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- PDB-5kdr: The crystal structure of carboxyltransferase from Staphylococcus ... -

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Basic information

Entry
Database: PDB / ID: 5kdr
TitleThe crystal structure of carboxyltransferase from Staphylococcus Aureus bound to the antimicrobial agent moiramide B.
Components(Acetyl-coenzyme A carboxylase carboxyl transferase subunit ...) x 2
KeywordsTRANSFERASE / ANTIBIOTIC / MOIRAMIDE B / acetyl-CoA carboxylase / carboxyltransferase / enolate
Function / homology
Function and homology information


acetyl-CoA carboxytransferase / carboxyl- or carbamoyltransferase activity / acetyl-CoA carboxylase complex / malonyl-CoA biosynthetic process / acetyl-CoA carboxylase activity / fatty acid biosynthetic process / zinc ion binding / ATP binding
Similarity search - Function
Acetyl-CoA carboxylase, alpha subunit / Acetyl co-enzyme A carboxylase carboxyltransferase-like / Acetyl-coA carboxylase zinc finger domain / Acetyl-CoA carboxylase zinc finger domain / Acetyl-CoA carboxylase carboxyl transferase, beta subunit / Acetyl-coenzyme A carboxyltransferase, C-terminal / Acetyl-coenzyme A (CoA) carboxyltransferase C-terminal domain profile. / Acetyl-coenzyme A carboxyltransferase, N-terminal / Acetyl-coenzyme A (CoA) carboxyltransferase N-terminal domain profile. / Acetyl-CoA carboxylase ...Acetyl-CoA carboxylase, alpha subunit / Acetyl co-enzyme A carboxylase carboxyltransferase-like / Acetyl-coA carboxylase zinc finger domain / Acetyl-CoA carboxylase zinc finger domain / Acetyl-CoA carboxylase carboxyl transferase, beta subunit / Acetyl-coenzyme A carboxyltransferase, C-terminal / Acetyl-coenzyme A (CoA) carboxyltransferase C-terminal domain profile. / Acetyl-coenzyme A carboxyltransferase, N-terminal / Acetyl-coenzyme A (CoA) carboxyltransferase N-terminal domain profile. / Acetyl-CoA carboxylase / Carboxyl transferase domain / 2-enoyl-CoA Hydratase; Chain A, domain 1 / 2-enoyl-CoA Hydratase; Chain A, domain 1 / ClpP/crotonase-like domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Moiramide B / Acetyl-coenzyme A carboxylase carboxyl transferase subunit alpha / Acetyl-coenzyme A carboxylase carboxyl transferase subunit beta / Acetyl-coenzyme A carboxylase carboxyl transferase subunit alpha / Acetyl-coenzyme A carboxylase carboxyl transferase subunit beta
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsSilvers, M.A. / Pakhomova, S. / Neau, D. / Silvers, W.C. / Anzalone, N. / Taylor, C.M. / Waldrop, G.L.
CitationJournal: Biochemistry / Year: 2016
Title: Crystal Structure of Carboxyltransferase from Staphylococcus aureus Bound to the Antibacterial Agent Moiramide B.
Authors: Silvers, M.A. / Pakhomova, S. / Neau, D.B. / Silvers, W.C. / Anzalone, N. / Taylor, C.M. / Waldrop, G.L.
History
DepositionJun 8, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 10, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2016Group: Database references
Revision 1.2Sep 7, 2016Group: Database references
Revision 1.3Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _chem_comp.pdbx_synonyms / _citation.journal_id_CSD ..._chem_comp.pdbx_synonyms / _citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Acetyl-coenzyme A carboxylase carboxyl transferase subunit alpha
B: Acetyl-coenzyme A carboxylase carboxyl transferase subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,4718
Polymers68,6022
Non-polymers8696
Water37821
1
A: Acetyl-coenzyme A carboxylase carboxyl transferase subunit alpha
B: Acetyl-coenzyme A carboxylase carboxyl transferase subunit beta
hetero molecules

