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- PDB-2nm0: Crystal Structure of SCO1815: a Beta-Ketoacyl-Acyl Carrier Protei... -

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Basic information

Entry
Database: PDB / ID: 2nm0
TitleCrystal Structure of SCO1815: a Beta-Ketoacyl-Acyl Carrier Protein Reductase from Streptomyces coelicolor A3(2)
ComponentsProbable 3-oxacyl-(Acyl-carrier-protein) reductase
KeywordsOXIDOREDUCTASE
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 speciesStreptomyces coelicolor (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 Å
AuthorsKhosla, C. / Tang, Y. / Lee, H.Y. / Tang, Y. / Kim, C.Y. / Mathews, I.I.
Citation
Journal: Biochemistry / Year: 2006
Title: Structural and functional studies on SCO1815: a beta-ketoacyl-acyl carrier protein reductase from Streptomyces coelicolor A3(2).
Authors: Tang, Y. / Lee, H.Y. / Tang, Y. / Kim, C.Y. / Mathews, I. / Khosla, C.
#1: Journal: Biochemistry / Year: 2003
Title: Ketosynthases in the initiation and elongation modules of aromatic polyketide synthases have orthogonal acyl carrier protein specificity
Authors: Tang, Y. / Lee, T.S. / Khobayashi, S. / Khosla, C.
#2: Journal: Biochemistry / Year: 2004
Title: The acyltransferase homologue from the initiation module of the R1128 polyketide synthase is an acyl-ACP thioesterase that edits acetyl primer units
Authors: Tang, Y. / Khppisch, A.T. / Khosla, C.
History
DepositionOct 20, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 2, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Jul 24, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.4Aug 30, 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 / struct_ncs_dom_lim / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Probable 3-oxacyl-(Acyl-carrier-protein) reductase
B: Probable 3-oxacyl-(Acyl-carrier-protein) reductase


Theoretical massNumber of molelcules
Total (without water)53,9492
Polymers53,9492
Non-polymers00
Water5,459303
1
A: Probable 3-oxacyl-(Acyl-carrier-protein) reductase
B: Probable 3-oxacyl-(Acyl-carrier-protein) reductase

A: Probable 3-oxacyl-(Acyl-carrier-protein) reductase
B: Probable 3-oxacyl-(Acyl-carrier-protein) reductase


Theoretical massNumber of molelcules
Total (without water)107,8984
Polymers107,8984
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_554-x,-x+y,-z-2/31
Buried area9870 Å2
ΔGint-70 kcal/mol
Surface area33870 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)113.759, 113.759, 73.937
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: GLY / End label comp-ID: GLY / Refine code: 4 / Auth seq-ID: 1 - 233 / Label seq-ID: 20 - 252

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Probable 3-oxacyl-(Acyl-carrier-protein) reductase / Beta-Ketoacyl-Acyl Carrier Protein Reductase


Mass: 26974.617 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces coelicolor (bacteria) / Strain: A3(2) / Gene: SCO1815 / Plasmid: pYT3 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
References: UniProt: Q9S274, 3-oxoacyl-[acyl-carrier-protein] reductase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 303 / 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: 2.56 Å3/Da / Density % sol: 52.05 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 20% PEG MME 2000, 10 mM NiCl2, 100 mM Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 1.03155 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 26, 2004 / Details: mirrors
RadiationMonochromator: Single Crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03155 Å / Relative weight: 1
ReflectionResolution: 1.99→49.3 Å / Num. all: 37985 / Num. obs: 37985 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 14.4 % / Rmerge(I) obs: 0.08 / Rsym value: 0.08 / Net I/σ(I): 14.9
Reflection shellResolution: 1.99→2.07 Å / Redundancy: 14.5 % / Rmerge(I) obs: 0.497 / Mean I/σ(I) obs: 7.8 / Rsym value: 0.496 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
HKL-2000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1IO1

1io1


Resolution: 1.99→27.33 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.94 / SU B: 2.975 / SU ML: 0.087 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.155 / ESU R Free: 0.143 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2238 1895 5 %RANDOM
Rwork0.18866 ---
all0.19042 36058 --
obs0.19042 36058 99.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.95 Å2
Baniso -1Baniso -2Baniso -3
1--0.26 Å2-0.13 Å20 Å2
2---0.26 Å20 Å2
3---0.39 Å2
Refinement stepCycle: LAST / Resolution: 1.99→27.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3268 0 0 303 3571
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0223306
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3961.9694468
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.445436
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.06523.235136
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.79815548
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7151532
X-RAY DIFFRACTIONr_chiral_restr0.0980.2528
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022476
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.210.21503
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3040.22344
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1930.2276
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2570.273
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2930.219
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2661.52230
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.10523466
X-RAY DIFFRACTIONr_scbond_it2.97931191
X-RAY DIFFRACTIONr_scangle_it4.6944.51002
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 1635 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
medium positional0.390.5
medium thermal1.852
LS refinement shellResolution: 1.99→2.04 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.26 114 -
Rwork0.193 2515 -
obs--95.36 %

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