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- PDB-4dmm: 3-oxoacyl-[acyl-carrier-protein] reductase from Synechococcus elo... -

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Basic information

Entry
Database: PDB / ID: 4dmm
Title3-oxoacyl-[acyl-carrier-protein] reductase from Synechococcus elongatus PCC 7942 in complex with NADP
Components3-oxoacyl-[acyl-carrier-protein] reductase
KeywordsOXIDOREDUCTASE / Rossmann Fold / OXOACYL-ACP REDUCTASE / NADP binding / Fatty acid biosynthsis
Function / homology
Function and homology information


3-oxoacyl-[acyl-carrier-protein] reductase / 3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity / fatty acid biosynthetic process / NAD binding
Similarity search - Function
3-oxoacyl-(acyl-carrier-protein) reductase / PKS_KR / Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / Enoyl-(Acyl carrier protein) reductase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 3-oxoacyl-[acyl-carrier-protein] reductase
Similarity search - Component
Biological speciesSynechococcus elongatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.38 Å
AuthorsChen, C. / Zhuang, N.N. / Lee, K.H.
CitationJournal: to be published
Title: 3-oxoacyl-[acyl-carrier-protein] reductase from Synechococcus elongatus PCC 7942 in complex with NADP
Authors: Chen, C. / Zhuang, N.N. / Lee, K.H.
History
DepositionFeb 8, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 22, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 3-oxoacyl-[acyl-carrier-protein] reductase
B: 3-oxoacyl-[acyl-carrier-protein] reductase
C: 3-oxoacyl-[acyl-carrier-protein] reductase
D: 3-oxoacyl-[acyl-carrier-protein] reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,0698
Polymers110,7434
Non-polymers2,3264
Water3,387188
1
A: 3-oxoacyl-[acyl-carrier-protein] reductase
B: 3-oxoacyl-[acyl-carrier-protein] reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,2114
Polymers55,3722
Non-polymers8392
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4550 Å2
ΔGint-40 kcal/mol
Surface area19000 Å2
MethodPISA
2
C: 3-oxoacyl-[acyl-carrier-protein] reductase
D: 3-oxoacyl-[acyl-carrier-protein] reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,8584
Polymers55,3722
Non-polymers1,4872
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5660 Å2
ΔGint-24 kcal/mol
Surface area18610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.9790, 116.9240, 125.5170
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
3-oxoacyl-[acyl-carrier-protein] reductase


Mass: 27685.752 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechococcus elongatus (bacteria) / Strain: PCC 7942 / Gene: Synpcc7942_0684 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q31QF3, 3-oxoacyl-[acyl-carrier-protein] reductase
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE / Nicotinamide adenine dinucleotide phosphate


Mass: 743.405 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 188 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.12 Å3/Da / Density % sol: 41.97 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 21% PEG3350, 0.1M HEPES, 0.16M Lithium sulfate monohydrate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 6C1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 14, 2007
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.38→42.78 Å / Num. all: 38351 / Num. obs: 36373 / % possible obs: 94.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellHighest resolution: 2.38 Å / % possible all: 94.8

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Processing

Software
NameVersionClassification
HKL-2000data collection
AMoREphasing
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.38→42.78 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.932 / SU B: 14.248 / SU ML: 0.151 / Cross valid method: THROUGHOUT / ESU R: 0.395 / ESU R Free: 0.234 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21553 1914 5 %RANDOM
Rwork0.16383 ---
obs0.16642 36373 99.78 %-
all-38351 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.156 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å20 Å20 Å2
2---0.02 Å20 Å2
3---0.05 Å2
Refinement stepCycle: LAST / Resolution: 2.38→42.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6922 0 149 188 7259
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0227147
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0451.9999718
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7315956
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.76223.76250
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.142151140
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7061556
X-RAY DIFFRACTIONr_chiral_restr0.1570.21195
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025201
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_it1.0331.54728
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.90927459
X-RAY DIFFRACTIONr_scbond_it3.19832419
X-RAY DIFFRACTIONr_scangle_it5.2244.52259
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.383→2.444 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 146 -
Rwork0.187 2555 -
obs-36373 97.61 %
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)
10.38670.21690.2240.53130.1460.17620.09550.0256-0.0799-0.0115-0.04560.02680.0186-0.0017-0.04990.08330.0174-0.03650.0589-0.0070.099315.08729.955217.3172
20.3040.06220.09560.33510.10360.54940.02970.09240.0162-0.0263-0.0099-0.0165-0.07930.0894-0.01980.07190.00490.01470.10830.040.068936.802751.11914.5198
31.36530.4950.46760.21870.18010.17870.1472-0.17910.05510.05-0.1123-0.03090.0763-0.0598-0.0350.1226-0.0276-0.04180.07370.02690.119539.270151.402445.5617
41.0730.34010.37690.32950.14220.25640.2196-0.3185-0.04530.0358-0.18630.02030.0191-0.1317-0.03340.1369-0.0848-0.00730.16180.01810.029612.548736.197547.4959
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 249
2X-RAY DIFFRACTION1A301
3X-RAY DIFFRACTION1A401 - 465
4X-RAY DIFFRACTION2B4 - 249
5X-RAY DIFFRACTION2B301
6X-RAY DIFFRACTION2B401 - 458
7X-RAY DIFFRACTION3C4 - 249
8X-RAY DIFFRACTION3C301
9X-RAY DIFFRACTION3C401 - 438
10X-RAY DIFFRACTION4D4 - 249
11X-RAY DIFFRACTION4D301
12X-RAY DIFFRACTION4D401 - 427

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