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- PDB-2q85: Crystal Structure of E. Coli Mur B bound to a Naphthyl Tetronic A... -

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Basic information

Entry
Database: PDB / ID: 2q85
TitleCrystal Structure of E. Coli Mur B bound to a Naphthyl Tetronic Acid inihibitor
ComponentsUDP-N-acetylenolpyruvoylglucosamine reductase
KeywordsOXIDOREDUCTASE
Function / homology
Function and homology information


UDP-N-acetylmuramate dehydrogenase / UDP-N-acetylmuramate dehydrogenase activity / peptidoglycan biosynthetic process / FAD binding / cell wall organization / flavin adenine dinucleotide binding / regulation of cell shape / cell cycle / cell division / cytosol / cytoplasm
Similarity search - Function
Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 1 / UDP-N-acetylenolpyruvoylglucosamine reductase, C-terminal domain / UDP-N-acetylenolpyruvoylglucosamine reductase / UDP-N-acetylenolpyruvoylglucosamine reductase, C-terminal / UDP-N-acetylenolpyruvoylglucosamine reductase, C-terminal domain superfamily / UDP-N-acetylenolpyruvoylglucosamine reductase, C-terminal domain / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase, domain 2 / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 2 / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 3 - #10 / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 3 ...Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 1 / UDP-N-acetylenolpyruvoylglucosamine reductase, C-terminal domain / UDP-N-acetylenolpyruvoylglucosamine reductase / UDP-N-acetylenolpyruvoylglucosamine reductase, C-terminal / UDP-N-acetylenolpyruvoylglucosamine reductase, C-terminal domain superfamily / UDP-N-acetylenolpyruvoylglucosamine reductase, C-terminal domain / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase, domain 2 / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 2 / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 3 - #10 / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 3 / FAD linked oxidase, N-terminal / FAD binding domain / FAD-binding, type PCMH, subdomain 1 / FAD-binding domain, PCMH-type / PCMH-type FAD-binding domain profile. / FAD-binding, type PCMH, subdomain 2 / FAD-binding, type PCMH-like superfamily / Alpha-Beta Complex / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-973 / FLAVIN-ADENINE DINUCLEOTIDE / UDP-N-acetylenolpyruvoylglucosamine reductase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.51 Å
AuthorsChopra, R. / Bard, J. / Svenson, K. / Mansour, T.
CitationJournal: TO BE PUBLISHED
Title: Crystal Structure of E. Coli Mur B bound to a napthyl tetronic acid inhibitor
Authors: Mansour, T. / Caulfield, C.E. / Rasmussen, B. / Chopra, R. / Krishnamurthy, G. / Morris, K.M. / Svenson, K. / Bard, J. / Smeltzer, C. / Naughton, S. / Antane, S. / Yang, Y. / Severin, A. / ...Authors: Mansour, T. / Caulfield, C.E. / Rasmussen, B. / Chopra, R. / Krishnamurthy, G. / Morris, K.M. / Svenson, K. / Bard, J. / Smeltzer, C. / Naughton, S. / Antane, S. / Yang, Y. / Severin, A. / Quagliato, D. / Petersen, P.J. / Singh, G.
History
DepositionJun 8, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 26, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 30, 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Assembly

Deposited unit
A: UDP-N-acetylenolpyruvoylglucosamine reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,0263
Polymers37,8921
Non-polymers1,1342
Water3,891216
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.993, 89.301, 50.943
Angle α, β, γ (deg.)90.00, 111.11, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein UDP-N-acetylenolpyruvoylglucosamine reductase / UDP-N- acetylmuramate dehydrogenase


Mass: 37891.910 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P08373, EC: 1.1.1.158
#2: Chemical ChemComp-973 / (5Z)-3-(4-CHLOROPHENYL)-4-HYDROXY-5-(1-NAPHTHYLMETHYLENE)FURAN-2(5H)-ONE


Mass: 348.779 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H13ClO3
#3: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 216 / 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: 2.35 Å3/Da / Density % sol: 47.67 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 25% Polyethyleneglycol 8000, 0.1 M Tris, pH 8.5, 0.1 M Calcium Acetate, Vapor Diffusion, Hanging Drop, temperature 291K, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Apr 23, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.5→35.87 Å / Num. all: 12098 / Num. obs: 11573 / % possible obs: 95.7 % / Observed criterion σ(I): 1.5 / Biso Wilson estimate: 40.3 Å2
Reflection shellResolution: 2.5→2.59 Å / Num. unique all: 1188 / % possible all: 0.871

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Processing

Software
NameVersionClassificationNB
REFMACrefinement
PDB_EXTRACT2data extraction
CrystalCleardata collection
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1mbt

1mbt


Resolution: 2.51→35.87 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.884 / SU B: 9.766 / SU ML: 0.218 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 3.816 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.244 964 95.1 %RANDOM
Rwork0.166 ---
obs0.24 11573 95.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.352 Å2
Baniso -1Baniso -2Baniso -3
1-0.69 Å20 Å20.89 Å2
2--0.09 Å20 Å2
3----0.14 Å2
Refinement stepCycle: LAST / Resolution: 2.51→35.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2662 0 78 216 2956
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0222810
X-RAY DIFFRACTIONr_bond_other_d0.0010.021837
X-RAY DIFFRACTIONr_angle_refined_deg0.7221.9783837
X-RAY DIFFRACTIONr_angle_other_deg0.72934486
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.2325340
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.81224.846130
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.29415442
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.9831514
X-RAY DIFFRACTIONr_chiral_restr0.0420.2419
X-RAY DIFFRACTIONr_gen_planes_refined0.0010.023130
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02550
X-RAY DIFFRACTIONr_nbd_refined0.1480.2530
X-RAY DIFFRACTIONr_nbd_other0.1590.21939
X-RAY DIFFRACTIONr_nbtor_refined0.1660.21353
X-RAY DIFFRACTIONr_nbtor_other0.0780.21388
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0630.2129
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0620.211
X-RAY DIFFRACTIONr_symmetry_vdw_other0.110.235
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0730.28
X-RAY DIFFRACTIONr_mcbond_it0.0991.52190
X-RAY DIFFRACTIONr_mcbond_other0.0051.5692
X-RAY DIFFRACTIONr_mcangle_it0.10322730
X-RAY DIFFRACTIONr_scbond_it0.03331415
X-RAY DIFFRACTIONr_scangle_it0.0534.51107
LS refinement shellResolution: 2.51→2.571 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.347 712 -
Rwork0.142 42 -
obs-754 87.1 %

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