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- PDB-1p4n: Crystal Structure of Weissella viridescens FemX:UDP-MurNAc-pentap... -

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Basic information

Entry
Database: PDB / ID: 1p4n
TitleCrystal Structure of Weissella viridescens FemX:UDP-MurNAc-pentapeptide complex
Components
  • FemX
  • UDP-MurNAc-pentapeptide
KeywordsTransferase/Transferase Substrate / FemX / Transferase-Transferase Substrate complex
Function / homology
Function and homology information


UDP-N-acetylmuramoylpentapeptide-lysine N6-alanyltransferase / UDP-N-acetylmuramoylpentapeptide-lysine N6-alanyltransferase activity / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape
Similarity search - Function
FemABX peptidyl transferase / : / FemAB family / FemABX peptidyl transferase family profile. / Gcn5-related N-acetyltransferase (GNAT) / Acyl-CoA N-acyltransferase / Aminopeptidase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / UDP-N-acetylmuramoylpentapeptide-lysine N(6)-alanyltransferase
Similarity search - Component
Biological speciesWeissella viridescens (bacteria)
Staphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / difference fourier synthesis / Resolution: 1.9 Å
AuthorsBiarrotte-Sorin, S. / Maillard, A. / Delettre, J. / Sougakoff, W. / Arthur, M. / Mayer, C.
CitationJournal: Structure / Year: 2004
Title: Crystal structures of Weissella viridescens FemX and its complex with UDP-MurNAc-pentapeptide: insights into FemABX family substrates recognition.
Authors: Biarrotte-Sorin, S. / Maillard, A.P. / Delettre, J. / Sougakoff, W. / Arthur, M. / Mayer, C.
History
DepositionApr 23, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 10, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 27, 2011Group: Database references / Derived calculations / Non-polymer description
Revision 1.4Aug 1, 2012Group: Structure summary
Revision 1.5Aug 16, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_validate_polymer_linkage / struct_conn / 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.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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 600HETEROGEN The residue FGA is gamma-glutamic acid but does not make classical peptide bond. It makes ...HETEROGEN The residue FGA is gamma-glutamic acid but does not make classical peptide bond. It makes peptide bond on the side chain at the Cgamma.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: FemX
B: UDP-MurNAc-pentapeptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,6047
Polymers39,3472
Non-polymers2575
Water8,395466
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2460 Å2
ΔGint-30 kcal/mol
Surface area15530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.201, 100.610, 46.538
Angle α, β, γ (deg.)90.00, 115.64, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein FemX


Mass: 38195.801 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Weissella viridescens (bacteria) / Gene: femx / Plasmid: pTYB2 / Production host: Escherichia coli (E. coli) / Strain (production host): ER2566
References: GenBank: 11999275, UniProt: Q9EY50*PLUS, UDP-N-acetylmuramoylpentapeptide-lysine N6-alanyltransferase
#2: Protein/peptide UDP-MurNAc-pentapeptide


Mass: 1150.943 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria)
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 466 / 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: 2.23 Å3/Da / Density % sol: 44.8 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG 2K, NaCl, sodium cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
110 mg/mlprotein1drop
225 %PEG20001reservoir
3300 mM1reservoirNaCl
4100 mMcacodylate1reservoirpH6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.979711 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 14, 2002
Details: two crystals monochromator between two cylindrical parabolic mirrors
RadiationMonochromator: Sagitally focused Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979711 Å / Relative weight: 1
ReflectionResolution: 1.9→15.57 Å / Num. obs: 27221 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 12.7 Å2 / Rsym value: 0.073 / Net I/σ(I): 7.5
Reflection shellResolution: 1.9→2 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 3.7 / Num. unique all: 3947 / Rsym value: 0.19 / % possible all: 98
Reflection
*PLUS
Num. measured all: 102033 / Rmerge(I) obs: 0.073
Reflection shell
*PLUS
% possible obs: 98 % / Rmerge(I) obs: 0.19

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Processing

Software
NameVersionClassification
CNS1refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
CNSphasing
RefinementMethod to determine structure: difference fourier synthesis
Starting model: PDB ENTRY 1NE9

1ne9


Resolution: 1.9→15.57 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1090877 / Data cutoff high rms absF: 1090877 / Data cutoff low absF: 0 / Isotropic thermal model: OVERALL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.207 1351 5 %RANDOM
Rwork0.172 ---
all0.185 ---
obs0.172 27014 97.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 54.1592 Å2 / ksol: 0.39732 e/Å3
Displacement parametersBiso mean: 16.3 Å2
Baniso -1Baniso -2Baniso -3
1--2.08 Å20 Å23.16 Å2
2---0.35 Å20 Å2
3---2.43 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.21 Å
Luzzati d res low-6 Å
Luzzati sigma a0.2 Å0.19 Å
Refinement stepCycle: LAST / Resolution: 1.9→15.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2763 0 15 466 3244
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d22.8
X-RAY DIFFRACTIONc_improper_angle_d0.82
X-RAY DIFFRACTIONc_mcbond_it1.9
X-RAY DIFFRACTIONc_mcangle_it2.48
X-RAY DIFFRACTIONc_scbond_it1.8
X-RAY DIFFRACTIONc_scangle_it2.6
LS refinement shellResolution: 1.9→2 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.265 212 4.8 %
Rwork0.209 4207 -
obs-3947 96.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
Refinement
*PLUS
Highest resolution: 1.9 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.8
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.8
LS refinement shell
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 2 Å

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