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- PDB-5doz: Crystal structure of JamJ enoyl reductase (NADPH bound) -

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Basic information

Entry
Database: PDB / ID: 5doz
TitleCrystal structure of JamJ enoyl reductase (NADPH bound)
ComponentsJamJ
KeywordsOXIDOREDUCTASE / Enoyl reductase / Polyketide synthase / NADPH / cyclopropane
Function / homology
Function and homology information


(3S)-3-hydroxyacyl-CoA dehydrogenase (NAD+) activity / DIM/DIP cell wall layer assembly / fatty acid synthase activity / phosphopantetheine binding / 3-oxoacyl-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process / nucleotide binding / plasma membrane / cytoplasm
Similarity search - Function
Methyltransferase, Helix-turn-helix domain / : / Beta-ketoacyl synthase-like, N-terminal / CurL-like, PKS C-terminal / Zinc-binding dehydrogenase / Methyltransferase type 12 / Methyltransferase domain / Enoyl-CoA hydratase/isomerase, conserved site / Enoyl-CoA hydratase/isomerase signature. / : ...Methyltransferase, Helix-turn-helix domain / : / Beta-ketoacyl synthase-like, N-terminal / CurL-like, PKS C-terminal / Zinc-binding dehydrogenase / Methyltransferase type 12 / Methyltransferase domain / Enoyl-CoA hydratase/isomerase, conserved site / Enoyl-CoA hydratase/isomerase signature. / : / Polyketide synthase dehydratase N-terminal domain / Polyketide synthase, dehydratase domain / PKS_DH / PKS_PP_betabranch / : / Polyketide synthase dehydratase domain / : / Polyketide and metazoan fatty acid synthase dehydratase (PKS/mFAS DH) domain profile. / Polyketide synthase, dehydratase domain superfamily / Polyketide synthase, ketoreductase domain / KR domain / Quinone Oxidoreductase; Chain A, domain 1 / Medium-chain alcohol dehydrogenases, catalytic domain / Enoyl-CoA hydratase/isomerase / Enoyl-CoA hydratase/isomerase / Malonyl-CoA ACP transacylase, ACP-binding / : / Acyl transferase / Acyl transferase domain / Acyl transferase domain in polyketide synthase (PKS) enzymes. / Acyl transferase domain superfamily / Alcohol dehydrogenase, N-terminal / Alcohol dehydrogenase GroES-like domain / Acyl transferase/acyl hydrolase/lysophospholipase / Polyketide synthase, enoylreductase domain / Enoylreductase / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / Beta-ketoacyl synthase, active site / Ketosynthase family 3 (KS3) active site signature. / PKS_KR / Beta-ketoacyl synthase / Ketosynthase family 3 (KS3) domain profile. / Beta-ketoacyl synthase, N-terminal / Beta-ketoacyl synthase, C-terminal / Polyketide synthase, beta-ketoacyl synthase domain / Beta-ketoacyl synthase, N-terminal domain / Beta-ketoacyl synthase, C-terminal domain / GroES-like superfamily / ClpP/crotonase-like domain superfamily / Thiolase-like / Phosphopantetheine attachment site / Phosphopantetheine attachment site. / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Chem-NDP / JamJ
Similarity search - Component
Biological speciesLyngbya majuscula (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.26 Å
AuthorsKhare, D. / Smith, J.L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)DK-042303 United States
CitationJournal: Structure / Year: 2015
Title: Structural Basis for Cyclopropanation by a Unique Enoyl-Acyl Carrier Protein Reductase.
Authors: Khare, D. / Hale, W.A. / Tripathi, A. / Gu, L. / Sherman, D.H. / Gerwick, W.H. / Hakansson, K. / Smith, J.L.
History
DepositionSep 11, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 18, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 16, 2015Group: Database references
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 2023Group: 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 viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: JamJ
B: JamJ
C: JamJ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,0367
Polymers113,7403
Non-polymers2,2954
Water6,503361
1
A: JamJ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,7183
Polymers37,9131
Non-polymers8042
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: JamJ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,6592
Polymers37,9131
Non-polymers7451
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: JamJ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,6592
Polymers37,9131
Non-polymers7451
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)110.702, 110.702, 92.826
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

#1: Protein JamJ


Mass: 37913.445 Da / Num. of mol.: 3 / Fragment: UNP residues 260-594
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lyngbya majuscula (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: Q6E7K0
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 361 / Source method: isolated from a natural source / Formula: H2O
Source detailsAs per the authors the source organism is Moorea producens 3L. Moorea producens 3L was formerly ...As per the authors the source organism is Moorea producens 3L. Moorea producens 3L was formerly known as Lyngbya majuscula

