	70
X-RAY DIFFRACTION	r_nbd_other	0.185	0.2	445
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.105	0.2	56
X-RAY DIFFRACTION	r_mcbond_it	5.117	4.523	7452
X-RAY DIFFRACTION	r_mcbond_other	5.116	4.523	7452
X-RAY DIFFRACTION	r_mcangle_it	6.952	8.112	9294
X-RAY DIFFRACTION	r_mcangle_other	6.952	8.112	9295
X-RAY DIFFRACTION	r_scbond_it	5.707	4.912	7306
X-RAY DIFFRACTION	r_scbond_other	5.706	4.911	7303
X-RAY DIFFRACTION	r_scangle_it	8.185	8.803	10638
X-RAY DIFFRACTION	r_scangle_other	8.183	8.801	10633
X-RAY DIFFRACTION	r_lrange_it	9.97	43.173	16457
X-RAY DIFFRACTION	r_lrange_other	9.972	43.127	16433
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.024	0.05	9974
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.028	0.05	9974
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.023	0.05	9975
X-RAY DIFFRACTION	r_ncsr_local_group_4	0.024	0.05	9985
X-RAY DIFFRACTION	r_ncsr_local_group_5	0.02	0.05	9973
X-RAY DIFFRACTION	r_ncsr_local_group_6	0.032	0.05	9980
X-RAY DIFFRACTION	r_ncsr_local_group_7	0.026	0.05	10002
X-RAY DIFFRACTION	r_ncsr_local_group_8	0.024	0.05	9989
X-RAY DIFFRACTION	r_ncsr_local_group_9	0.025	0.05	9985
X-RAY DIFFRACTION	r_ncsr_local_group_10	0.03	0.05	9983
X-RAY DIFFRACTION	r_ncsr_local_group_11	0.031	0.05	9985
X-RAY DIFFRACTION	r_ncsr_local_group_12	0.028	0.05	9977
X-RAY DIFFRACTION	r_ncsr_local_group_13	0.023	0.05	9994
X-RAY DIFFRACTION	r_ncsr_local_group_14	0.022	0.05	9979
X-RAY DIFFRACTION	r_ncsr_local_group_15	0.023	0.05	9980

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)	Weight position
1	1	A	X-RAY DIFFRACTION	Local ncs	0.02445	0.0501
1	2	A	X-RAY DIFFRACTION	Local ncs	0.02445	0.0501
2	3	A	X-RAY DIFFRACTION	Local ncs	0.02771	0.0501
2	4	A	X-RAY DIFFRACTION	Local ncs	0.02771	0.0501
3	5	A	X-RAY DIFFRACTION	Local ncs	0.02271	0.0501
3	6	A	X-RAY DIFFRACTION	Local ncs	0.02271	0.0501
4	7	A	X-RAY DIFFRACTION	Local ncs	0.02366	0.0501
4	8	A	X-RAY DIFFRACTION	Local ncs	0.02366	0.0501
5	9	A	X-RAY DIFFRACTION	Local ncs	0.01986	0.0501
5	10	A	X-RAY DIFFRACTION	Local ncs	0.01986	0.0501
6	11	A	X-RAY DIFFRACTION	Local ncs	0.03205	0.0501
6	12	A	X-RAY DIFFRACTION	Local ncs	0.03205	0.0501
7	13	A	X-RAY DIFFRACTION	Local ncs	0.0259	0.0501
7	14	A	X-RAY DIFFRACTION	Local ncs	0.0259	0.0501
8	15	A	X-RAY DIFFRACTION	Local ncs	0.02424	0.0501
8	16	A	X-RAY DIFFRACTION	Local ncs	0.02424	0.0501
9	17	A	X-RAY DIFFRACTION	Local ncs	0.02467	0.0501
9	18	A	X-RAY DIFFRACTION	Local ncs	0.02467	0.0501
10	19	A	X-RAY DIFFRACTION	Local ncs	0.0299	0.0501
10	20	A	X-RAY DIFFRACTION	Local ncs	0.0299	0.0501
11	21	A	X-RAY DIFFRACTION	Local ncs	0.03096	0.0501
11	22	A	X-RAY DIFFRACTION	Local ncs	0.03096	0.0501
12	23	A	X-RAY DIFFRACTION	Local ncs	0.02803	0.0501
12	24	A	X-RAY DIFFRACTION	Local ncs	0.02803	0.0501
13	25	A	X-RAY DIFFRACTION	Local ncs	0.0233	0.0501
13	26	A	X-RAY DIFFRACTION	Local ncs	0.0233	0.0501
14	27	A	X-RAY DIFFRACTION	Local ncs	0.02227	0.0501
14	28	A	X-RAY DIFFRACTION	Local ncs	0.02227	0.0501
15	29	A	X-RAY DIFFRACTION	Local ncs	0.02349	0.0501
15	30	A	X-RAY DIFFRACTION	Local ncs	0.02349	0.0501

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 (%)
2-2.052		0	0.363	12130	X-RAY DIFFRACTION	99.967
2.052-2.108	0.344	1168	0.337	10631	X-RAY DIFFRACTION	99.9407
2.108-2.169		0	0.308	11490	X-RAY DIFFRACTION	99.9565
2.169-2.236	0.325	1079	0.477	8352	X-RAY DIFFRACTION	84.4618
2.236-2.309	0.416	962	0.601	8327	X-RAY DIFFRACTION	85.6366
2.309-2.39		0	0.276	10466	X-RAY DIFFRACTION	99.7902
2.39-2.48	0.302	858	0.26	9265	X-RAY DIFFRACTION	99.7438
2.48-2.581	0.286	755	0.251	8971	X-RAY DIFFRACTION	99.7232
2.581-2.696		0	0.26	9353	X-RAY DIFFRACTION	99.659
2.696-2.827	0.314	681	0.26	8233	X-RAY DIFFRACTION	99.5755
2.827-2.98	0.29	592	0.252	7927	X-RAY DIFFRACTION	99.6141
2.98-3.16	0.308	510	0.249	7572	X-RAY DIFFRACTION	99.5933
3.16-3.377	0.278	358	0.248	7176	X-RAY DIFFRACTION	98.9753
3.377-3.647	0.319	95	0.261	6787	X-RAY DIFFRACTION	96.6709
3.647-3.994	0.404	376	0.256	5941	X-RAY DIFFRACTION	96.2224
3.994-4.463	0.211	540	0.174	5356	X-RAY DIFFRACTION	98.7274
4.463-5.149	0.202	210	0.15	5055	X-RAY DIFFRACTION	99.3396
5.149-6.296	0.224	174	0.193	4327	X-RAY DIFFRACTION	99.6237
6.296-8.861	0.2	223	0.172	3330	X-RAY DIFFRACTION	99.8595
8.861-63.06	0.206	134	0.186	1972	X-RAY DIFFRACTION	99.9525

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi