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- PDB-3h0p: 2.0 Angstrom Crystal Structure of an Acyl Carrier Protein S-malon... -

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Basic information

Entry
Database: PDB / ID: 3h0p
Title2.0 Angstrom Crystal Structure of an Acyl Carrier Protein S-malonyltransferase from Salmonella typhimurium.
ComponentsS-malonyltransferase
KeywordsTRANSFERASE / acyl carrier protein / S-malonyltransferase / idp00956 / FabD / Fatty acid biosynthesis / Lipid synthesis / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


[acyl-carrier-protein] S-malonyltransferase / [acyl-carrier-protein] S-malonyltransferase activity / fatty acid biosynthetic process / cytosol
Similarity search - Function
Malonyl CoA-acyl carrier protein transacylase / Malonyl CoA-acyl carrier protein transacylase, FabD-type / : / Malonyl-CoA ACP transacylase, ACP-binding / Malonyl-Coenzyme A Acyl Carrier Protein, domain 2 / Malonyl-Coenzyme A Acyl Carrier Protein; domain 2 / Malonyl-CoA ACP transacylase, ACP-binding / Acyl transferase domain superfamily / Acyl transferase / Acyl transferase domain ...Malonyl CoA-acyl carrier protein transacylase / Malonyl CoA-acyl carrier protein transacylase, FabD-type / : / Malonyl-CoA ACP transacylase, ACP-binding / Malonyl-Coenzyme A Acyl Carrier Protein, domain 2 / Malonyl-Coenzyme A Acyl Carrier Protein; domain 2 / Malonyl-CoA ACP transacylase, ACP-binding / Acyl transferase domain superfamily / Acyl transferase / Acyl transferase domain / Acyl transferase domain in polyketide synthase (PKS) enzymes. / Acyl transferase/acyl hydrolase/lysophospholipase / Alpha-Beta Plaits / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Malonyl CoA-acyl carrier protein transacylase
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsMinasov, G. / Wawrzak, Z. / Skarina, T. / Onopriyenko, O. / Peterson, S.N. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID) / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: TO BE PUBLISHED
Title: 2.0 Angstrom Crystal Structure of an Acyl Carrier Protein S-malonyltransferase from Salmonella typhimurium.
Authors: Minasov, G. / Wawrzak, Z. / Skarina, T. / Onopriyenko, O. / Peterson, S.N. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionApr 10, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 21, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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 / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 22, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: S-malonyltransferase
B: S-malonyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,5395
Polymers66,2512
Non-polymers2883
Water7,981443
1
A: S-malonyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,2212
Polymers33,1251
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: S-malonyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,3183
Polymers33,1251
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.589, 92.169, 77.075
Angle α, β, γ (deg.)90.00, 92.84, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein S-malonyltransferase / Malonyl CoA-acyl carrier protein transacylase / MCT


Mass: 33125.379 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Strain: LT2 / Gene: fabD, STM1194 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: O85140, [acyl-carrier-protein] S-malonyltransferase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 443 / 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: 2.49 Å3/Da / Density % sol: 50.7 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Protein Solution: 0.3M NaCl, 10mM HEPES (pH 7.5); Screen Solution: 1M Lithium Sulphate, 0.1M Bis-Tris-Propane HCl (pH 7.0), VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.98011 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 21, 2009 / Details: mirrors
RadiationMonochromator: Si {1,1,1} / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98011 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. all: 41818 / Num. obs: 41818 / % possible obs: 95.5 % / Observed criterion σ(I): -3 / Redundancy: 5.3 % / Biso Wilson estimate: 20 Å2 / Rmerge(I) obs: 0.096 / Net I/σ(I): 16.6
Reflection shellResolution: 2→2.03 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.482 / Mean I/σ(I) obs: 3.7 / Num. unique all: 2146 / % possible all: 97.8

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Processing

Software
NameVersionClassification
Blu-IceMaxdata collection
MrBUMPphasing
REFMAC5.5.0044refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2G2Y

