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- PDB-5dov: Crystal structure of JamJ enoyl reductase (apo form) -

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Basic information

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


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 / : / Polyketide synthase dehydratase domain / PKS_PP_betabranch / Polyketide synthase, dehydratase domain superfamily / : / Polyketide and metazoan fatty acid synthase dehydratase (PKS/mFAS DH) domain profile. / Polyketide synthase, ketoreductase domain / KR domain / Enoyl-CoA hydratase/isomerase / Enoyl-CoA hydratase/isomerase / Quinone Oxidoreductase; Chain A, domain 1 / Medium-chain alcohol dehydrogenases, catalytic domain / 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 / PKS_KR / Beta-ketoacyl synthase, active site / Ketosynthase family 3 (KS3) active site signature. / 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
Biological speciesLyngbya majuscula (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,9544
Polymers80,7702
Non-polymers1842
Water7,458414
1
A: JamJ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,5693
Polymers40,3851
Non-polymers1842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: JamJ


Theoretical massNumber of molelcules
Total (without water)40,3851
Polymers40,3851
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.905, 57.166, 66.132
Angle α, β, γ (deg.)95.27, 106.75, 105.12
Int Tables number1
Space group name H-MP1

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Components

#1: Protein JamJ


Mass: 40385.105 Da / Num. of mol.: 2 / 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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 414 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.17 Å3/Da / Density % sol: 43.22 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 30% PEG 4000, 0.2 M MgCl2 and 0.1 M Tris pH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 15, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.8→46.5 Å / Num. obs: 63164 / % possible obs: 95.2 % / Redundancy: 2.2 % / Rmerge(I) obs: 0.074 / Net I/σ(I): 14.2

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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: 5DP1

5dp1


Resolution: 1.8→46.5 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.948 / SU B: 5.844 / SU ML: 0.09 / Cross valid method: THROUGHOUT / ESU R: 0.145 / ESU R Free: 0.135 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2234 2949 5 %RANDOM
Rwork0.1837 ---
obs0.18575 55547 93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.793 Å2
Baniso -1Baniso -2Baniso -3
1--0.6 Å2-0.42 Å2-0.82 Å2
2---0.31 Å20.26 Å2
3---1.25 Å2
Refinement stepCycle: 1 / Resolution: 1.8→46.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5315 0 12 414 5741
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0195471
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3431.9447423
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9145681
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.03424.762252
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.16415952
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4911524
X-RAY DIFFRACTIONr_chiral_restr0.0940.2841
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214110
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_it1.4592.1142694
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.3673.163367
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.0462.4622777
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined6.25819.0678508
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: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.312 227 -
Rwork0.268 4176 -
obs--94.14 %
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)
10.28010.00830.05410.4422-0.4440.9102-0.00030.0251-0.0685-0.0736-0.0248-0.05280.03460.06250.0250.0330.00340.01650.0457-0.01340.029919.29899.2997-14.9406
20.9330.1714-0.2010.2913-0.19780.14390.05260.01380.15230.0229-0.00160.06-0.0155-0.0027-0.0510.02550.00440.02230.04490.00590.046713.496634.0533-13.2461
31.479-0.14010.10731.1952-0.92210.7170.07860.12590.2278-0.1122-0.0936-0.00250.08420.09240.01490.03-0.00950.02030.09040.03570.06727.186739.6126-20.4557
40.5435-0.0899-0.05620.84870.13880.71940.0452-0.01630.0273-0.0492-0.05150.049-0.035-0.06320.00630.01050.0070.00420.02370.00440.01212.175721.3382-12.3113
50.24440.09040.11360.32990.05330.2638-0.02530.01160.03080.01540.0623-0.010.0114-0.0393-0.0370.01570.00010.00710.05070.0040.052938.025447.33842.5906
60.4669-0.08770.10940.54030.12420.1422-0.1023-0.0225-0.03710.07250.0702-0.0076-0.02240.00250.03210.05320.01420.0130.04810.00380.038544.894624.996317.9315
70.5517-0.79660.26571.83390.23240.7337-0.01180.0139-0.0229-0.08420.00890-0.0940.04090.00290.0292-0.02470.01670.0355-0.00670.043938.621815.7485.766
80.7566-0.0095-0.34030.8791-0.36430.51-0.037-0.00970.05680.14350.0274-0.0392-0.00720.01310.00960.03450.0112-0.0060.0238-0.00810.011141.562639.814413.9748
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 114
2X-RAY DIFFRACTION2A115 - 208
3X-RAY DIFFRACTION3A209 - 275
4X-RAY DIFFRACTION4A276 - 335
5X-RAY DIFFRACTION5B-2 - 117
6X-RAY DIFFRACTION6B118 - 232
7X-RAY DIFFRACTION7B233 - 273
8X-RAY DIFFRACTION8B274 - 335

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