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- PDB-6udf: Crystal structure of Enoyl-[acyl-carrier-protein] reductase [NADH... -

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Open data

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Basic information

Entry

Database: PDB / ID: 6udf

Title

Crystal structure of Enoyl-[acyl-carrier-protein] reductase [NADH] (InhA) from Mycobacterium kansasii

Components

Enoyl-[acyl-carrier-protein] reductase [NADH]

Keywords

OXIDOREDUCTASE / SSGCID / Mycobacterium kansasii / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / Enoyl-[acyl-carrier-protein] reductase [NADH] / InhA

Function / homology

Function and homology information

enoyl-[acyl-carrier-protein] reductase (NADH) / enoyl-[acyl-carrier-protein] reductase (NADH) activity / fatty acid biosynthetic process / response to antibiotic / nucleotide binding
Similarity search - Function

Biological species

Mycobacterium kansasii (bacteria)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 1.95 Å

Authors

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Citation

Journal: to be published
Title: Crystal stucture of Enoyl-[acyl-carrier-protein] reductase [NADH] (InhA) from Mycobacterium kansasii
Authors: Abendroth, J. / Davies, D.R. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E.

History

Deposition	Sep 19, 2019	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 16, 2019	Provider: repository / Type: Initial release
Revision 1.1	Oct 11, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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	6udf.cif.gz	147.3 KB	Display	PDBx/mmCIF format
PDB format	pdb6udf.ent.gz	95.2 KB	Display	PDB format
PDBx/mmJSON format	6udf.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	6udf_validation.pdf.gz	425.3 KB	Display	wwPDB validaton report
Full document	6udf_full_validation.pdf.gz	425.5 KB	Display
Data in XML	6udf_validation.xml.gz	14.2 KB	Display
Data in CIF	6udf_validation.cif.gz	21 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ud/6udf ftp://data.pdbj.org/pub/pdb/validation_reports/ud/6udf	HTTPS FTP

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Related structure data

Related structure data	2h7i PDB Unreleased entryS S: Starting model for refinement
Similar structure data	1p44-2 2h9i-1 2ntv-1 6sq7-1 4tzk-1 7kxa-1 4u0j-1 4dqu-1 6yuu-1 1p44-1 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
Other databases	TargetTrack: MykaA.20209.a TargetTrack: MykaA.00472.a

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#90 - Jun 2007 Fatty Acid Synthase similarity (3) #77 - May 2006 Glucose Oxidase similarity (1)

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Assembly

Deposited unit

A: Enoyl-[acyl-carrier-protein] reductase [NADH]

hetero molecules

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

1

A: Enoyl-[acyl-carrier-protein] reductase [NADH]

hetero molecules

A: Enoyl-[acyl-carrier-protein] reductase [NADH]

hetero molecules

A: Enoyl-[acyl-carrier-protein] reductase [NADH]

hetero molecules

A: Enoyl-[acyl-carrier-protein] reductase [NADH]

hetero molecules

defined by author&software
Evidence: gel filtration
120 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	92.980, 92.980, 182.620
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	98
Space group name H-M	I4₁22
Space group name Hall	I4bw2bw
Symmetry operation	#1: x,y,z #2: -y+1/2,x,z+3/4 #3: y+1/2,-x,z+3/4 #4: x+1/2,-y,-z+3/4 #5: -x+1/2,y,-z+3/4 #6: -x,-y,z #7: y,x,-z #8: -y,-x,-z #9: x+1/2,y+1/2,z+1/2 #10: -y+1,x+1/2,z+5/4 #11: y+1,-x+1/2,z+5/4 #12: x+1,-y+1/2,-z+5/4 #13: -x+1,y+1/2,-z+5/4 #14: -x+1/2,-y+1/2,z+1/2 #15: y+1/2,x+1/2,-z+1/2 #16: -y+1/2,-x+1/2,-z+1/2

