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- PDB-3nfd: Chronobacterium ammoniagenes ACPS-CoA complex -

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Basic information

Entry
Database: PDB / ID: 3nfd
TitleChronobacterium ammoniagenes ACPS-CoA complex
ComponentsPhosphopantetheine protein transferase, Ppt1p
KeywordsTRANSFERASE / acyl carrier protein synthase / Mycobacterium tuberculosis / acyl carrier protein / fatty acid synthase
Function / homology
Function and homology information


holo-[acyl-carrier-protein] synthase / holo-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process / magnesium ion binding / cytoplasm
Similarity search - Function
4'-phosphopantetheinyl transferase domain / Holo-[acyl carrier protein] synthase / Phosphopantetheine-protein transferase domain / 4'-phosphopantetheinyl transferase domain / 4'-phosphopantetheinyl transferase domain superfamily / 4'-phosphopantetheinyl transferase superfamily / Ribosomal Protein L22; Chain A / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
COENZYME A / Holo-[acyl-carrier-protein] synthase
Similarity search - Component
Biological speciesCorynebacterium ammoniagenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 Å
AuthorsGokulan, K.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2011
Title: Mycobacterium tuberculosis acyl carrier protein synthase adopts two different pH-dependent structural conformations.
Authors: Gokulan, K. / Aggarwal, A. / Shipman, L. / Besra, G.S. / Sacchettini, J.C.
History
DepositionJun 10, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 5, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 25, 2012Group: Database references / Structure summary
Revision 1.3Jul 17, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.name ..._software.classification / _software.name / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Nov 27, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _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

Downloads & links

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Assembly

Deposited unit
A: Phosphopantetheine protein transferase, Ppt1p
B: Phosphopantetheine protein transferase, Ppt1p
C: Phosphopantetheine protein transferase, Ppt1p
D: Phosphopantetheine protein transferase, Ppt1p
E: Phosphopantetheine protein transferase, Ppt1p
F: Phosphopantetheine protein transferase, Ppt1p
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,34612
Polymers101,7416
Non-polymers4,6056
Water4,125229
1
A: Phosphopantetheine protein transferase, Ppt1p
B: Phosphopantetheine protein transferase, Ppt1p
C: Phosphopantetheine protein transferase, Ppt1p
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,1736
Polymers50,8703
Non-polymers2,3033
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7970 Å2
ΔGint-41 kcal/mol
Surface area18250 Å2
MethodPISA
2
D: Phosphopantetheine protein transferase, Ppt1p
E: Phosphopantetheine protein transferase, Ppt1p
F: Phosphopantetheine protein transferase, Ppt1p
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,1736
Polymers50,8703
Non-polymers2,3033
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8000 Å2
ΔGint-41 kcal/mol
Surface area17770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.779, 56.019, 88.279
Angle α, β, γ (deg.)80.88, 76.23, 60.92
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Phosphopantetheine protein transferase, Ppt1p


Mass: 16956.828 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium ammoniagenes (bacteria)
Gene: PPT1 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 / References: UniProt: O31302
#2: Chemical
ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 229 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsACCORDING TO THE AUTHORS THE DISCREPANCIES MAY BE DUE TO ERRORS AT THE GENOMIC SEQUENCING

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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: 2.25 Å3/Da / Density % sol: 45.42 %
Crystal growMethod: evaporation / pH: 6.5
Details: 25% PEG MME 5K, 0.1 M MES, 200 mM ammonium sulfate, pH 6.5, EVAPORATION

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 1-BM-C / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 10, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.89→30.52 Å / Num. all: 52264 / Num. obs: 52264 / % possible obs: 73 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 58.1
Reflection shellResolution: 1.89→1.95 Å / Redundancy: 0.8 % / Rmerge(I) obs: 0.15 / Mean I/σ(I) obs: 6.4 / % possible all: 44.2

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Processing

Software
NameVersionClassification
REFMAC5.2.0000refinement
CNSrefinement
ADSCQuantumdata collection
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.89→20 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.906 / SU B: 3.329 / SU ML: 0.102 / Cross valid method: THROUGHOUT / ESU R: 0.263 / ESU R Free: 0.211 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25933 2539 5 %RANDOM
Rwork0.21209 ---
obs0.21451 47784 70.34 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 24.913 Å2
Baniso -1Baniso -2Baniso -3
1-1.02 Å20.42 Å2-0.3 Å2
2---0.92 Å2-0.43 Å2
3----0.22 Å2
Refinement stepCycle: LAST / Resolution: 1.89→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6433 0 162 229 6824
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0216692
X-RAY DIFFRACTIONr_bond_other_d0.0020.026229
X-RAY DIFFRACTIONr_angle_refined_deg2.0361.959064
X-RAY DIFFRACTIONr_angle_other_deg1.293314397
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8585816
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.95422.99311
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.99151099
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.71564
X-RAY DIFFRACTIONr_chiral_restr0.2940.2995
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.027404
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021390
X-RAY DIFFRACTIONr_nbd_refined0.2590.21435
X-RAY DIFFRACTIONr_nbd_other0.1990.26463
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0910.24051
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.220.2179
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3390.247
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2890.2134
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3720.210
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3241.54533
X-RAY DIFFRACTIONr_mcbond_other0.2491.51686
X-RAY DIFFRACTIONr_mcangle_it1.6726564
X-RAY DIFFRACTIONr_scbond_it2.27732827
X-RAY DIFFRACTIONr_scangle_it3.474.52500
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.89→1.936 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.298 114
Rwork0.221 1932

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