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- PDB-7rm7: The X-ray crystal structure of the N-terminal domain of Staphyloc... -

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Basic information

Entry
Database: PDB / ID: 7rm7
TitleThe X-ray crystal structure of the N-terminal domain of Staphylococcus aureus Fatty Acid Kinase A (FakA, residues 1-208) in complex with ADP to 1.025 Angstrom resolution
ComponentsFatty Acid Kinase A
KeywordsLIGASE / Fatty acid kinase A / phosphorylation / fatty acid / N-terminus domain
Function / homology
Function and homology information


glycerone kinase activity / glycerol metabolic process
Similarity search - Function
: / Fatty acid kinase subunit A-like, middle domain / DAK2 domain-containing protein YloV / Uncharacterised protein, DhaK domain / Fatty acid kinase subunit A-like, C-terminal / Dak1_2 / DhaL domain / DhaL domain superfamily / DAK2 domain / DhaL domain profile. / Dak2
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Uncharacterized protein SA1069
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.025 Å
AuthorsCuypers, M.G. / Subramanian, C. / Rock, C.O. / White, S.W.
CitationJournal: To Be Published
Title: The X-ray crystal structure of the N-terminal domain of Staphylococcus aureus Fatty Acid Kinase A (FakA, residues 1-208) in complex with ADP to 1.025 Angstrom resolution
Authors: Cuypers, M.G. / Subramanian, C. / Rock, C.O. / White, S.W.
History
DepositionJul 26, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 2, 2022Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fatty Acid Kinase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0878
Polymers24,4461
Non-polymers6417
Water6,503361
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1390 Å2
ΔGint-40 kcal/mol
Surface area10550 Å2
Unit cell
Length a, b, c (Å)42.665, 57.399, 81.195
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Fatty Acid Kinase A


Mass: 24445.777 Da / Num. of mol.: 1 / Fragment: N-terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: Q7A5Z4
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 361 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.03 Å3/Da / Density % sol: 39.51 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.2M MgCl2, 0.1M Tris Hcl pH8.5, 30%PEG4000 (JCSG core IV #21)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Mar 23, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.025→34.24 Å / Num. obs: 95789 / % possible obs: 95.5 % / Redundancy: 6.8 % / Biso Wilson estimate: 8.3 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.02 / Net I/σ(I): 19.6
Reflection shellResolution: 1.025→1.04 Å / Mean I/σ(I) obs: 2 / Num. unique obs: 3447 / CC1/2: 0.65 / Rpim(I) all: 0.396 / % possible all: 70.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
SHELXDEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.025→34.24 Å / Cor.coef. Fo:Fc: 0.985 / Cor.coef. Fo:Fc free: 0.978 / SU B: 0.911 / SU ML: 0.02 / Cross valid method: FREE R-VALUE / ESU R: 0.022 / ESU R Free: 0.024
Details: Phasing was performed using this data set as a remote wavelength coupled with the SAD data from a cobalt-derivatized crystal (PDB ID 7RZK). Hydrogens have been used if present in the input file
RfactorNum. reflection% reflection
Rfree0.1441 4782 4.996 %
Rwork0.1177 90938 -
all0.119 --
obs-95720 95.158 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 16.035 Å2
Baniso -1Baniso -2Baniso -3
1--1.134 Å2-0 Å2-0 Å2
2---0.38 Å20 Å2
3---1.514 Å2
Refinement stepCycle: LAST / Resolution: 1.025→34.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1659 0 38 361 2058
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0121906
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171814
X-RAY DIFFRACTIONr_angle_refined_deg2.0461.6232605
X-RAY DIFFRACTIONr_angle_other_deg0.671.5654219
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3615265
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.68226.17381
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.70415349
X-RAY DIFFRACTIONr_dihedral_angle_4_deg28.729154
X-RAY DIFFRACTIONr_chiral_restr0.1030.2251
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.022298
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02393
X-RAY DIFFRACTIONr_nbd_refined0.2740.2495
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1920.21701
X-RAY DIFFRACTIONr_nbtor_refined0.1820.21000
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.070.2926
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2580.2229
X-RAY DIFFRACTIONr_metal_ion_refined0.0920.27
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.430.230
X-RAY DIFFRACTIONr_nbd_other0.2920.296
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.290.253
X-RAY DIFFRACTIONr_mcbond_it5.5681.1511000
X-RAY DIFFRACTIONr_mcbond_other5.5691.149999
X-RAY DIFFRACTIONr_mcangle_it6.1571.7071285
X-RAY DIFFRACTIONr_mcangle_other6.1551.7081286
X-RAY DIFFRACTIONr_scbond_it6.2631.532906
X-RAY DIFFRACTIONr_scbond_other6.2631.532906
X-RAY DIFFRACTIONr_scangle_it7.4932.1561320
X-RAY DIFFRACTIONr_scangle_other7.492.1561321
X-RAY DIFFRACTIONr_lrange_it8.63117.9122424
X-RAY DIFFRACTIONr_lrange_other8.00715.9162319
X-RAY DIFFRACTIONr_rigid_bond_restr14.25733720
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.025-1.0520.3122610.2935081X-RAY DIFFRACTION72.6407
1.052-1.080.2292890.2146117X-RAY DIFFRACTION89.2325
1.08-1.1120.1673330.1576335X-RAY DIFFRACTION95.6671
1.112-1.1460.1513350.1416164X-RAY DIFFRACTION96.0396
1.146-1.1830.1533120.1346055X-RAY DIFFRACTION96.6601
1.183-1.2250.1293290.1235841X-RAY DIFFRACTION96.7995
1.225-1.2710.1593010.1225677X-RAY DIFFRACTION97.3774
1.271-1.3230.1482920.1175501X-RAY DIFFRACTION97.5417
1.323-1.3820.1292740.1155299X-RAY DIFFRACTION97.9782
1.382-1.4490.1512620.1115078X-RAY DIFFRACTION98.2882
1.449-1.5280.1342420.1064900X-RAY DIFFRACTION98.4303
1.528-1.620.132410.0994572X-RAY DIFFRACTION98.708
1.62-1.7320.1352180.14398X-RAY DIFFRACTION98.9496
1.732-1.870.1362120.1094077X-RAY DIFFRACTION98.9845
1.87-2.0490.1222330.0973744X-RAY DIFFRACTION99.3753
2.049-2.290.1181760.0943414X-RAY DIFFRACTION99.281
2.29-2.6430.1221560.0953063X-RAY DIFFRACTION99.5054
2.643-3.2340.141600.1062565X-RAY DIFFRACTION99.163
3.234-4.5630.143930.1122012X-RAY DIFFRACTION96.7371
4.563-34.240.254630.2151045X-RAY DIFFRACTION86.1586
Refinement TLS params.Method: refined / Origin x: 14.9801 Å / Origin y: 5.2362 Å / Origin z: -12.5135 Å
111213212223313233
T0.0196 Å20.0006 Å2-0.0002 Å2-0.0153 Å2-0.0009 Å2--0.0005 Å2
L0.0655 °20.0079 °20.02 °2-0.0374 °2-0.0074 °2--0.0965 °2
S0.0009 Å °0.005 Å °-0.0057 Å °-0.0006 Å °0.0014 Å °0.0002 Å °0.0025 Å °0.0033 Å °-0.0023 Å °
Refinement TLS groupSelection: ALL

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