Components on special symmetry positions

ID	Model	Components
1	1	A-478- HOH
2	1	A-531- HOH

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Components

#1: Protein	Enoyl-[acyl-carrier-protein] reductase [NADH] Mass: 29896.293 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium kansasii (bacteria) / Gene: inhA, BZL29_3124, BZL30_8369 / Plasmid: MykaA.00472.a.B1 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) Strain (production host): BL21(DE3) References: UniProt: A0A1V3XDT0, enoyl-[acyl-carrier-protein] reductase (NADH)
#2: Chemical	ChemComp-FMT / FORMIC ACID Mass: 46.025 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH₂O₂
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 259 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N

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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: 3.3 Å³/Da / Density % sol: 62.8 %
Crystal grow	Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7 Details: Optimization condition around Microlytic MCSG1 screen, condition F8: 3000mM sodium formate pH 7.0: MykaA.00472.a.B1.PS38576, at 27.1mg/ml: cryo: 20%EG: tray 311486 b1: puck ybk8-4.

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å

Detector

Type: RIGAKU SATURN 944+ / Detector: CCD / Date: Aug 23, 2019 / Details: Rigaku VariMax

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 1.5418 Å / Relative weight: 1

Reflection

Resolution: 1.95→50 Å / Num. obs: 29565 / % possible obs: 99.8 % / Redundancy: 12.1 % / B_iso Wilson estimate: 28.65 Å² / CC_1/2: 1 / R_merge(I) obs: 0.045 / R_rim(I) all: 0.047 / Χ²: 1.024 / Net I/σ(I): 36.94

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. unique obs	CC_1/2	R_rim(I) all	% possible all
1.95-2	6.898	0.544	3.53	2154	0.9	0.588	99.9
2-2.06	8.198	0.394	5.55	2111	0.953	0.42	99.9
2.06-2.12	9.133	0.326	7.3	2047	0.972	0.346	99.9
2.12-2.18	10.107	0.234	10.86	1966	0.988	0.246	99.9
2.18-2.25	10.746	0.197	13.4	1951	0.991	0.207	100
2.25-2.33	11.466	0.168	15.89	1849	0.995	0.176	99.7
2.33-2.42	12.612	0.14	19.75	1780	0.998	0.146	99.5
2.42-2.52	14.249	0.124	23.87	1736	0.998	0.129	99.7
2.52-2.63	14.283	0.106	27.12	1682	0.998	0.11	99.9
2.63-2.76	14.408	0.083	32.82	1589	0.999	0.086	99.6
2.76-2.91	14.427	0.067	39.07	1528	0.999	0.07	99.6
2.91-3.08	14.442	0.055	47.41	1436	0.999	0.056	100
3.08-3.3	14.4	0.041	58.57	1375	1	0.042	99.7
3.3-3.56	14.375	0.032	73.19	1270	1	0.033	99.8
3.56-3.9	14.255	0.027	90.61	1179	1	0.028	99.7
3.9-4.36	14.274	0.022	99.34	1063	1	0.023	98.9
4.36-5.04	14.083	0.02	106.29	959	1	0.021	99.9
5.04-6.17	13.89	0.023	95.24	834	0.999	0.024	100
6.17-8.72	13.452	0.019	103.35	661	1	0.02	100
8.72-50	11.686	0.016	109.7	395	1	0.017	98.5

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Processing

Software

Name	Version	Classification
PHENIX		refinement
XDS		data reduction
XSCALE		data scaling
PDB_EXTRACT	3.25	data extraction
MoRDa		phasing
Coot		model building
PHENIX		model building

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 2h7i

2h7i
PDB Unreleased entry

Resolution: 1.95→46.49 Å / SU ML: 0.2041 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.5248

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.193	1974	6.68 %	0
R_work	0.1619	-	-	-
obs	0.1639	29548	99.79 %	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Displacement parameters

B_iso mean: 33.86 Å²

Refinement step

Cycle: LAST / Resolution: 1.95→46.49 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2002	0	6	259	2267

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0062	2088
X-RAY DIFFRACTION	f_angle_d	0.8211	2844
X-RAY DIFFRACTION	f_chiral_restr	0.0521	330
X-RAY DIFFRACTION	f_plane_restr	0.0056	370
X-RAY DIFFRACTION	f_dihedral_angle_d	10.4871	1263