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.89 Å3/Da / Density % sol: 57.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 20% PEG 3350, 0.25 M sodium acetate, 100 mM Bis Tris propane pH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 19, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.5
11-h,-k,l20.5
ReflectionResolution: 2.25→45.6 Å / Num. obs: 59866 / % possible obs: 99.6 % / Redundancy: 2.1 % / Rmerge(I) obs: 0.073 / Net I/σ(I): 12.3
Reflection shellHighest resolution: 2.25 Å / Rmerge(I) obs: 0.609 / Mean I/σ(I) obs: 1.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5DOV

5dov


Resolution: 2.26→42.59 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.94 / SU B: 5.801 / SU ML: 0.087 / Cross valid method: THROUGHOUT / ESU R: 0.053 / ESU R Free: 0.041 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.21718 3015 5.1 %RANDOM
Rwork0.18045 ---
obs0.18234 56585 99.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 45.113 Å2
Baniso -1Baniso -2Baniso -3
1-7.49 Å20 Å20 Å2
2--7.49 Å20 Å2
3----14.99 Å2
Refinement stepCycle: LAST / Resolution: 2.26→42.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7905 0 148 361 8414
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0198238
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0341.96611193
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9915993
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.79224.72375
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.271151407
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.7611536
X-RAY DIFFRACTIONr_chiral_restr0.0680.21257
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0216148
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6913.1373982
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.2274.7034971
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.5643.2254256
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined4.47426.16212631
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.256→2.314 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.32 204 -
Rwork0.246 4128 -
obs--98.68 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°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)
10.92960.22060.92711.17560.46652.1042-0.0042-0.26390.1162-0.0993-0.04170.0696-0.0984-0.22370.04590.05670.01610.01430.1383-0.03590.15220.143258.33032.231
20.27320.30660.25740.39240.28960.38990.05350.0216-0.049-0.0070.0033-0.03880.01670.0278-0.05670.1212-0.0014-0.0080.11470.00020.180114.075851.552-7.2657
30.98680.4120.31350.6099-0.25540.95740.0317-0.03150.01030.03020.0593-0.0522-0.1510.1603-0.0910.0545-0.06960.01940.1461-0.01240.191131.211166.35230.7178
40.85180.40110.18590.72720.28430.6083-0.0008-0.0035-0.0304-0.0435-0.00480.01320.01020.05950.00570.0940.00010.00510.07220.0060.147117.055555.848-3.0386
51.1794-0.1758-0.40541.14411.59142.28650.1277-0.00710.04250.1401-0.16660.06480.1774-0.15810.03890.0947-0.02670.02070.1233-0.00280.15726.4509-3.10816.1888
60.0243-0.1111-0.05141.15130.11170.63190.01080.030.0119-0.02050.0188-0.0429-0.0010.0672-0.02950.08860.0044-0.01030.13260.00580.174418.598.09078.0355
70.1778-0.07580.39591.18660.23291.384-0.0132-0.02550.0385-0.03630.0478-0.0566-0.2667-0.0576-0.03460.1605-0.00120.00880.02960.03590.17913.735828.289616.2588
80.3376-0.2834-0.08021.46420.33590.53070.02710.02850.0046-0.0225-0.0145-0.0189-0.03230.0592-0.01270.06430.007-0.00190.09710.01250.144915.25210.953212.3607
91.44330.23191.15333.231-4.40297.56570.19530.3143-0.0972-0.0771-0.1026-0.06630.29990.4963-0.09270.08810.11450.04780.195-0.0160.170956.365921.676542.5612
100.6428-0.39880.55120.757-1.00431.60190.1585-0.07080.04640.0005-0.1210.05160.08660.053-0.03750.1388-0.0456-0.01160.1166-0.0640.105439.066726.651149.4948
111.845-0.81561.22252.0124-0.8962.1548-0.1127-0.44860.33130.1813-0.0230.0026-0.3034-0.33450.13580.0918-0.00020.03380.1567-0.11550.10229.628138.658749.5629
123.39821.9608-1.1141.183-0.64190.3652-0.06820.2053-0.0067-0.20480.05870.05020.0216-0.06850.00950.50840.2026-0.16930.0971-0.06970.056641.112723.605534.598
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 70
2X-RAY DIFFRACTION2A71 - 171
3X-RAY DIFFRACTION3A172 - 259
4X-RAY DIFFRACTION4A260 - 335
5X-RAY DIFFRACTION5B4 - 87
6X-RAY DIFFRACTION6B88 - 171
7X-RAY DIFFRACTION7B172 - 258
8X-RAY DIFFRACTION8B259 - 335
9X-RAY DIFFRACTION9C4 - 34
10X-RAY DIFFRACTION10C35 - 191
11X-RAY DIFFRACTION11C192 - 309
12X-RAY DIFFRACTION12C310 - 335

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