PDB-8a8y: Structure of truncated 1-deoxy-D-xylulose 5-phosphate synthase (D...

ID or keywords:

Entry

Database: PDB / ID: 8a8y

Title

Structure of truncated 1-deoxy-D-xylulose 5-phosphate synthase (DXS) from Klebsiella pneumoniae

Components

1-deoxy-D-xylulose-5-phosphate synthase

Keywords

TRANSFERASE / Primary metabolism / synthase

Function / homology

Function and homology information

1-deoxy-D-xylulose-5-phosphate synthase / 1-deoxy-D-xylulose 5-phosphate biosynthetic process / 1-deoxy-D-xylulose-5-phosphate synthase activity / thiamine biosynthetic process / terpenoid biosynthetic process / isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway / thiamine pyrophosphate binding / magnesium ion binding / cytosol
Similarity search - Function

Biological species

Klebsiella pneumoniae (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.10000431701 Å

Authors

Adam, S. / Hirsch, A.

Funding support

Germany, 1items

Citation

Journal: To Be Published
Title: Structure of truncated 1-deoxy-D-xylulose 5-phosphate synthase (DXS) from Klebsiella pneumoniae
Authors: Adam, S. / Hirsch, A.

History

Deposition	Jun 24, 2022	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jul 5, 2023	Provider: repository / Type: Initial release
Revision 1.1	Feb 7, 2024	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8a8y.cif.gz	651.5 KB	Display	PDBx/mmCIF format
PDB format	pdb8a8y.ent.gz	452.8 KB	Display	PDB format
PDBx/mmJSON format	8a8y.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8a8y_validation.pdf.gz	437.6 KB	Display	wwPDB validaton report
Full document	8a8y_full_validation.pdf.gz	442.9 KB	Display
Data in XML	8a8y_validation.xml.gz	36.4 KB	Display
Data in CIF	8a8y_validation.cif.gz	52.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/a8/8a8y ftp://data.pdbj.org/pub/pdb/validation_reports/a8/8a8y	HTTPS FTP

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Related structure data

Related structure data	2o1sS S: Starting model for refinement
Similar structure data	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	#153 - Sep 2012 Pyruvate Dehydrogenase Complex similarity (7) #154 - Oct 2012 Citric Acid Cycle similarity (4) #263 - Nov 2021 Acetohydroxyacid Synthase similarity (1)

Deposited unit

A: 1-deoxy-D-xylulose-5-phosphate synthase

B: 1-deoxy-D-xylulose-5-phosphate synthase

127 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	119.164, 144.247, 142.911
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	20
Space group name H-M	C222₁
Space group name Hall	C2c2
Symmetry operation	#1: x,y,z #2: x,-y,-z #3: -x,y,-z+1/2 #4: -x,-y,z+1/2 #5: x+1/2,y+1/2,z #6: x+1/2,-y+1/2,-z #7: -x+1/2,y+1/2,-z+1/2 #8: -x+1/2,-y+1/2,z+1/2

#1: Protein	1-deoxy-D-xylulose-5-phosphate synthase / 1-deoxyxylulose-5-phosphate synthase / DXP synthase / DXPS Mass: 63254.125 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Klebsiella pneumoniae (bacteria) Gene: dxs_3, dxs, dxs_1, dxs_2, BN49_1346, DRB11_07540, FXN67_12755, GPZ86_21160, NCTC11679_04435, NCTC13465_06397, NCTC3279_00555, NCTC5047_01280, NCTC5052_00313, NCTC9140_02292, NCTC9645_03343, ...Gene: dxs_3, dxs, dxs_1, dxs_2, BN49_1346, DRB11_07540, FXN67_12755, GPZ86_21160, NCTC11679_04435, NCTC13465_06397, NCTC3279_00555, NCTC5047_01280, NCTC5052_00313, NCTC9140_02292, NCTC9645_03343, NCTC9661_05006, SAMEA3512100_02923, SAMEA3649733_02709, SAMEA4364603_02966 Production host: Escherichia coli (E. coli) References: UniProt: A0A0S3F934, 1-deoxy-D-xylulose-5-phosphate synthase
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 392 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

1-deoxy-D-xylulose-5-phosphate synthase / 1-deoxyxylulose-5-phosphate synthase / DXP synthase / DXPS

Mass: 63254.125 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Klebsiella pneumoniae (bacteria)
Gene: dxs_3, dxs, dxs_1, dxs_2, BN49_1346, DRB11_07540, FXN67_12755, GPZ86_21160, NCTC11679_04435, NCTC13465_06397, NCTC3279_00555, NCTC5047_01280, NCTC5052_00313, NCTC9140_02292, NCTC9645_03343, ...
Production host:

Escherichia coli (E. coli)
References: UniProt: A0A0S3F934, 1-deoxy-D-xylulose-5-phosphate synthase

#2: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 392 / 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: 2.92 Å³/Da / Density % sol: 57.89 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, hanging drop / Details: PEG 8000, Magnesium chloride, TRIS

