PDB-28yl: Crystal structure of the zeamine pathway ketoreductase Zmn13-KR, ...

ID or keywords:

Entry

Database: PDB / ID: 28yl

Title

Crystal structure of the zeamine pathway ketoreductase Zmn13-KR, in complex with NADH

Components

3-oxoacyl-[acyl-carrier-protein] reductase FabG

Keywords

OXIDOREDUCTASE / Short-chain dehydrogenase/reductase (SDR) superfamily / Rossmann fold / catalytic domain / NADH-dependent reduction

Function / homology

3-oxoacyl-[acyl-carrier-protein] reductase / 3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity / short chain dehydrogenase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding domain superfamily / ISOPROPYL ALCOHOL / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / 3-oxoacyl-[acyl-carrier-protein] reductase FabG

Function and homology information

Biological species

Serratia plymuthica RVH1 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.9 Å

Authors

Boone, L. / Desiderati, G. / Voet, A.R.D. / Masschelein, J.

Funding support

Belgium, 2items

Citation

Journal: To Be Published
Title: Structural insights into Zmn13-KR: a first step towards engineering improved zeamine antibiotics
Authors: Boone, L. / Desiderati, G. / El Arnouki Belhaji, F. / Voet, A.R.D. / Masschelein, J.

History

Deposition	Mar 2, 2026	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Mar 25, 2026	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	28yl.cif.gz	207.3 KB	Display	PDBx/mmCIF format
PDB format	pdb28yl.ent.gz	161 KB	Display	PDB format
PDBx/mmJSON format	28yl.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/8y/28yl ftp://data.pdbj.org/pub/pdb/validation_reports/8y/28yl	HTTPS FTP

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Related structure data

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	#188 - Aug 2015 Tetrahydrobiopterin Biosynthesis similarity (1) #90 - Jun 2007 Fatty Acid Synthase similarity (1) #102 - Jun 2008 Lactate Dehydrogenase similarity (1) #93 - Sep 2007 Citrate Synthase similarity (1) #216 - Dec 2017 Biodegradable Plastic similarity (1) #70 - Oct 2005 Designer Proteins similarity (1)

Deposited unit

D: 3-oxoacyl-[acyl-carrier-protein] reductase FabG

B: 3-oxoacyl-[acyl-carrier-protein] reductase FabG

A: 3-oxoacyl-[acyl-carrier-protein] reductase FabG

C: 3-oxoacyl-[acyl-carrier-protein] reductase FabG

hetero molecules

111 kDa, 4 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)	80.342, 109.321, 208.278
Angle α, β, γ (deg.)	90, 90, 90
Int Tables number	20
Space group name H-M	C222₁

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	D
2	1	B
3	2	D
4	2	A
5	3	D
6	3	C
7	4	B
8	4	A
9	5	B
10	5	C
11	6	A
12	6	C

NCS domain segments:

End auth comp-ID: LEU / End label comp-ID: LEU

Dom-ID	Component-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	1	MET	MET	D	A	1 - 255	4 - 258
2	1	1	MET	MET	B	B	1 - 255	4 - 258
3	2	2	MET	MET	D	A	1 - 255	4 - 258
4	2	2	MET	MET	A	C	1 - 255	4 - 258
5	3	3	SER	SER	D	A	2 - 255	5 - 258
6	3	3	SER	SER	C	D	2 - 255	5 - 258
7	4	4	MET	MET	B	B	1 - 255	4 - 258
8	4	4	MET	MET	A	C	1 - 255	4 - 258
9	5	5	SER	SER	B	B	2 - 255	5 - 258
10	5	5	SER	SER	C	D	2 - 255	5 - 258
11	6	6	SER	SER	A	C	2 - 255	5 - 258
12	6	6	SER	SER	C	D	2 - 255	5 - 258

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

#1: Protein	3-oxoacyl-[acyl-carrier-protein] reductase FabG / Putative 3-oxoacyl-ACP reductase / SDR family NAD(P)-dependent oxidoreductase Mass: 27077.959 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Serratia plymuthica RVH1 (bacteria) / Gene: zmn13, fabG_16, I6G64_16280, NCTC12961_05043 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: T2I4E6, 3-oxoacyl-[acyl-carrier-protein] reductase
#2: Chemical	ChemComp-NAI / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH Mass: 665.441 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂₁H₂₉N₇O₁₄P₂ / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Chemical	ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL Mass: 60.095 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃H₈O / Comment: alkaloid*YM
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 272 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
Has protein modification	N

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.14 Å³/Da / Density % sol: 42.47 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.2 Details: 0.1 M HEPES, 10% (v/v) isopropanol, 5% (v/v) glycerol

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.8731 Å
Detector	Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Apr 29, 2025
Radiation	Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.8731 Å / Relative weight: 1
Reflection	Resolution: 1.9→64.74 Å / Num. obs: 70494 / % possible obs: 97.7 % / Redundancy: 3.9 % / B_iso Wilson estimate: 26.1 Å² / CC_1/2: 0.996 / R_merge(I) obs: 0.103 / R_pim(I) all: 0.056 / R_rim(I) all: 0.118 / Χ²: 1.01 / Net I/σ(I): 7.2
Reflection shell	Resolution: 1.9→1.94 Å / R_merge(I) obs: 0.577 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 4428 / CC_1/2: 0.748 / R_pim(I) all: 0.327 / R_rim(I) all: 0.668 / Χ²: 0.96 / % possible all: 95.3

