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- PDB-2rjt: Crystal Structure Analysis of a Surface Entropy Reduction Mutant ... -

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Basic information

Entry
Database: PDB / ID: 2rjt
TitleCrystal Structure Analysis of a Surface Entropy Reduction Mutant of S. pneumoniae FabF
ComponentsBeta-ketoacyl-ACP synthase II
KeywordsTRANSFERASE / KASII / beta-ketoacyl acyl carrier protein synthase / thiolase / FabF / Acyltransferase
Function / homology
Function and homology information


beta-ketoacyl-[acyl-carrier-protein] synthase II / 3-oxoacyl-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process / metal ion binding
Similarity search - Function
3-oxoacyl-[acyl-carrier-protein] synthase 2 / Beta-ketoacyl synthase / Thiolase/Chalcone synthase / Peroxisomal Thiolase; Chain A, domain 1 / Ketosynthase family 3 (KS3) domain profile. / Beta-ketoacyl synthase / Beta-ketoacyl synthase, active site / Ketosynthase family 3 (KS3) active site signature. / Polyketide synthase, beta-ketoacyl synthase domain / Beta-ketoacyl synthase, N-terminal ...3-oxoacyl-[acyl-carrier-protein] synthase 2 / Beta-ketoacyl synthase / Thiolase/Chalcone synthase / Peroxisomal Thiolase; Chain A, domain 1 / Ketosynthase family 3 (KS3) domain profile. / Beta-ketoacyl synthase / Beta-ketoacyl synthase, active site / Ketosynthase family 3 (KS3) active site signature. / Polyketide synthase, beta-ketoacyl synthase domain / Beta-ketoacyl synthase, N-terminal / Beta-ketoacyl synthase, C-terminal / Beta-ketoacyl synthase, N-terminal domain / Beta-ketoacyl synthase, C-terminal domain / Thiolase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
3-oxoacyl-[acyl-carrier-protein] synthase 2
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.75 Å
AuthorsSoisson, S.M. / Parthasarathy, G. / Becker, J.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2008
Title: Surface-entropy reduction approaches to manipulate crystal forms of beta-ketoacyl acyl carrier protein synthase II from Streptococcus pneumoniae.
Authors: Parthasarathy, G. / Cummings, R. / Becker, J.W. / Soisson, S.M.
History
DepositionOct 15, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 22, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 28, 2012Group: Database references
Revision 1.3Oct 25, 2017Group: Refinement description / Category: software
Revision 1.4Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta-ketoacyl-ACP synthase II
D: Beta-ketoacyl-ACP synthase II
C: Beta-ketoacyl-ACP synthase II
B: Beta-ketoacyl-ACP synthase II


Theoretical massNumber of molelcules
Total (without water)181,8284
Polymers181,8284
Non-polymers00
Water32,2651791
1
A: Beta-ketoacyl-ACP synthase II
B: Beta-ketoacyl-ACP synthase II


Theoretical massNumber of molelcules
Total (without water)90,9142
Polymers90,9142
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5950 Å2
MethodPISA
2
D: Beta-ketoacyl-ACP synthase II
C: Beta-ketoacyl-ACP synthase II


Theoretical massNumber of molelcules
Total (without water)90,9142
Polymers90,9142
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.417, 115.872, 278.923
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein
Beta-ketoacyl-ACP synthase II / / 3-oxoacyl-Acyl-carrier-protein / synthase II


Mass: 45457.074 Da / Num. of mol.: 4 / Fragment: spFabF(1-412) / Mutation: E22A, E94A, E325A, E383A,E409A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Gene: fabF / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q9FBC2, beta-ketoacyl-[acyl-carrier-protein] synthase I
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1791 / 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: 2.5 Å3/Da / Density % sol: 50.75 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 5-12% PEG3350, 0.1M MES, 1% benzamidine-HCl, 10% ethylene glycol, 1mM DTT, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 14, 2004
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. obs: 180912 / % possible obs: 99.6 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.059 / Χ2: 1.052 / Net I/σ(I): 13.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.75-1.813.20.475175740.679197.9
1.81-1.893.30.344178840.726199.2
1.89-1.973.50.295180071.02199.8
1.97-2.073.90.175180430.9131100
2.07-2.24.50.122180440.9931100
2.2-2.384.70.106181201.261100
2.38-2.6150.068181251.0641100
2.61-2.995.50.054181821.1541100
2.99-3.776.90.05182871.0941100
3.77-507.10.049186461.169199.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
TNTrefinement
PDB_EXTRACT3data extraction
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
BUSTER-TNT2.1.1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→45.9 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.207 9058 5.01 %RANDOM
Rwork0.167 ---
obs0.169 180813 99.32 %-
Displacement parametersBiso mean: 30.05 Å2
Baniso -1Baniso -2Baniso -3
1-5.477 Å20 Å20 Å2
2---2.642 Å20 Å2
3----2.835 Å2
Refinement stepCycle: LAST / Resolution: 1.75→45.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12162 0 0 1791 13953
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.011124692
X-RAY DIFFRACTIONt_angle_deg1.332168532
X-RAY DIFFRACTIONt_dihedral_angle_d16.28622150
X-RAY DIFFRACTIONIMPROPER ANGLES (DEGREES)
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.0042888
X-RAY DIFFRACTIONt_gen_planes0.01518748
X-RAY DIFFRACTIONt_it1.5931246920
X-RAY DIFFRACTIONt_nbd0.1082055
LS refinement shellResolution: 1.75→1.86 Å / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.252 1437 5.1 %
Rwork0.22 26720 -
all0.222 28157 -
obs--99.32 %

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