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 3, 2022
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97 Å / Relative weight: 1
Reflection	Resolution: 2.1→91.9 Å / Num. obs: 71565 / % possible obs: 99.6 % / Redundancy: 4.5 % / B_iso Wilson estimate: 35.355127569 Å² / R_merge(I) obs: 0.089 / Net I/σ(I): 9.9
Reflection shell	Resolution: 2.1→2.21 Å / R_merge(I) obs: 0.72 / Num. unique obs: 10344

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Processing

Software

Name	Version	Classification
PHENIX	1.11.1_2575	refinement
XDS		data reduction
SCALA		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 2o1s

2o1s

Resolution: 2.10000431701→45.934906016 Å / SU ML: 0.219294682671 / Cross valid method: FREE R-VALUE / σ(F): 1.35282638344 / Phase error: 20.7565773698
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.201051462019	3562	4.98042505593 %
R_work	0.17914882105	67958	-
obs	0.18023954443	71520	99.4922445573 %

Solvent computation

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

Displacement parameters

B_iso mean: 52.2053769734 Å²

Refinement step

Cycle: LAST / Resolution: 2.10000431701→45.934906016 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7384	0	0	392	7776

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.00237804848585	7526
X-RAY DIFFRACTION	f_angle_d	0.527250609394	10204
X-RAY DIFFRACTION	f_chiral_restr	0.0427122065955	1171
X-RAY DIFFRACTION	f_plane_restr	0.00256755404267	1321
X-RAY DIFFRACTION	f_dihedral_angle_d	15.0981131547	4507

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 (%)
2.1000044-2.1288	0.301884447985	142	0.264533394056	2731	X-RAY DIFFRACTION	99.6877168633
2.1288-2.1592	0.302141025334	147	0.259928607137	2670	X-RAY DIFFRACTION	99.6815286624
2.1592-2.1914	0.292789948279	154	0.239411317601	2687	X-RAY DIFFRACTION	99.7191997192
2.1914-2.2257	0.277190274387	158	0.234097161392	2638	X-RAY DIFFRACTION	98.5200845666
2.2257-2.2621	0.266624591521	135	0.224723829359	2683	X-RAY DIFFRACTION	99.4354269584
2.2621-2.3011	0.262299705836	137	0.215975333993	2707	X-RAY DIFFRACTION	99.649614576
2.3011-2.343	0.246671846094	162	0.210140758368	2685	X-RAY DIFFRACTION	99.7197898424
2.343-2.3881	0.236763795338	151	0.212934046736	2683	X-RAY DIFFRACTION	99.5783555868
2.3881-2.4368	0.24087176571	155	0.197456682448	2684	X-RAY DIFFRACTION	99.5790950544
2.4368-2.4898	0.199382044274	131	0.196555988319	2698	X-RAY DIFFRACTION	99.6828752643
2.4898-2.5477	0.244954634254	144	0.194704236982	2716	X-RAY DIFFRACTION	99.6515679443
2.5477-2.6114	0.250310314621	129	0.197474870425	2715	X-RAY DIFFRACTION	99.5101469559
2.6114-2.682	0.218365133506	157	0.191540620558	2683	X-RAY DIFFRACTION	99.5094604064
2.682-2.7609	0.233265470216	138	0.19072529895	2735	X-RAY DIFFRACTION	99.4806094183
2.7609-2.85	0.210546588862	142	0.183911113876	2691	X-RAY DIFFRACTION	99.9294532628
2.85-2.9519	0.20944950157	144	0.180462225702	2723	X-RAY DIFFRACTION	99.8954703833
2.9519-3.07	0.227362579162	147	0.177246955219	2706	X-RAY DIFFRACTION	99.5116846878
3.07-3.2097	0.193825811704	127	0.173949304981	2753	X-RAY DIFFRACTION	99.6884735202
3.2097-3.3789	0.174971270669	125	0.162763260263	2711	X-RAY DIFFRACTION	98.780912574
3.3789-3.5905	0.156459026393	134	0.158032792478	2757	X-RAY DIFFRACTION	99.8963372495
3.5905-3.8676	0.198332560976	144	0.15296515775	2748	X-RAY DIFFRACTION	99.8274076631
3.8676-4.2566	0.166430752284	137	0.14782183215	2759	X-RAY DIFFRACTION	99.6558843772
4.2566-4.8719	0.151527539465	137	0.138137427925	2753	X-RAY DIFFRACTION	99.4152046784
4.8719-6.1358	0.155199719283	137	0.171831911154	2786	X-RAY DIFFRACTION	99.2866847826
6.1358-45.933	0.208120028051	148	0.205539276647	2856	X-RAY DIFFRACTION	98.1699346405