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Processing

Software

Name	Version	Classification
REFMAC	v5.8.0431 (refmacat 0.4.126)	refinement
XDS	Jan 19, 2025	data reduction
Aimless	v0.8.2	data scaling
MOLREP	v11.9.02	phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.9→64.739 Å / Cor.coef. F_o:F_c: 0.964 / Cor.coef. F_o:F_c free: 0.949 / SU B: 5.034 / SU ML: 0.134 / Cross valid method: THROUGHOUT / ESU R: 0.168 / ESU R Free: 0.15 / Details: Hydrogens have not been used

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2246	3536	5.018 %	RANDOM
R_work	0.1844	66932	-	-
all	0.186	-	-	-
obs	-	70468	97.266 %	-

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: 31.741 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.009 Å²	-0 Å²	-0 Å²
2-	-	0.009 Å²	-0 Å²
3-	-	-	0.001 Å²

Refinement step

Cycle: LAST / Resolution: 1.9→64.739 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7203	0	208	272	7683

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.006	0.012	7667
X-RAY DIFFRACTION	r_angle_refined_deg	1.454	1.788	10463
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.375	5	1009
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	7.105	5	80
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.542	10	1158
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	13.612	10	272
X-RAY DIFFRACTION	r_chiral_restr	0.103	0.2	1265
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	5653
X-RAY DIFFRACTION	r_nbd_refined	0.208	0.2	3841
X-RAY DIFFRACTION	r_nbtor_refined	0.306	0.2	5270
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.131	0.2	435
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.238	0.2	122
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.195	0.2	19
X-RAY DIFFRACTION	r_mcbond_it	2.553	2.97	4012
X-RAY DIFFRACTION	r_mcangle_it	3.74	5.31	5016
X-RAY DIFFRACTION	r_scbond_it	3.772	3.329	3655
X-RAY DIFFRACTION	r_scangle_it	5.606	5.954	5441
X-RAY DIFFRACTION	r_lrange_it	7.405	34.724	11976
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.079	0.05	7296
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.077	0.05	7311
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.079	0.05	7271
X-RAY DIFFRACTION	r_ncsr_local_group_4	0.083	0.05	7284
X-RAY DIFFRACTION	r_ncsr_local_group_5	0.088	0.05	7172
X-RAY DIFFRACTION	r_ncsr_local_group_6	0.087	0.05	7064

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)	Weight position
1	1	D	X-RAY DIFFRACTION	Local ncs	0.07852	0.05009
1	2	B	X-RAY DIFFRACTION	Local ncs	0.07852	0.05009
2	3	D	X-RAY DIFFRACTION	Local ncs	0.07684	0.05009
2	4	A	X-RAY DIFFRACTION	Local ncs	0.07684	0.05009
3	5	D	X-RAY DIFFRACTION	Local ncs	0.07924	0.05009
3	6	C	X-RAY DIFFRACTION	Local ncs	0.07924	0.05009
4	7	B	X-RAY DIFFRACTION	Local ncs	0.08265	0.05009
4	8	A	X-RAY DIFFRACTION	Local ncs	0.08265	0.05009
5	9	B	X-RAY DIFFRACTION	Local ncs	0.08782	0.05009
5	10	C	X-RAY DIFFRACTION	Local ncs	0.08782	0.05009
6	11	A	X-RAY DIFFRACTION	Local ncs	0.08719	0.05009
6	12	C	X-RAY DIFFRACTION	Local ncs	0.08719	0.05009

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
1.9-1.949	0.321	258	0.322	4796	0.322	5304	0.897	0.891	95.2866	0.264
1.949-2.003	0.318	286	0.316	4877	0.316	5197	0.909	0.91	99.3458	0.249
2.003-2.061	0.282	250	0.282	4738	0.282	5028	0.929	0.931	99.2045	0.225
2.061-2.124	0.288	232	0.253	4614	0.255	4893	0.937	0.948	99.0394	0.199
2.124-2.194	0.275	218	0.236	4437	0.238	4707	0.938	0.957	98.8953	0.19
2.194-2.271	0.296	212	0.225	4295	0.228	4567	0.935	0.963	98.6862	0.187
2.271-2.356	0.291	223	0.219	4145	0.223	4438	0.943	0.965	98.4227	0.18
2.356-2.452	0.242	219	0.195	3966	0.197	4265	0.959	0.974	98.1243	0.167
2.452-2.561	0.232	204	0.197	3794	0.199	4092	0.967	0.974	97.7028	0.167
2.561-2.686	0.215	189	0.181	3654	0.183	3940	0.969	0.98	97.5381	0.157
2.686-2.831	0.263	201	0.177	3314	0.181	3736	0.963	0.98	94.0846	0.157
2.831-3.002	0.212	176	0.168	3251	0.171	3536	0.971	0.983	96.9174	0.152
3.002-3.209	0.217	144	0.165	3111	0.168	3349	0.972	0.983	97.1932	0.155
3.209-3.465	0.216	145	0.16	2859	0.163	3103	0.972	0.984	96.8095	0.153
3.465-3.795	0.185	150	0.149	2630	0.151	2885	0.981	0.987	96.3605	0.145
3.795-4.241	0.179	116	0.144	2405	0.145	2626	0.982	0.989	96.0015	0.142
4.241-4.894	0.154	100	0.126	2080	0.127	2306	0.986	0.991	94.536	0.128
4.894-5.985	0.198	88	0.165	1749	0.167	1974	0.983	0.985	93.0598	0.168
5.985-8.428	0.228	71	0.158	1423	0.161	1580	0.981	0.988	94.557	0.157
8.428-64.739	0.134	54	0.152	794	0.151	922	0.99	0.985	91.974	0.157

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