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- PDB-2h1y: Crystal structure of malonyl-CoA:Acyl carrier protein transacylas... -

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Basic information

Entry
Database: PDB / ID: 2h1y
TitleCrystal structure of malonyl-CoA:Acyl carrier protein transacylase (MCAT) from Helicobacter pylori
ComponentsMalonyl coenzyme A-acyl carrier protein transacylase
KeywordsTRANSFERASE / FabD / MCAT
Function / homology
Function and homology information


[acyl-carrier-protein] S-malonyltransferase / [acyl-carrier-protein] S-malonyltransferase activity
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 speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsZhang, L. / Liu, W. / Shen, X. / Jiang, H.
CitationJournal: Protein Sci. / Year: 2007
Title: Malonyl-CoA: acyl carrier protein transacylase from Helicobacter pylori: Crystal structure and its interaction with acyl carrier protein
Authors: Zhang, L. / Liu, W. / Xiao, J. / Hu, T. / Chen, J. / Chen, K. / Jiang, H. / Shen, X.
History
DepositionMay 17, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 22, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Oct 25, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Malonyl coenzyme A-acyl carrier protein transacylase
B: Malonyl coenzyme A-acyl carrier protein transacylase


Theoretical massNumber of molelcules
Total (without water)71,6072
Polymers71,6072
Non-polymers00
Water46826
1
A: Malonyl coenzyme A-acyl carrier protein transacylase


Theoretical massNumber of molelcules
Total (without water)35,8031
Polymers35,8031
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Malonyl coenzyme A-acyl carrier protein transacylase


Theoretical massNumber of molelcules
Total (without water)35,8031
Polymers35,8031
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.616, 76.175, 99.768
Angle α, β, γ (deg.)90.00, 101.22, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Malonyl coenzyme A-acyl carrier protein transacylase / MCAT / malonyl-CoA:Acyl carrier protein transacylase


Mass: 35803.258 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Strain: SS1 / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): M15
References: UniProt: Q56S05, [acyl-carrier-protein] S-malonyltransferase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 26 / 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: 2.27 Å3/Da / Density % sol: 45.81 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1M Hepes, 10% v/v PEG10000, 8% v/v MPD, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Mar 15, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 22318 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rmerge(I) obs: 0.065 / Rsym value: 0.065 / Χ2: 1.059 / Net I/σ(I): 14.2
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.452 / Mean I/σ(I) obs: 2.8 / Num. unique all: 2234 / Rsym value: 0.452 / Χ2: 1.019 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.2.0005refinement
PDB_EXTRACT2data extraction
CrystalCleardata reduction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1NM2

1nm2


Resolution: 2.5→36.7 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.919 / SU B: 11.948 / SU ML: 0.261 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 1.037 / ESU R Free: 0.324 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.262 1126 5.1 %RANDOM
Rwork0.215 ---
all0.217 ---
obs-22004 98.29 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 55.749 Å2
Baniso -1Baniso -2Baniso -3
1-2.26 Å20 Å20.45 Å2
2---0.73 Å20 Å2
3----1.36 Å2
Refinement stepCycle: LAST / Resolution: 2.5→36.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4852 0 0 26 4878
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0224934
X-RAY DIFFRACTIONr_angle_refined_deg1.4091.9776633
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5335621
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.98825.607214
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.30115934
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.891514
X-RAY DIFFRACTIONr_chiral_restr0.1010.2742
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023634
X-RAY DIFFRACTIONr_nbd_refined0.2290.22314
X-RAY DIFFRACTIONr_nbtor_refined0.3040.23379
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1420.2169
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1840.232
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2130.24
X-RAY DIFFRACTIONr_mcbond_it0.6071.53173
X-RAY DIFFRACTIONr_mcangle_it1.07524931
X-RAY DIFFRACTIONr_scbond_it1.42931957
X-RAY DIFFRACTIONr_scangle_it2.3194.51702
LS refinement shellResolution: 2.498→2.563 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.359 81 -
Rwork0.296 1502 -
obs-1583 94.11 %

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