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	2.37059340361	-0.460015460944	0.406609125516	3.31752706775	0.434229136644	2.64576063668	-0.195499093522	0.184572049458	0.765455017265	-0.109735172839	-0.026068905961	-0.291453248917	-1.01972985552	0.344772124433	0.225030800295	0.72107132867	-0.174176613167	-0.0872477682418	0.515527629002	0.0464537760284	0.588879201994	-4.50997369119	-11.8999695493	17.2252325317
2	2.1279016269	0.919158915482	0.51173904237	3.4480377322	0.687584943627	2.33751292097	-0.128123896714	-0.336074992727	0.299578074517	0.333196516504	-0.127104171602	0.0817537008859	-0.382950811035	-0.0218990341317	0.260493651284	0.475767341692	-0.00632631857031	-0.0368319139313	0.401173831942	-0.0382575143831	0.373106791354	-14.5089711296	-22.2755118612	25.5411203662
3	1.64153727709	-0.590882666036	2.11278827361	0.587628409266	-0.52481161799	3.74342187214	-0.0742820885002	0.0279762123967	0.280780116527	0.0197306841769	-0.0964143839474	-0.00666417409024	-0.342094587767	0.00523182663574	0.207651503151	0.326073195602	0.000239939289373	0.0163056069127	0.357223462049	0.00654735398556	0.391757633078	-30.7391327265	-21.3372784522	2.20302380366
4	1.69589287297	-0.324897787069	-0.734307738636	0.507308312763	0.102891123452	2.12293874762	0.0550757447156	0.164565662618	0.0266290858479	-0.0931300617241	-0.0169579400796	0.0281150689477	0.0422243066738	-0.0599003303627	-0.0306912798385	0.267323978299	-0.0141519507619	-0.0331407586447	0.289956097361	0.00879845424432	0.280660373507	-25.0295577481	-33.9049469117	-12.3437066025
5	2.21043854452	0.907314596568	0.278948023947	2.8579497036	-0.666448240054	1.25751596799	0.0537217250652	0.229514056208	0.261468507081	-0.122863809242	-0.0699418220518	0.036213470389	-0.0613714879753	0.182952010077	0.00382028722311	0.294702115278	-0.0091649162008	0.00719244690442	0.418420096283	0.0503704923513	0.302127753717	-8.71416833845	-34.4603505235	-19.2924130925
6	3.81827465862	0.168929016435	0.706883994394	3.15498611875	0.767030229613	3.07342696336	-0.0333371762871	-0.182642394761	-0.995511056652	0.26498023801	0.0418642231423	0.306655674486	0.989147254005	-0.540303108084	-0.0523364010989	0.734318193847	-0.199779111983	0.0605349973483	0.560170086782	0.0966746993546	0.793135703601	-45.6533841382	-61.3995878743	23.4688828027
7	3.1516254997	-0.482998205808	0.0326725174569	4.16235393216	-1.15474518361	2.48304906081	-0.0310210797667	0.220394535506	-0.462282700417	-0.214456581627	0.150674846814	-0.0566014236507	0.588808506425	-0.106835226787	-0.122178120934	0.46942565411	-0.0612944980584	-0.00816301817327	0.485551995898	-0.0517689312789	0.395016645795	-40.4864391913	-46.9092819356	12.9855576472
8	1.83869304838	0.676572778844	-1.2195811395	4.20977609216	-1.39410879723	3.54857679299	-0.00684705263355	-0.0982185005278	-0.0139458067138	0.199090502541	0.14228316333	0.381064760405	0.0408377303793	-0.239815004345	-0.111631471293	0.309342960886	0.012080630742	0.0283096103786	0.372063237699	0.0131157767808	0.302630263835	-37.7600105741	-39.2759294845	22.8195954331
9	2.9621872851	-1.15819530102	-0.962923050778	1.00259038165	0.325778849311	0.678680872008	-0.112178170133	-0.132209055258	-0.295163901471	0.104310308941	0.0232648975924	0.0440883605395	0.0356641930521	0.0634127421472	0.113869144367	0.363688345365	-0.00875806144358	-0.0200821041763	0.347897280325	0.0491423779774	0.295102494472	-11.7563475243	-49.7690947006	20.6457732704
10	2.40320008735	-0.232685523315	0.796133173764	2.36744246268	1.04041414355	4.88219901199	-0.0368160255277	-0.149192338904	-0.00494260691231	0.130754803636	-0.0490003725182	0.117187937827	0.148958833411	-0.25162386825	0.089729823925	0.205492280581	-0.00835292681133	0.00380619197527	0.271061420847	0.030185371589	0.23024627818	-10.4200955935	-42.767959132	11.6870822149
11	1.48669213271	-0.307582401527	0.438077433603	0.605789234273	-0.196504166294	1.43872354969	0.0961158859301	0.05683150936	-0.215136046814	-0.0894349330411	-0.0429822517258	-0.0427076455267	0.243909792966	0.0451196501142	-0.0523638487884	0.314656916696	0.0042848992937	-0.00122291992849	0.289916556862	-0.00547026376594	0.320786680679	-5.21937311842	-55.58855042	-6.34374367831

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 6 through 140 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 141 through 237 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 238 through 324 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 325 through 530 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 531 through 586 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 4 through 66 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 67 through 140 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 141 through 237 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 238 through 324 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 325 through 400 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 401 through 586 )

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