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- PDB-1amu: PHENYLALANINE ACTIVATING DOMAIN OF GRAMICIDIN SYNTHETASE 1 IN A C... -

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Basic information

Entry
Database: PDB / ID: 1amu
TitlePHENYLALANINE ACTIVATING DOMAIN OF GRAMICIDIN SYNTHETASE 1 IN A COMPLEX WITH AMP AND PHENYLALANINE
ComponentsGRAMICIDIN SYNTHETASE 1
KeywordsPEPTIDE SYNTHETASE / GRSA / ADENYLATE FORMING
Function / homology
Function and homology information


phenylalanine racemase (ATP-hydrolysing) / phenylalanine racemase (ATP-hydrolyzing) activity / ligase activity / antibiotic biosynthetic process / ATP binding
Similarity search - Function
Rossmann fold - #980 / Luciferase; domain 3 / Luciferase; Domain 3 / Non-ribosomal peptide synthase / ANL, C-terminal domain / Condensation domain / Condensation domain / Amino acid adenylation domain / AMP-binding enzyme, C-terminal domain / AMP-binding enzyme C-terminal domain ...Rossmann fold - #980 / Luciferase; domain 3 / Luciferase; Domain 3 / Non-ribosomal peptide synthase / ANL, C-terminal domain / Condensation domain / Condensation domain / Amino acid adenylation domain / AMP-binding enzyme, C-terminal domain / AMP-binding enzyme C-terminal domain / AMP-binding, conserved site / Chloramphenicol acetyltransferase-like domain superfamily / Putative AMP-binding domain signature. / GMP Synthetase; Chain A, domain 3 / AMP-dependent synthetase/ligase / AMP-binding enzyme / Phosphopantetheine attachment site / Phosphopantetheine attachment site. / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / Roll / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / PHENYLALANINE / Gramicidin S synthase 1 / Gramicidin S synthase 1
Similarity search - Component
Biological speciesBrevibacillus brevis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.9 Å
AuthorsConti, E. / Stachelhaus, T. / Marahiel, M.A. / Brick, P.
Citation
Journal: EMBO J. / Year: 1997
Title: Structural basis for the activation of phenylalanine in the non-ribosomal biosynthesis of gramicidin S.
Authors: Conti, E. / Stachelhaus, T. / Marahiel, M.A. / Brick, P.
#1: Journal: J.Biol.Chem. / Year: 1995
Title: Modular Structure of Peptide Synthetases Revealed by Dissection of the Multifunctional Enzyme Grsa
Authors: Stachelhaus, T. / Marahiel, M.A.
History
DepositionJun 18, 1997Processing site: BNL
Revision 1.0Jul 1, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / 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 / _diffrn_source.pdbx_synchrotron_site / _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.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.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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.ptnr2_auth_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_conn.ptnr2_label_seq_id / _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: GRAMICIDIN SYNTHETASE 1
B: GRAMICIDIN SYNTHETASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,52910
Polymers128,2642
Non-polymers1,2668
Water10,251569
1
A: GRAMICIDIN SYNTHETASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,7655
Polymers64,1321
Non-polymers6334
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: GRAMICIDIN SYNTHETASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,7655
Polymers64,1321
Non-polymers6334
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.680, 154.770, 65.300
Angle α, β, γ (deg.)90.00, 93.91, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein GRAMICIDIN SYNTHETASE 1 / GRSA


Mass: 64131.793 Da / Num. of mol.: 2
Fragment: ADENYLATE FORMING DOMAIN, RESIDUES 1 - 556 PLUS A 7 RESIDUE C-TERMINAL TAG - SHHHHHH
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brevibacillus brevis (bacteria) / Gene: GRSA / Plasmid: PQE60 / Production host: Escherichia coli (E. coli) / Strain (production host): M15(PREP4)
References: UniProt: P14687, UniProt: P0C061*PLUS, phenylalanine racemase (ATP-hydrolysing)

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Non-polymers , 5 types, 577 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-PHE / PHENYLALANINE / Phenylalanine


Type: L-peptide linking / Mass: 165.189 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H11NO2
#5: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE / Adenosine monophosphate


Mass: 347.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 569 / 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: 2.5 Å3/Da / Density % sol: 50 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 6.5
Details: CRYSTALS WERE GROWN USING THE VAPOR DIFFUSION TECHNIQUE. THE PROTEIN AT 15 MG/ML IN 10 MM TRIS-HCL PH7.8, 50 MM NACL, 15% GLYCEROL, 2 MM ATP, 2 MM L-PHE AND 4 MM MGCL2 WAS EQUILIBRATED WITH ...Details: CRYSTALS WERE GROWN USING THE VAPOR DIFFUSION TECHNIQUE. THE PROTEIN AT 15 MG/ML IN 10 MM TRIS-HCL PH7.8, 50 MM NACL, 15% GLYCEROL, 2 MM ATP, 2 MM L-PHE AND 4 MM MGCL2 WAS EQUILIBRATED WITH AN EQUAL VOLUME OF RESERVOIR SOLUTION CONTAINING 28-32%(W/V) METHOXY POLYETHYLENE GLYCOL 5000, 200 MM AMMONIUM SULFATE, AND 100 MM ADA PH6.5 AT 18C., vapor diffusion, temperature 291K
Crystal grow
*PLUS
Temperature: 18 ℃ / pH: 7.8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
115 mg/mlprotein1drop
210 mMTris-HCl1drop
350 mM1dropNaCl
415 %glycerol1drop
52 mMATP1drop
62 mML-phenylalanine1drop
74 mM1dropMgCl2
828-32 %(w/v)MePEG50001reservoir
9200 mMammonium sulfate1reservoir
10100 mMADA1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.88
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Sep 9, 1996
RadiationMonochromator: Y / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.88 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. obs: 91144 / % possible obs: 96.4 % / Redundancy: 2.5 % / Rmerge(I) obs: 0.051 / Net I/σ(I): 7.3
Reflection shellResolution: 1.9→2 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.232 / Mean I/σ(I) obs: 2.7 / % possible all: 88.3
Reflection
*PLUS
Num. measured all: 230285
Reflection shell
*PLUS
% possible obs: 88.3 %

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
CCP4SUITEdata reduction
X-PLOR3.1model building
X-PLOR3.1refinement
CCP4data scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MIR / Resolution: 1.9→20 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 0 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.246 3656 4 %RANDOM
Rwork0.213 ---
obs0.213 91142 95.3 %-
Displacement parametersBiso mean: 33 Å2
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7897 0 54 569 8520
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.37
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.1
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.1
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.5
X-RAY DIFFRACTIONx_mcangle_it2
X-RAY DIFFRACTIONx_scbond_it2
X-RAY DIFFRACTIONx_scangle_it2
Refine LS restraints NCSNCS model details: UNRESTRAINED
LS refinement shellResolution: 1.9→1.99 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.331 437 3.31 %
Rwork0.331 9969 -
obs--87.12 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM19.SOLTOPH.SOL
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.1
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.1

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