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- PDB-4r0m: Structure of McyG A-PCP complexed with phenylalanyl-adenylate -

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Basic information

Entry
Database: PDB / ID: 4r0m
TitleStructure of McyG A-PCP complexed with phenylalanyl-adenylate
ComponentsMcyG protein
KeywordsLIGASE / phenylalanyl-AMP / adenylation domain / Acetyl-CoA synthetase-like domain / Acyl carrier protein-like domain / peptidyl carrier protein like domain / phenylalanyl-AMP binding
Function / homology
Function and homology information


phosphopantetheine binding / transferase activity
Similarity search - Function
: / Methyltransferase type 12 / Methyltransferase domain / ACP-like / ANL, C-terminal domain / ANL, N-terminal domain / Polyketide synthase, ketoreductase domain / KR domain / Malonyl-CoA ACP transacylase, ACP-binding / Polyketide synthase, C-terminal extension ...: / Methyltransferase type 12 / Methyltransferase domain / ACP-like / ANL, C-terminal domain / ANL, N-terminal domain / Polyketide synthase, ketoreductase domain / KR domain / Malonyl-CoA ACP transacylase, ACP-binding / Polyketide synthase, C-terminal extension / Ketoacyl-synthetase C-terminal extension / ANL, N-terminal domain / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A / Acyl transferase domain superfamily / Acyl transferase / Acyl transferase domain / Acyl transferase domain in polyketide synthase (PKS) enzymes. / Acyl transferase/acyl hydrolase/lysophospholipase / AMP-binding, conserved site / Putative AMP-binding domain signature. / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / GMP Synthetase; Chain A, domain 3 / Beta-ketoacyl synthase / AMP-dependent synthetase/ligase / AMP-binding enzyme / Beta-ketoacyl synthase, active site / Ketosynthase family 3 (KS3) active site signature. / Polyketide synthase, beta-ketoacyl synthase domain / Beta-ketoacyl synthase, N-terminal / Beta-ketoacyl synthase, C-terminal / Beta-ketoacyl synthase, N-terminal domain / Beta-ketoacyl synthase, C-terminal domain / Thiolase-like / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / NAD(P)-binding domain superfamily / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-[PHENYLALANINYL-PHOSPHATE] / McyG protein
Similarity search - Component
Biological speciesMicrocystis aeruginosa PCC 7806 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.45 Å
AuthorsTan, X.F. / Dai, Y.N. / Zhou, K. / Jiang, Y.L. / Ren, Y.M. / Chen, Y.X. / Zhou, C.Z.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2015
Title: Structure of the adenylation-peptidyl carrier protein didomain of the Microcystis aeruginosa microcystin synthetase McyG.
Authors: Tan, X.F. / Dai, Y.N. / Zhou, K. / Jiang, Y.L. / Ren, Y.M. / Chen, Y. / Zhou, C.Z.
History
DepositionAug 1, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 15, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Database references / Derived calculations / Category: citation / citation_author / struct_conn
Item: _citation.country / _citation.journal_id_CSD ..._citation.country / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: McyG protein
A: McyG protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,2324
Polymers146,2432
Non-polymers9892
Water46826
1
B: McyG protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,6162
Polymers73,1221
Non-polymers4941
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
A: McyG protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,6162
Polymers73,1221
Non-polymers4941
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)120.710, 120.710, 262.780
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein McyG protein


Mass: 73121.586 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Microcystis aeruginosa PCC 7806 (bacteria)
Gene: mcyG, IPF_370 / Production host: Escherichia coli (E. coli) / References: UniProt: A8YJW1
#2: Chemical ChemComp-FA5 / ADENOSINE-5'-[PHENYLALANINYL-PHOSPHATE]


Type: RNA linking / Mass: 494.395 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H23N6O8P
#3: Water ChemComp-HOH / 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: 3.78 Å3/Da / Density % sol: 67.45 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1.8M (NH4)2SO4, 0.1M NaKHPO4, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979228 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 10, 2012
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979228 Å / Relative weight: 1
ReflectionResolution: 2.45→54.845 Å / Num. all: 81516 / Num. obs: 81008 / % possible obs: 99.4 % / Observed criterion σ(F): -3 / Observed criterion σ(I): 0
Reflection shellResolution: 2.45→2.58 Å / % possible all: 98.7

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SOLVEphasing
REFMAC5.6.0117refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.45→54.845 Å / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.27348 4063 RANDOM
Rwork0.24671 --
obs0.24807 76945 -
all-78148 -
Refinement stepCycle: LAST / Resolution: 2.45→54.845 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9475 0 68 26 9569
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.029739
X-RAY DIFFRACTIONr_angle_refined_deg0.9561.97313215
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.5351190
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.15725.58448
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.817151692
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1651535
X-RAY DIFFRACTIONr_chiral_restr0.060.21511
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0217254
LS refinement shellResolution: 2.45→2.514 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.362 296 -
Rwork0.34 5324 -
obs--98.37 %

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