A: Acetyl-coenzyme A carboxylase carboxyl transferase subunit alpha
B: Acetyl-coenzyme A carboxylase carboxyl transferase subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)138,94116
Polymers137,2034
Non-polymers1,73812
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area15340 Å2
ΔGint-150 kcal/mol
Surface area41560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)153.807, 49.445, 100.048
Angle α, β, γ (deg.)90.00, 91.94, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Acetyl-coenzyme A carboxylase carboxyl transferase subunit ... , 2 types, 2 molecules AB

#1: Protein Acetyl-coenzyme A carboxylase carboxyl transferase subunit alpha / Acetyl-CoA carboxylase carboxyltransferase subunit alpha


Mass: 36684.738 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (strain USA300) (bacteria)
Strain: USA300 / Gene: accA, SAUSA300_1646 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q2FG38, UniProt: Q2FXM7*PLUS, acetyl-CoA carboxylase
#2: Protein Acetyl-coenzyme A carboxylase carboxyl transferase subunit beta / Acetyl-CoA carboxylase carboxyltransferase subunit beta


Mass: 31916.793 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (strain bovine RF122 / ET3-1) (bacteria)
Strain: bovine RF122 / ET3-1 / Gene: accD, SAB1559c / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q2YTE0, UniProt: Q2FXM6*PLUS, acetyl-CoA carboxylase

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Non-polymers , 5 types, 27 molecules

#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-YT5 / Moiramide B / (2~{E},4~{E})-~{N}-[(1~{S})-3-[[(2~{S})-3-methyl-1-[(3~{R},4~{S})-4-methyl-2,5-bis(oxidanylidene)pyrrolidin-3-yl]-1-oxi danylidene-butan-2-yl]amino]-3-oxidanylidene-1-phenyl-propyl]hexa-2,4-dienamide


Mass: 453.531 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H31N3O5
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 21 / 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: 2.77 Å3/Da / Density % sol: 55.61 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 0.1 M MES, 1.6 M NH4SO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 20, 2016 / Details: KB mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.6→40 Å / Num. obs: 23238 / % possible obs: 99.1 % / Redundancy: 3.7 % / Rsym value: 0.06 / Net I/σ(I): 6.8
Reflection shellResolution: 2.6→2.72 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.46 / % possible all: 98.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2F9I