2g2y


Resolution: 2→29.54 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.905 / SU B: 9.152 / SU ML: 0.117 / TLS residual ADP flag: LIKELY RESIDUAL
Isotropic thermal model: Isotropic Individual Temperature Factors Refined
Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.201 / ESU R Free: 0.18 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2434 2079 5 %RANDOM
Rwork0.18975 ---
all0.19246 39714 --
obs0.19246 39714 95.1 %-
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: 12.37 Å2
Baniso -1Baniso -2Baniso -3
1-0.89 Å2-0 Å20.58 Å2
2---0.75 Å2-0 Å2
3----0.08 Å2
Refinement stepCycle: LAST / Resolution: 2→29.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4540 0 15 443 4998
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0224708
X-RAY DIFFRACTIONr_bond_other_d0.0010.023035
X-RAY DIFFRACTIONr_angle_refined_deg1.261.9646429
X-RAY DIFFRACTIONr_angle_other_deg0.8337498
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.7045629
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.86525.667180
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.76715744
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.8181516
X-RAY DIFFRACTIONr_chiral_restr0.0810.2745
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0215351
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02855
X-RAY DIFFRACTIONr_mcbond_it1.0461.53113
X-RAY DIFFRACTIONr_mcbond_other0.3331.51260
X-RAY DIFFRACTIONr_mcangle_it1.70524979
X-RAY DIFFRACTIONr_scbond_it3.07631595
X-RAY DIFFRACTIONr_scangle_it4.7514.51450
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.276 144 -
Rwork0.212 2772 -
obs-2772 91.3 %
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)
11.8047-0.09910.15972.47670.25211.3660.1008-0.1854-0.020.0586-0.17640.0850.0996-0.16470.07560.0395-0.00190.01860.0716-0.00350.01716.80718.987338.7881
22.03151.18530.70974.4660.43141.68750.0344-0.1175-0.1328-0.11880.0624-0.44050.11490.1916-0.09690.01470.01410.01410.06120.01020.097330.57694.150834.9113
31.4557-0.03920.06012.79910.57720.54160.0224-0.120.0068-0.1734-0.0366-0.1769-0.0652-0.0290.01420.02950.00950.01480.07140.00990.021324.166812.771634.8175
40.6979-0.4112-0.19592.02810.82822.03290.0742-0.04810.0972-0.0363-0.077-0.00460.0161-0.04320.00280.0249-0.0077-0.00150.01-0.00840.024513.841728.145642.4422
51.547-0.4348-0.33143.57880.10250.97520.038-0.0255-0.0833-0.1415-0.18130.4204-0.0218-0.06640.14330.0107-0.0071-0.0210.063-0.02350.06817.988611.198837.1651
61.03860.14780.11282.8080.74741.18530.02840.09490.1437-0.0739-0.0765-0.0069-0.088-0.00540.0480.02870.00030.00160.02020.0130.02218.066412.851278.0281
76.1311-1.79390.66382.4805-0.15282.4311-0.09910.00080.22390.13860.1308-0.5058-0.0010.2186-0.03170.00840.0052-0.03370.0396-0.01260.148131.82166.892783.0731
81.3373-0.0453-0.02532.640.57640.76930.02250.0229-0.03980.1248-0.0658-0.1163-0.0157-0.00790.04330.03340.0033-0.00890.03880.01110.015421.59265.082781.026
90.73250.2670.10941.66511.04041.73110.04250.0766-0.0681-0.0552-0.07110.0038-0.0292-0.07390.02860.02470.01520.00830.017-0.00480.016612.132-10.714869.9309
101.7311.02780.44192.82760.14660.98730.0348-0.04040.03510.0993-0.10390.15110.0228-0.10330.06910.00810.0030.00970.0434-0.01990.03176.69344.572579.1235
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 20
2X-RAY DIFFRACTION2A21 - 42
3X-RAY DIFFRACTION3A43 - 119
4X-RAY DIFFRACTION4A120 - 248
5X-RAY DIFFRACTION5A249 - 309
6X-RAY DIFFRACTION6B1 - 30
7X-RAY DIFFRACTION7B31 - 42
8X-RAY DIFFRACTION8B43 - 118
9X-RAY DIFFRACTION9B119 - 232
10X-RAY DIFFRACTION10B233 - 309

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