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- PDB-3kzu: Crystal structure of 3-oxoacyl-(acyl carrier protein) synthase II... -

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Basic information

Entry
Database: PDB / ID: 3kzu
TitleCrystal structure of 3-oxoacyl-(acyl carrier protein) synthase II from Brucella melitensis
Components3-oxoacyl-(Acyl-carrier-protein) synthase ii
KeywordsTRANSFERASE / acyl carrier protein / Seattle Structural Genomics Center for Infectious Disease / SSGCID / 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 / cytosol
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, active site / Ketosynthase family 3 (KS3) active site signature. / Beta-ketoacyl synthase / Ketosynthase family 3 (KS3) domain profile. / Beta-ketoacyl synthase, N-terminal / Beta-ketoacyl synthase, C-terminal ...3-oxoacyl-[acyl-carrier-protein] synthase 2 / Beta-ketoacyl synthase / Thiolase/Chalcone synthase / Peroxisomal Thiolase; Chain A, domain 1 / Beta-ketoacyl synthase, active site / Ketosynthase family 3 (KS3) active site signature. / Beta-ketoacyl synthase / Ketosynthase family 3 (KS3) domain profile. / Beta-ketoacyl synthase, N-terminal / Beta-ketoacyl synthase, C-terminal / Polyketide synthase, beta-ketoacyl synthase domain / 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 speciesBrucella melitensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: TO BE PUBLISHED
Title: Crystal structure of 3-oxoacyl-(acyl carrier protein) synthase II from Brucella melitensis
Authors: Edwards, T.E. / Abendroth, J. / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
History
DepositionDec 8, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 15, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: 3-oxoacyl-(Acyl-carrier-protein) synthase ii
B: 3-oxoacyl-(Acyl-carrier-protein) synthase ii
C: 3-oxoacyl-(Acyl-carrier-protein) synthase ii
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,9909
Polymers135,5163
Non-polymers4746
Water22,8431268
1
A: 3-oxoacyl-(Acyl-carrier-protein) synthase ii
B: 3-oxoacyl-(Acyl-carrier-protein) synthase ii
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,6606
Polymers90,3442
Non-polymers3164
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6930 Å2
ΔGint-58 kcal/mol
Surface area25570 Å2
MethodPISA
2
C: 3-oxoacyl-(Acyl-carrier-protein) synthase ii
hetero molecules

C: 3-oxoacyl-(Acyl-carrier-protein) synthase ii
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,6606
Polymers90,3442
Non-polymers3164
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area6670 Å2
ΔGint-58 kcal/mol
Surface area25400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.020, 62.320, 177.720
Angle α, β, γ (deg.)90.000, 109.180, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1114A0 - 420
2114B0 - 420
3114C0 - 420

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Components

#1: Protein 3-oxoacyl-(Acyl-carrier-protein) synthase ii


Mass: 45171.855 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brucella melitensis (bacteria) / Gene: BMEI1473 / Production host: Escherichia coli (E. coli)
References: UniProt: Q8YFP7, beta-ketoacyl-[acyl-carrier-protein] synthase I
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1268 / 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: 2.28 Å3/Da / Density % sol: 45.99 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Hampton CSHT condition B5: 0.2 M lithium sulfate, 0.1 M Tris pH 8.5, 30% w/v PEG 4000, 25% ethylene glycol as cryo-protectant, 51.0 mg/mL protein, crystal tracking ID 205856b5, VAPOR ...Details: Hampton CSHT condition B5: 0.2 M lithium sulfate, 0.1 M Tris pH 8.5, 30% w/v PEG 4000, 25% ethylene glycol as cryo-protectant, 51.0 mg/mL protein, crystal tracking ID 205856b5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 0.979464 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 19, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979464 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. all: 536301 / Num. obs: 119229 / % possible obs: 96.7 % / Observed criterion σ(I): -3 / Redundancy: 4.5 % / Biso Wilson estimate: 22.489 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 21.32
Reflection shellResolution: 1.75→1.8 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.285 / Mean I/σ(I) obs: 4.4 / Num. measured obs: 32363 / Num. unique all: 8234 / Num. unique obs: 8234 / % possible all: 90.5

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Phasing

Phasing MRRfactor: 37.93 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3 Å42.63 Å
Translation3 Å42.63 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3E60

3e60


Resolution: 1.75→50 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.953 / WRfactor Rfree: 0.165 / WRfactor Rwork: 0.136 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.898 / SU B: 4.32 / SU ML: 0.062 / SU R Cruickshank DPI: 0.104 / SU Rfree: 0.1 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.104 / ESU R Free: 0.1 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.181 5996 5 %RANDOM
Rwork0.148 ---
obs0.15 119225 96.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 77.9 Å2 / Biso mean: 10.905 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--0.81 Å20 Å20.09 Å2
2--1.44 Å20 Å2
3----0.57 Å2
Refinement stepCycle: LAST / Resolution: 1.75→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9221 0 27 1268 10516
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0219593
X-RAY DIFFRACTIONr_angle_refined_deg1.3431.96513054
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.54751312
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.24923.01402
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.204151526
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6861594
X-RAY DIFFRACTIONr_chiral_restr0.0970.21497
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0217367
X-RAY DIFFRACTIONr_mcbond_it0.6361.56300
X-RAY DIFFRACTIONr_mcangle_it1.084210067
X-RAY DIFFRACTIONr_scbond_it2.02733293
X-RAY DIFFRACTIONr_scangle_it3.3194.52959
Refine LS restraints NCS

Ens-ID: 1 / Number: 3028 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1AMEDIUM POSITIONAL0.280.5
2BMEDIUM POSITIONAL0.260.5
3CMEDIUM POSITIONAL0.330.5
1AMEDIUM THERMAL0.782
2BMEDIUM THERMAL0.72
3CMEDIUM THERMAL0.822
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.251 397 -
Rwork0.213 7827 -
all-8224 -
obs--90.6 %
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)
10.90610.0694-0.20220.1976-0.00160.41010.05460.05290.1013-0.02160.0274-0.0506-0.07410.0573-0.0820.0591-0.0240.01160.0272-0.01680.056736.9194.241520.1375
21.06320.0239-0.31680.25350.08160.47960.0383-0.18290.01550.02850.0073-0.0177-0.01010.0349-0.04560.0398-0.0126-0.01370.0381-0.00190.014316.8545-3.320941.4068
30.67490.0534-0.28780.2044-0.03910.4874-0.0343-0.0052-0.0155-0.01430.0009-0.02030.0330.02430.03340.01530.0031-0.00710.0370.00240.012743.4531-29.081877.3287
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 420
2X-RAY DIFFRACTION1A421 - 422
3X-RAY DIFFRACTION1A423 - 1238
4X-RAY DIFFRACTION2B1 - 420
5X-RAY DIFFRACTION2B421 - 422
6X-RAY DIFFRACTION2B423 - 1252
7X-RAY DIFFRACTION3C1 - 420
8X-RAY DIFFRACTION3C421 - 422
9X-RAY DIFFRACTION3C423 - 1268

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