2f9i


Resolution: 2.6→40 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.902 / SU B: 33.226 / SU ML: 0.329 / Cross valid method: THROUGHOUT / ESU R: 0.582 / ESU R Free: 0.324 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27586 1112 4.8 %RANDOM
Rwork0.22946 ---
obs0.23171 22099 98.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 67.113 Å2
Baniso -1Baniso -2Baniso -3
1--1.74 Å2-0 Å21.29 Å2
2--3.59 Å2-0 Å2
3----1.93 Å2
Refinement stepCycle: LAST / Resolution: 2.6→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4264 0 53 21 4338
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0194383
X-RAY DIFFRACTIONr_bond_other_d0.0020.024267
X-RAY DIFFRACTIONr_angle_refined_deg1.0051.9795891
X-RAY DIFFRACTIONr_angle_other_deg0.7863.0049831
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2265547
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.8524.503191
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.42215802
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.4011527
X-RAY DIFFRACTIONr_chiral_restr0.0550.2660
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024905
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02956
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5282.2092203
X-RAY DIFFRACTIONr_mcbond_other0.5282.2112204
X-RAY DIFFRACTIONr_mcangle_it0.9543.3052745
X-RAY DIFFRACTIONr_mcangle_other0.9543.3072746
X-RAY DIFFRACTIONr_scbond_it0.9222.3252180
X-RAY DIFFRACTIONr_scbond_other0.9192.3252180
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.0993.4693147
X-RAY DIFFRACTIONr_long_range_B_refined3.62417.4464886
X-RAY DIFFRACTIONr_long_range_B_other3.59117.4284882
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.351 97 -
Rwork0.35 1561 -
obs--97.93 %
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)
16.43774.1448-1.01383.1149-1.37621.93010.14920.0838-0.1154-0.3465-0.21750.17490.760.34870.06840.981-0.0542-0.06360.98250.01240.6722-17.471-15.81953.318
27.60771.9773-0.15281.6232-2.42965.1973-0.0658-0.1684-0.0417-0.038-0.0304-0.07970.1296-0.16160.09610.7036-0.0317-0.03530.5738-0.01080.5285-11.554-5.14448.896
33.2096-0.01480.37180.8182-0.1533.2966-0.0303-0.7361-0.05560.24690.15970.15910.2907-0.3159-0.12930.11080.02520.04680.56090.00050.4279-11.064-2.42716.377
44.71290.3569-2.45472.0669-0.51096.1336-0.3991-0.4531-0.52610.18870.3649-0.08221.20740.26750.03410.28110.086-0.02440.45760.05720.45092.662-7.79212.841
53.5935-0.32410.09793.8343-0.84562.386-0.0408-1.077-0.09660.4656-0.0397-0.160.22090.0250.08050.16160.0421-0.03460.7322-0.06420.39951.666-1.24425.667
65.72031.51961.82119.181-4.5454.4751-0.1181-0.60320.58230.6954-0.114-0.5475-0.4131-0.03550.2320.41730.0505-0.00340.726-0.15180.45641.284.48533.788
72.73410.43461.30570.73230.23492.2658-0.0695-1.11410.66610.33080.03950.1733-0.2864-0.35760.030.22180.12190.06460.8611-0.20880.6489-6.05310.42425.107
816.04689.321812.61328.12547.54079.9320.2602-0.30020.71790.154-0.7734-0.12640.2121-0.26350.51330.6640.0299-0.02250.65980.0370.658541.444-13.69915.454
98.01751.1476-0.360411.2941-3.60274.09320.4626-0.5176-0.4491.0413-0.5079-0.13020.3321-0.07690.04520.35370.0678-0.03160.56-0.01640.639639.304-12.2479.033
107.31710.8215-1.68185.8123-1.49590.7322-0.17960.1091-0.3411-0.08660.02090.03130.18610.01350.15870.44990.12090.08640.52510.0020.619733.439-8.7528.263
116.34663.9657-3.06195.05870.02896.18910.3438-1.37790.17090.4475-0.2788-0.7822-0.93061.5145-0.0650.321-0.0851-0.25750.8066-0.08120.649827.7117.33618.496
123.0219-0.0046-0.19951.610.33255.2949-0.1328-0.920.17860.32860.1709-0.44490.43380.4082-0.03820.10270.0479-0.09620.7527-0.08960.577725.3743.98420.775
133.3564-0.83760.84531.30550.29053.0298-0.2021-0.4220.44230.21910.0485-0.2007-0.0221-0.12960.15370.03910.0154-0.04670.4689-0.10070.47215.5367.55313.197
145.00480.24540.95010.34241.20825.37660.1126-0.2602-0.14090.1764-0.0678-0.14150.6225-0.2708-0.04480.0941-0.0207-0.05150.4143-0.02590.435216.074-4.649.097
150.150.11980.58771.58081.18552.79910.081-0.0556-0.0198-0.3120.0021-0.2099-0.1962-0.2354-0.08310.9195-0.05790.02470.7691-0.03410.83919.476-16.96118.177
165.0546-0.5419-0.46515.20080.13656.14570.00130.07120.1548-0.6843-0.024-0.43090.37970.55770.02260.12110.03480.0180.4513-0.050.37921.669-0.479-1.259
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 39
2X-RAY DIFFRACTION2A40 - 52
3X-RAY DIFFRACTION3A53 - 153
4X-RAY DIFFRACTION4A154 - 178
5X-RAY DIFFRACTION5A179 - 242
6X-RAY DIFFRACTION6A243 - 261
7X-RAY DIFFRACTION7A262 - 314
8X-RAY DIFFRACTION8B29 - 33
9X-RAY DIFFRACTION9B34 - 49
10X-RAY DIFFRACTION10B50 - 64
11X-RAY DIFFRACTION11B65 - 91
12X-RAY DIFFRACTION12B92 - 147
13X-RAY DIFFRACTION13B148 - 203
14X-RAY DIFFRACTION14B204 - 232
15X-RAY DIFFRACTION15B233 - 248
16X-RAY DIFFRACTION16B249 - 283

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