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

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Basic information

Entry
Database: PDB / ID: 4dml
Title3-oxoacyl-[acyl-carrier-protein] reductase from Synechococcus elongatus PCC 7942
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-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
3-oxoacyl-[acyl-carrier-protein] reductase
Similarity search - Component
Biological speciesSynechococcus elongatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.5 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
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
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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


Theoretical massNumber of molelcules
Total (without water)110,7434
Polymers110,7434
Non-polymers00
Water32418
1
A: 3-oxoacyl-[acyl-carrier-protein] reductase
C: 3-oxoacyl-[acyl-carrier-protein] reductase


Theoretical massNumber of molelcules
Total (without water)55,3722
Polymers55,3722
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3110 Å2
ΔGint-22 kcal/mol
Surface area19350 Å2
MethodPISA
2
B: 3-oxoacyl-[acyl-carrier-protein] reductase
D: 3-oxoacyl-[acyl-carrier-protein] reductase


Theoretical massNumber of molelcules
Total (without water)55,3722
Polymers55,3722
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3080 Å2
ΔGint-21 kcal/mol
Surface area19150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.9110, 117.9320, 125.3290
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 18 / 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: 2.13 Å3/Da / Density % sol: 42.32 %
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: 0.9795, 0.9796, 0.9718
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 14, 2007
RadiationMonochromator: GRAPHITE / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97951
20.97961
30.97181
ReflectionResolution: 2.5→43.34 Å / Num. all: 33516 / Num. obs: 31758 / % possible obs: 94.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellHighest resolution: 2.5 Å / % possible all: 94.8

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Processing

Software
NameVersionClassification
HKL-2000data collection
SOLVEphasing
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 2.5→43.34 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.89 / SU B: 22.588 / SU ML: 0.224 / Cross valid method: THROUGHOUT / ESU R: 0.653 / ESU R Free: 0.311 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26201 1695 5.1 %RANDOM
Rwork0.19712 ---
obs0.20035 31758 99.87 %-
all-33516 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.681 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å20 Å2
2--0.02 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.5→43.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6898 0 0 18 6916
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0226963
X-RAY DIFFRACTIONr_angle_refined_deg1.7491.9719440
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7075951
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.27623.735249
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.338151136
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.7691556
X-RAY DIFFRACTIONr_chiral_restr0.1170.21157
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025124
X-RAY DIFFRACTIONr_mcbond_it0.7861.54711
X-RAY DIFFRACTIONr_mcangle_it1.48427432
X-RAY DIFFRACTIONr_scbond_it2.51232252
X-RAY DIFFRACTIONr_scangle_it4.2314.52008
LS refinement shellResolution: 2.501→2.566 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.421 140 -
Rwork0.303 2281 -
obs-31758 98.29 %
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)
10.51980.49350.40990.49070.39320.61060.1423-0.03940.02850.1572-0.07610.00210.08710.0054-0.06610.187-0.0126-0.00890.06570.00680.081938.970554.615444.4521
20.4980.43440.11510.97610.18880.18220.03720.07840.1180.06280.01750.20050.10050.0591-0.05470.0690.0307-0.03260.090.02860.161914.252731.779517.8105
30.79320.68330.70990.62150.58810.86510.3706-0.36720.20670.3503-0.4040.18060.2138-0.27480.03350.2918-0.20410.18340.2781-0.10660.123412.228739.72947.6145
40.48590.57570.13170.69040.11920.397-0.05880.09470.041-0.04540.10760.0624-0.08380.1024-0.04880.0682-0.00550.010.14580.03470.093536.277852.444213.6117
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 249
2X-RAY DIFFRACTION1A301 - 302
3X-RAY DIFFRACTION2B4 - 249
4X-RAY DIFFRACTION2B301 - 304
5X-RAY DIFFRACTION3C4 - 249
6X-RAY DIFFRACTION3C301 - 306
7X-RAY DIFFRACTION4D4 - 248
8X-RAY DIFFRACTION4D301 - 306

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