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- PDB-4ewp: Crystal structure of FabH from Micrococcus luteus -

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Basic information

Entry
Database: PDB / ID: 4ewp
TitleCrystal structure of FabH from Micrococcus luteus
Components3-oxoacyl-[acyl-carrier-protein] synthase 3
KeywordsTRANSFERASE / synthase
Function / homology
Function and homology information


beta-ketoacyl-[acyl-carrier-protein] synthase III / beta-ketoacyl-acyl-carrier-protein synthase III activity / 3-oxoacyl-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process / cytoplasm
Similarity search - Function
3-oxoacyl-[acyl-carrier-protein] synthase 3 / 3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III / 3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III / 3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III, C-terminal / 3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III C terminal / Thiolase/Chalcone synthase / Peroxisomal Thiolase; Chain A, domain 1 / Thiolase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Beta-ketoacyl-[acyl-carrier-protein] synthase III
Similarity search - Component
Biological speciesMicrococcus luteus NCTC 2665 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.198 Å
AuthorsPereira, J.H. / Goh, E.-B. / Keasling, J.D. / Beller, H.R. / Adams, P.D.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2012
Title: Structure of FabH and factors affecting the distribution of branched fatty acids in Micrococcus luteus.
Authors: Pereira, J.H. / Goh, E.B. / Keasling, J.D. / Beller, H.R. / Adams, P.D.
History
DepositionApr 27, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 3, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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] synthase 3
B: 3-oxoacyl-[acyl-carrier-protein] synthase 3
C: 3-oxoacyl-[acyl-carrier-protein] synthase 3
D: 3-oxoacyl-[acyl-carrier-protein] synthase 3
E: 3-oxoacyl-[acyl-carrier-protein] synthase 3
F: 3-oxoacyl-[acyl-carrier-protein] synthase 3


Theoretical massNumber of molelcules
Total (without water)220,7006
Polymers220,7006
Non-polymers00
Water15,799877
1
A: 3-oxoacyl-[acyl-carrier-protein] synthase 3
B: 3-oxoacyl-[acyl-carrier-protein] synthase 3


Theoretical massNumber of molelcules
Total (without water)73,5672
Polymers73,5672
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8140 Å2
ΔGint-49 kcal/mol
Surface area23440 Å2
MethodPISA
2
C: 3-oxoacyl-[acyl-carrier-protein] synthase 3
D: 3-oxoacyl-[acyl-carrier-protein] synthase 3


Theoretical massNumber of molelcules
Total (without water)73,5672
Polymers73,5672
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8180 Å2
ΔGint-48 kcal/mol
Surface area23450 Å2
MethodPISA
3
E: 3-oxoacyl-[acyl-carrier-protein] synthase 3
F: 3-oxoacyl-[acyl-carrier-protein] synthase 3


Theoretical massNumber of molelcules
Total (without water)73,5672
Polymers73,5672
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8150 Å2
ΔGint-47 kcal/mol
Surface area23430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.140, 85.026, 96.916
Angle α, β, γ (deg.)69.82, 71.37, 85.66
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
3-oxoacyl-[acyl-carrier-protein] synthase 3 / 3-oxoacyl-[acyl-carrier-protein] synthase III / Beta-ketoacyl-ACP synthase III


Mass: 36783.391 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Micrococcus luteus NCTC 2665 (bacteria)
Strain: ATCC 4698 / DSM 20030 / JCM 1464 / NBRC 3333 / NCIMB 9278 / NCTC 2665 / VKM Ac-2230
Gene: fabH, HMPREF0569_0014, Mlut_09310 / Production host: Escherichia coli (E. coli)
References: UniProt: C5CAR9, beta-ketoacyl-[acyl-carrier-protein] synthase III
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 877 / 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: 2.66 Å3/Da / Density % sol: 53.75 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 9
Details: 0.1 M Bis-Tris propane pH 9.0, 10% PEG 200, 18% PEG 8,000, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.9774 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 10, 2010
RadiationMonochromator: Double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9774 Å / Relative weight: 1
ReflectionResolution: 2.198→49.8 Å / % possible obs: 96.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2

