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- PDB-3hqj: Structure-function analysis of Mycobacterium tuberculosis acyl ca... -

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Basic information

Entry
Database: PDB / ID: 3hqj
TitleStructure-function analysis of Mycobacterium tuberculosis acyl carrier protein synthase (AcpS).
ComponentsHolo-[acyl-carrier-protein] synthase
KeywordsTRANSFERASE / an/fold / Structural Genomics / Israel Structural Proteomics Center / ISPC / Cytoplasm / Fatty acid biosynthesis / Lipid synthesis / Magnesium / Metal-binding
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 / Holo-[acyl-carrier-protein] synthase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsDym, O. / Albeck, S. / Peleg, Y. / Schwarz, A. / Shakked, Z. / Burstein, Y. / Zimhony, O. / Israel Structural Proteomics Center (ISPC)
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Structure-function analysis of the acyl carrier protein synthase (AcpS) from Mycobacterium tuberculosis.
Authors: Dym, O. / Albeck, S. / Peleg, Y. / Schwarz, A. / Shakked, Z. / Burstein, Y. / Zimhony, O.
History
DepositionJun 7, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 15, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 13, 2021Group: Advisory / Database references / Derived calculations
Category: database_2 / pdbx_database_related ...database_2 / pdbx_database_related / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn / 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 / _pdbx_database_related.db_name / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Holo-[acyl-carrier-protein] synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,9525
Polymers14,1121
Non-polymers8404
Water79344
1
A: Holo-[acyl-carrier-protein] synthase
hetero molecules

A: Holo-[acyl-carrier-protein] synthase
hetero molecules

A: Holo-[acyl-carrier-protein] synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,85715
Polymers42,3363
Non-polymers2,52112
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Unit cell
Length a, b, c (Å)77.443, 77.443, 77.443
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number195
Space group name H-MP23
Components on special symmetry positions
IDModelComponents
11A-143-

HOH

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Components

#1: Protein Holo-[acyl-carrier-protein] synthase / Holo-ACP synthase / 4'-phosphopantetheinyl transferase acpS


Mass: 14111.939 Da / Num. of mol.: 1 / Mutation: A28M,V74M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: acpS, Rv2523c, MT2599, MTV009.08c / Production host: Escherichia coli (E. coli)
References: UniProt: P0A4W8, UniProt: P9WQD3*PLUS, holo-[acyl-carrier-protein] synthase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 44 / 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: 2.74 Å3/Da / Density % sol: 55.15 %
Crystal growTemperature: 294 K / pH: 6.5
Details: 100mM MgCl2, 50mM Na cacodylate pH=6.5, and 25% polyethylene glycol 200, Microbatch under oil, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Sep 5, 2007
RadiationMonochromator: YALE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. all: 11556 / Num. obs: 11568 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.95→2.02 Å / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1F7T

1f7t


Resolution: 1.95→50 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.899 / SU B: 2.846 / SU ML: 0.086 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.149 / ESU R Free: 0.146 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25167 553 4.8 %RANDOM
Rwork0.20906 ---
all0.211 11012 --
obs0.211 10999 99.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.946 Å2
Refinement stepCycle: LAST / Resolution: 1.95→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms860 0 30 44 934
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.021904
X-RAY DIFFRACTIONr_angle_refined_deg1.6991.971232
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0655109
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.92821.84238
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.43515135
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.7091510
X-RAY DIFFRACTIONr_chiral_restr0.1170.2142
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02668
X-RAY DIFFRACTIONr_nbd_refined0.2070.2380
X-RAY DIFFRACTIONr_nbtor_refined0.2970.2611
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1970.245
X-RAY DIFFRACTIONr_metal_ion_refined0.040.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.180.255
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3270.223
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.0640.22
X-RAY DIFFRACTIONr_mcbond_it1.0561.5573
X-RAY DIFFRACTIONr_mcangle_it1.7242891
X-RAY DIFFRACTIONr_scbond_it2.4613386
X-RAY DIFFRACTIONr_scangle_it3.5224.5341
LS refinement shellResolution: 1.95→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.271 35 -
Rwork0.211 790 -
obs--100 %

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