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- PDB-3ftp: Crystal structure of 3-Ketoacyl-(acyl-carrier-protein) reductase ... -

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Basic information

Entry
Database: PDB / ID: 3ftp
TitleCrystal structure of 3-Ketoacyl-(acyl-carrier-protein) reductase from Burkholderia pseudomallei at 2.05 A resolution
Components3-oxoacyl-[acyl-carrier protein] reductase
KeywordsOXIDOREDUCTASE / SSGCID / BURKHOLDERIA PSEUDOMALLEI / 3-KETOACYL-(ACYL-CARRIER-PROTEIN) REDUCTASE / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
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 / 3-oxoacyl-[acyl-carrier-protein] reductase
Similarity search - Component
Biological speciesBurkholderia pseudomallei (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: Plos One / Year: 2013
Title: Combining functional and structural genomics to sample the essential Burkholderia structome.
Authors: Baugh, L. / Gallagher, L.A. / Patrapuvich, R. / Clifton, M.C. / Gardberg, A.S. / Edwards, T.E. / Armour, B. / Begley, D.W. / Dieterich, S.H. / Dranow, D.M. / Abendroth, J. / Fairman, J.W. / ...Authors: Baugh, L. / Gallagher, L.A. / Patrapuvich, R. / Clifton, M.C. / Gardberg, A.S. / Edwards, T.E. / Armour, B. / Begley, D.W. / Dieterich, S.H. / Dranow, D.M. / Abendroth, J. / Fairman, J.W. / Fox, D. / Staker, B.L. / Phan, I. / Gillespie, A. / Choi, R. / Nakazawa-Hewitt, S. / Nguyen, M.T. / Napuli, A. / Barrett, L. / Buchko, G.W. / Stacy, R. / Myler, P.J. / Stewart, L.J. / Manoil, C. / Van Voorhis, W.C.
History
DepositionJan 13, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 27, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 30, 2013Group: Database references
Revision 1.3Sep 6, 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_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)112,3694
Polymers112,3694
Non-polymers00
Water8,647480
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12570 Å2
ΔGint-80 kcal/mol
Surface area32990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.620, 89.900, 120.240
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1116A1 - 250
2116B1 - 250
3116C1 - 250
4116D1 - 250

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Components

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


Mass: 28092.131 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia pseudomallei (bacteria) / Strain: 1710B / Gene: fabG, BPSL2440 / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q63S85, UniProt: Q3JQ67*PLUS, 3-oxoacyl-[acyl-carrier-protein] reductase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 480 / 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: 2.08 Å3/Da / Density % sol: 40.95 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 8
Details: PROPLEX-96 SCREEN C5: 100MM TRIS, 20% PEG 4000, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Aug 18, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.05→20 Å / Num. all: 59670 / Num. obs: 53192 / % possible obs: 89.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.3 % / Biso Wilson estimate: 39.59 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 17
Reflection shellResolution: 2.05→2.1 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 3.2 / Num. unique all: 4349 / % possible all: 84.5

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASERphasing
REFMAC5.5.0070refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1q7b, side chains modified by ccp4 program chainsaw

1q7b


Resolution: 2.05→19.68 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.911 / SU B: 5.586 / SU ML: 0.149 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.269 / ESU R Free: 0.223 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.268 2690 5.1 %RANDOM
Rwork0.208 ---
all0.211 52958 --
obs0.211 52958 88.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.48 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20 Å20 Å2
2---0.21 Å20 Å2
3---0.18 Å2
Refinement stepCycle: LAST / Resolution: 2.05→19.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6889 0 0 480 7369
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0226957
X-RAY DIFFRACTIONr_bond_other_d0.0010.024448
X-RAY DIFFRACTIONr_angle_refined_deg1.4981.9599445
X-RAY DIFFRACTIONr_angle_other_deg0.949310890
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3045975
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.4323.934244
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.649151070
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.0921552
X-RAY DIFFRACTIONr_chiral_restr0.0860.21155
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.028039
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021345
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_it0.831.54811
X-RAY DIFFRACTIONr_mcbond_other0.1911.52050
X-RAY DIFFRACTIONr_mcangle_it1.48527573
X-RAY DIFFRACTIONr_scbond_it2.31632146
X-RAY DIFFRACTIONr_scangle_it3.7734.51872
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Number: 2714 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDTypeRms dev position (Å)Weight position
Aloose positional0.335
Bloose positional0.435
Cloose positional0.45
Dloose positional0.345
Aloose thermal4.0710
Bloose thermal3.7810
Cloose thermal2.4710
Dloose thermal4.1110
LS refinement shellResolution: 2.05→2.1 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.411 200 -
Rwork0.357 3438 -
obs--84.37 %

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