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Processing

Software
NameVersionClassification
BOSdata collection
PHENIXmodel building
PHENIX(phenix.refine: dev_718)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.198→49.797 Å / SU ML: 0.68 / σ(F): 1.96 / Phase error: 21.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2098 5572 5.01 %RANDOM
Rwork0.1689 ---
all0.1689 111229 --
obs0.1709 111229 96.1 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 33.435 Å2 / ksol: 0.349 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.3381 Å26.7032 Å2-0.7289 Å2
2---3.0285 Å2-4.5501 Å2
3---3.3666 Å2
Refinement stepCycle: LAST / Resolution: 2.198→49.797 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15456 0 0 877 16333
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00715756
X-RAY DIFFRACTIONf_angle_d1.07121528
X-RAY DIFFRACTIONf_dihedral_angle_d14.075616
X-RAY DIFFRACTIONf_chiral_restr0.072520
X-RAY DIFFRACTIONf_plane_restr0.0052850
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.198-2.22310.27031450.22842695X-RAY DIFFRACTION73
2.2231-2.24930.26281800.23573154X-RAY DIFFRACTION87
2.2493-2.27670.30511730.24093227X-RAY DIFFRACTION89
2.2767-2.30550.28531910.23343351X-RAY DIFFRACTION91
2.3055-2.33590.28661920.21183358X-RAY DIFFRACTION93
2.3359-2.36790.26091930.21723499X-RAY DIFFRACTION94
2.3679-2.40170.24351720.22173434X-RAY DIFFRACTION96
2.4017-2.43760.27481830.21413564X-RAY DIFFRACTION96
2.4376-2.47560.29151910.23683518X-RAY DIFFRACTION97
2.4756-2.51620.29651780.22953584X-RAY DIFFRACTION97
2.5162-2.55960.24681860.20613554X-RAY DIFFRACTION97
2.5596-2.60620.25412040.20623582X-RAY DIFFRACTION97
2.6062-2.65630.26522080.19363509X-RAY DIFFRACTION98
2.6563-2.71050.2771640.19513611X-RAY DIFFRACTION98
2.7105-2.76940.22291820.18353603X-RAY DIFFRACTION98
2.7694-2.83380.22611770.17453646X-RAY DIFFRACTION98
2.8338-2.90470.20091690.17013628X-RAY DIFFRACTION98
2.9047-2.98320.23371770.17863624X-RAY DIFFRACTION98
2.9832-3.0710.21051930.17113596X-RAY DIFFRACTION99
3.071-3.17010.20181880.16753611X-RAY DIFFRACTION99
3.1701-3.28340.22761820.17383625X-RAY DIFFRACTION99
3.2834-3.41480.21162020.1613592X-RAY DIFFRACTION99
3.4148-3.57020.20672170.16153600X-RAY DIFFRACTION99
3.5702-3.75840.1851970.1613611X-RAY DIFFRACTION99
3.7584-3.99370.17781950.13633658X-RAY DIFFRACTION99
3.9937-4.30190.1491750.12343648X-RAY DIFFRACTION99
4.3019-4.73460.15552060.11563630X-RAY DIFFRACTION99
4.7346-5.41890.16051860.13323632X-RAY DIFFRACTION99
5.4189-6.82450.18531810.16283660X-RAY DIFFRACTION100
6.8245-49.80960.17741850.15753653X-RAY DIFFRACTION99
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)
11.1903-0.29660.32621.7073-0.06881.37270.04040.1304-0.108-0.067-0.0354-0.25120.15340.2587-0.02690.13430.0150.02380.1781-0.0130.1703-20.0643-15.5988-27.6953
21.0084-0.35770.25321.9785-0.16031.1603-0.06850.02730.08150.13510.00630.0732-0.1432-0.03060.01280.1353-0.02660.01390.12540.01780.1172-35.27725.0366-19.7377
31.9507-0.9148-0.64552.19690.67341.48350.07450.05110.06650.0493-0.07710.16020.0096-0.0988-0.03820.1292-0.02480.00990.11810.01710.11588.0016-31.7523-0.6571
42.3342-1.6573-1.06631.97640.89461.7922-0.4946-0.4537-0.24820.6260.5041-0.30850.66120.4668-0.06550.37630.2109-0.12340.26880.03470.167625.9006-50.08327.3249
51.3204-0.07290.2811.4199-0.17361.27650.0588-0.1315-0.073-0.06240.05950.3287-0.0197-0.4669-0.06610.1718-0.0242-0.02370.33480.05540.1821-33.623-21.241738.663
61.3842-0.05390.00161.47560.24221.21410.0322-0.03050.2445-0.11450.0483-0.0892-0.2744-0.0373-0.07450.2264-0.010.02980.1736-0.01340.1439-14.8369-5.158128.1471
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B
3X-RAY DIFFRACTION3chain C
4X-RAY DIFFRACTION4chain D
5X-RAY DIFFRACTION5chain E
6X-RAY DIFFRACTION6chain F

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