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- PDB-1nm2: Malonyl-CoA:ACP Transacylase -

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Basic information

Entry
Database: PDB / ID: 1nm2
TitleMalonyl-CoA:ACP Transacylase
Componentsmalonyl CoA:acyl carrier protein malonyltransferase
KeywordsTRANSFERASE / ALPHA/BETA HYDROLASE-LIKE CORE / ACETATE BOUND TO ACTIVE SITE MIMICKING A MALONYL GROUP
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 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 / Acyl transferase domain / Acyl transferase domain in polyketide synthase (PKS) enzymes. / Acyl transferase domain superfamily / Acyl transferase/acyl hydrolase/lysophospholipase ...: / 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 / Acyl transferase domain / Acyl transferase domain in polyketide synthase (PKS) enzymes. / Acyl transferase domain superfamily / Acyl transferase/acyl hydrolase/lysophospholipase / Alpha-Beta Plaits / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETIC ACID / NICKEL (II) ION / [acyl-carrier-protein] S-malonyltransferase
Similarity search - Component
Biological speciesStreptomyces coelicolor (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsKeatinge-Clay, A.T. / Shelat, A.A. / Savage, D.F. / Tsai, S. / Miercke, L.J.W. / O'Connell III, J.D. / Khosla, C. / Stroud, R.M.
CitationJournal: Structure / Year: 2003
Title: Catalysis, Specificity, and ACP Docking Site of Streptomyces coelicolor Malonyl-CoA:ACP Transacylase
Authors: Keatinge-Clay, A.T. / Shelat, A.A. / Savage, D.F. / Tsai, S. / Miercke, L.J.W. / O'Connell III, J.D. / Khosla, C. / Stroud, R.M.
History
DepositionJan 8, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 21, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Sep 5, 2018Group: Data collection / Structure summary / Category: struct / Item: _struct.title
Revision 1.4Aug 16, 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 / pdbx_struct_conn_angle / 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_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.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _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.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _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_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_ref_seq_dif.details / _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: malonyl CoA:acyl carrier protein malonyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,4264
Polymers32,2471
Non-polymers1793
Water1,946108
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.067, 54.486, 109.880
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein malonyl CoA:acyl carrier protein malonyltransferase


Mass: 32246.709 Da / Num. of mol.: 1 / Fragment: Malonyl-CoA:ACP Transacylase
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces coelicolor (bacteria) / Strain: A3(2) / Gene: FABD / Plasmid: pET28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P72391, [acyl-carrier-protein] S-malonyltransferase
#2: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#3: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H4O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 108 / 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 Å3/Da / Density % sol: 38.43 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 5.4
Details: PEG 4000, sodium acetate, ammonium acetate, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 297.0K
Crystal grow
*PLUS
pH: 7.4
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mMTris-HCl1droppH7.4
21 mMbeta-mercaptoethanol1drop
33 mg/mlprotein1drop
425 %PEG40001reservoir
5100 mMsodium acetate1reservoirpH4.8
6200 mMammonium acetate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.127 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jan 15, 2002
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.127 Å / Relative weight: 1
ReflectionResolution: 2→48.81 Å / Num. obs: 17011 / % possible obs: 93.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 16.7 Å2 / Limit h max: 21 / Limit h min: 0 / Limit k max: 26 / Limit k min: 0 / Limit l max: 54 / Limit l min: 0 / Observed criterion F max: 1282968.78 / Observed criterion F min: 12.5 / Rsym value: 0.081 / Net I/σ(I): 6.2
Reflection shellResolution: 2→2.13 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 1.7 / Num. unique all: 2268 / Rsym value: 0.412 / % possible all: 85.6
Reflection
*PLUS
Highest resolution: 2 Å / Num. measured all: 65258 / Rmerge(I) obs: 0.081
Reflection shell
*PLUS
% possible obs: 85.6 % / Rmerge(I) obs: 0.412

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Processing

Software
NameVersionClassificationNB
CNS1.1refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1MLA

1mla


Resolution: 2→48.81 Å / Rfactor Rfree error: 0.006 / Occupancy max: 1 / Occupancy min: 1 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.232 1701 10 %RANDOM
Rwork0.197 ---
all0.232 18132 --
obs0.232 17011 93.8 %-
Solvent computationSolvent model: CNS bulk solvent model used / Bsol: 51.2305 Å2 / ksol: 0.389125 e/Å3
Displacement parametersBiso max: 62.24 Å2 / Biso mean: 22.73 Å2 / Biso min: 11.39 Å2
Baniso -1Baniso -2Baniso -3
1--1.03 Å20 Å20 Å2
2--0.14 Å20 Å2
3---0.89 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.18 Å0.14 Å
Luzzati d res high-2
Refinement stepCycle: LAST / Resolution: 2→48.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2183 0 9 108 2300
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.005
X-RAY DIFFRACTIONx_angle_deg1.2
X-RAY DIFFRACTIONx_torsion_deg21.7
X-RAY DIFFRACTIONx_torsion_impr_deg0.79
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRfactor Rfree errorNum. reflection allNum. reflection obs% reflection obs (%)
2-2.090.2661839.80.23116820.022218186584.1
2.09-2.20.25522411.20.20517750.0172237199989.4
2.2-2.340.2271768.70.18518550.0172226203191.2
2.34-2.520.24521510.30.218740.0172238208993.3
2.52-2.770.2652109.70.20119460.0182256215695.6
2.77-3.170.21923310.70.18719480.0142271218196
3.17-40.2182199.70.17820490.0152285226899.3
4-48.810.223241100.21321810.0142425242299.9
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 2 Å / % reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDType
X-RAY DIFFRACTIONc_bond_d
X-RAY DIFFRACTIONc_angle_deg

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