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 (%)
1.95-2	0.2349	119	0.2135	1961	X-RAY DIFFRACTION	99.9
2-2.05	0.2146	138	0.1798	1943	X-RAY DIFFRACTION	99.95
2.05-2.11	0.2145	140	0.1832	1938	X-RAY DIFFRACTION	99.9
2.11-2.18	0.2089	157	0.1774	1916	X-RAY DIFFRACTION	100
2.18-2.26	0.2329	133	0.1737	1952	X-RAY DIFFRACTION	99.95
2.26-2.35	0.2295	162	0.1834	1929	X-RAY DIFFRACTION	99.76
2.35-2.46	0.2404	148	0.1851	1925	X-RAY DIFFRACTION	99.62
2.46-2.59	0.2646	141	0.1885	1964	X-RAY DIFFRACTION	99.72
2.59-2.75	0.2293	144	0.1841	1959	X-RAY DIFFRACTION	99.72
2.75-2.96	0.195	136	0.1804	1952	X-RAY DIFFRACTION	99.76
2.96-3.26	0.1943	148	0.172	1965	X-RAY DIFFRACTION	99.86
3.26-3.73	0.1565	120	0.1429	2026	X-RAY DIFFRACTION	99.81
3.73-4.7	0.1427	133	0.1215	2022	X-RAY DIFFRACTION	99.45
4.7-46.49	0.1797	155	0.1579	2122	X-RAY DIFFRACTION	99.82

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	3.31334260428	-0.244649225592	-0.501625310232	1.93568668883	-0.850655897035	2.36379209462	-0.0545718178973	-0.0520131694266	0.356127116429	0.182627771543	0.118594382828	-0.297138831389	-0.574642421409	0.208641046291	-0.0670232233422	0.453855697438	-0.0888618724202	0.0194374407566	0.172694946068	-0.0347883808753	0.316691354323	-37.3173663991	-17.6589069978	5.31015578551
2	4.4346218045	-0.709348325332	1.08978709145	2.7177381413	0.715451738798	3.78549857812	-0.0609503634381	-0.137293205541	0.447525028508	0.198251520641	-0.0173712011796	-0.0187665619038	-0.715245806521	-0.483221878921	0.0173938129905	0.645914655527	-0.0361299592548	0.0393961242677	0.191173853464	-0.00482944394563	0.350209148588	-44.469521068	-9.84767460786	8.09051630507
3	1.86376157997	1.30648551069	0.267943505108	2.77713798667	-0.544559990021	1.65439442337	-0.0220241215163	0.0169790203725	0.7046392481	-0.0625193255443	0.0725494572567	0.300305752685	-0.748462676452	-0.0486532474353	-0.0192644200801	0.681245250726	0.0282346030675	0.0926541785137	0.196412160804	0.00729208796149	0.420057222936	-49.029771119	-10.1886136931	-2.28177899913
4	1.33547998716	0.213198106868	0.253829186488	1.66080391954	0.0183707440425	1.38227100222	0.043844346082	0.0236432038358	0.203489529254	0.0154203441766	0.0277847191882	0.0457871101672	-0.414878522946	-0.0704974867493	-0.0913473916558	0.254611140547	0.0304024673652	0.0288550520032	0.130332587381	0.0111832581071	0.192001785966	-51.351271174	-27.782122511	1.05736265368
5	2.16845279319	4.03378179967	-1.0843797893	8.78546483657	-4.66728726183	6.23772948241	-0.471265010485	-0.388826333241	0.264892404996	0.603426184541	0.418794467479	-0.124976990313	-0.330036842239	-0.602501042957	0.120664636601	0.739127814953	0.0659799257022	-0.0674768429382	0.448199530548	-0.111937093082	0.465140594827	-54.2288580085	-27.7723404801	22.7121201623
6	1.5586994365	0.247109255639	0.0587505326963	1.69135471721	-0.0514341131586	2.31600677789	0.0707085427891	-0.16668083205	0.101285520971	0.364373959657	-0.0315464913336	-0.00525963332938	-0.270177147117	0.128448544049	-0.0659082936769	0.240935680549	-0.0262115643182	0.0204775720352	0.148189315785	-0.0385619779268	0.199333909366	-39.9198986416	-34.886561331	10.5555142374

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 2 through 31 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 32 through 53 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 54 through 82 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 83 through 196 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 197 through 209 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 210 through 269 )

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