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- PDB-1ox0: The crystal structure of beta-ketoacyl-[acyl carrier protein] syn... -

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Basic information

Entry
Database: PDB / ID: 1ox0
TitleThe crystal structure of beta-ketoacyl-[acyl carrier protein] synthase II from Streptococcus pneumoniae
ComponentsBeta ketoacyl-acyl carrier protein synthase
KeywordsTRANSFERASE
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 / Beta-ketoacyl synthase / Beta-ketoacyl synthase, active site / Ketosynthase family 3 (KS3) active site signature. / Ketosynthase family 3 (KS3) domain profile. / 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 / Beta-ketoacyl synthase / Beta-ketoacyl synthase, active site / Ketosynthase family 3 (KS3) active site signature. / Ketosynthase family 3 (KS3) domain profile. / 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 / Resolution: 1.3 Å
AuthorsPrice, A.C. / Rock, C.O. / White, S.W.
CitationJournal: J.Bacteriol. / Year: 2003
Title: The 1.3-Angstrom-Resolution Crystal Structure of beta-Ketoacyl-Acyl Carrier Protein Synthase II from Streptococcus pneumoniae.
Authors: Price, A.C. / Rock, C.O. / White, S.W.
History
DepositionMar 31, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 22, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Jan 31, 2018Group: Advisory / Experimental preparation / Category: exptl_crystal_grow / pdbx_unobs_or_zero_occ_atoms / Item: _exptl_crystal_grow.temp
Revision 1.4Feb 14, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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

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Assembly

Deposited unit
A: Beta ketoacyl-acyl carrier protein synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,0673
Polymers46,0191
Non-polymers492
Water5,855325
1
A: Beta ketoacyl-acyl carrier protein synthase
hetero molecules

A: Beta ketoacyl-acyl carrier protein synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,1346
Polymers92,0372
Non-polymers974
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area6910 Å2
ΔGint-65 kcal/mol
Surface area27140 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)63.666, 89.973, 62.202
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-761-

HOH

21A-781-

HOH

DetailsThe biological assembly is a dimer generated from the monomer in the asymmetric unit by the operation: 1-x, -y, z .

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Components

#1: Protein Beta ketoacyl-acyl carrier protein synthase / Beta ketoacyl-acyl carrier protein synthase II


Mass: 46018.551 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Strain: RN4220 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9FBC2, beta-ketoacyl-[acyl-carrier-protein] synthase I
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 325 / 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: 1.93 Å3/Da / Density % sol: 36.43 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7.75
Details: PEG 3350, magnesium acetate, Tris HCl, pH 7.75, VAPOR DIFFUSION, HANGING DROP, temperature 392K
Crystal grow
*PLUS
pH: 7.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
150 mMTris-HCl1reservoirpH7.5
21 mMEDTA1reservoir
31 mMdithiothreitol1reservoir
420 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.97919 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 17, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97919 Å / Relative weight: 1
ReflectionResolution: 1.3→15 Å / Num. all: 85878 / Num. obs: 85878 / % possible obs: 99.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 2
Reflection shellResolution: 1.3→1.32 Å / % possible all: 99.8
Reflection
*PLUS
Num. obs: 88233 / Redundancy: 8.5 % / Num. measured all: 1002530 / Rmerge(I) obs: 0.08
Reflection shell
*PLUS
% possible obs: 99.8 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.351 / Mean I/σ(I) obs: 3.6

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.3→15 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.972 / SU B: 0.538 / SU ML: 0.024 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.045 / ESU R Free: 0.042 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16005 2038 2.3 %RANDOM
Rwork0.13775 ---
all0.1382 85878 --
obs0.13825 85878 99.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 11.23 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å20 Å20 Å2
2---0.52 Å20 Å2
3---0.45 Å2
Refinement stepCycle: LAST / Resolution: 1.3→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3111 0 2 325 3438
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0213134
X-RAY DIFFRACTIONr_bond_other_d0.0250.022812
X-RAY DIFFRACTIONr_angle_refined_deg1.8131.944247
X-RAY DIFFRACTIONr_angle_other_deg1.04136534
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.275412
X-RAY DIFFRACTIONr_chiral_restr0.120.2477
X-RAY DIFFRACTIONr_gen_planes_refined0.0210.023577
X-RAY DIFFRACTIONr_gen_planes_other0.0360.02626
X-RAY DIFFRACTIONr_nbd_refined0.2470.2578
X-RAY DIFFRACTIONr_nbd_other0.2540.23114
X-RAY DIFFRACTIONr_nbtor_other0.0860.21616
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1260.2154
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3990.224
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3610.294
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1160.210
X-RAY DIFFRACTIONr_mcbond_it1.561.52043
X-RAY DIFFRACTIONr_mcangle_it2.26323261
X-RAY DIFFRACTIONr_scbond_it3.44231091
X-RAY DIFFRACTIONr_scangle_it4.9024.5986
X-RAY DIFFRACTIONr_rigid_bond_restr1.71923134
X-RAY DIFFRACTIONr_sphericity_free9.1663.5326
X-RAY DIFFRACTIONr_sphericity_bonded4.2623.53071
LS refinement shellResolution: 1.301→1.335 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.206 149
Rwork0.155 6168
Refinement
*PLUS
Highest resolution: 1.3 Å / Lowest resolution: 15 Å / Num. reflection obs: 83903 / Rfactor Rfree: 0.16 / Rfactor Rwork: 0.139
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.02
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.81

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