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- PDB-2gqu: Crystal Structure of UDP-N-Acetylenolpyruvylglucosamine Reductase... -

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Basic information

Entry
Database: PDB / ID: 2gqu
TitleCrystal Structure of UDP-N-Acetylenolpyruvylglucosamine Reductase (MurB) from Thermus caldophilus
ComponentsUDP-N-Acetylenolpyruvylglucosamine Reductase
KeywordsOXIDOREDUCTASE / peptidoglycan biosynthesis / enolpyruvyl-UDP-N-acetylglucosamine / flavin adenine dinucleotide / substrate complex / enzyme
Function / homology
Function and homology information


UDP-N-acetylmuramate dehydrogenase / UDP-N-acetylmuramate dehydrogenase activity / peptidoglycan biosynthetic process / FAD binding / cell wall organization / regulation of cell shape / cell cycle / cell division / cytosol
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-EPU / FLAVIN-ADENINE DINUCLEOTIDE / UDP-N-acetylenolpyruvoylglucosamine reductase
Similarity search - Component
Biological speciesThermus caldophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsEom, S.H. / Kim, M.-K.
CitationJournal: Proteins / Year: 2006
Title: Crystal structure of UDP-N-acetylenolpyruvylglucosamine reductase (MurB) from Thermus caldophilus
Authors: Kim, M.-K. / Cho, M.K. / Song, H.-E. / Kim, D. / Park, B.-H. / Lee, J.H. / Kang, G.B. / Kim, S.H. / Im, Y.J. / Lee, D.-S. / Eom, S.H.
History
DepositionApr 21, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 19, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

Downloads & links

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Assembly

Deposited unit
A: UDP-N-Acetylenolpyruvylglucosamine Reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,0923
Polymers29,6291
Non-polymers1,4632
Water7,332407
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)29.817, 46.850, 48.593
Angle α, β, γ (deg.)65.26, 76.13, 84.01
Int Tables number1
Space group name H-MP1

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Components

#1: Protein UDP-N-Acetylenolpyruvylglucosamine Reductase


Mass: 29629.191 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus caldophilus (bacteria) / Plasmid: pKK223-3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5SJC8*PLUS, EC: 1.1.1.158
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-EPU / URIDINE-DIPHOSPHATE-2(N-ACETYLGLUCOSAMINYL) BUTYRIC ACID / ENOLPYRUVYL-URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE


Mass: 677.400 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H29N3O19P2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 407 / 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: 2.02 Å3/Da / Density % sol: 39.08 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 100mM Mes-NaOH (pH 6.5), 18% (w/v) PEG 8000, 200mM CaCl2, 25mM substrate (EP-UDPGlcNAc), VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 26, 2005
RadiationMonochromator: Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. all: 29519 / Num. obs: 29087 / % possible obs: 95.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.6→1.63 Å / % possible all: 89.2

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
ADSCdata collection
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→25.96 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.94 / SU B: 3.821 / SU ML: 0.063 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.213 / ESU R Free: 0.113 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2232 1467 5 %RANDOM
Rwork0.16972 ---
obs0.17245 27619 95.13 %-
all-27619 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.219 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0 Å20.02 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.6→25.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2066 0 97 407 2570
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0222208
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4012.0432997
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0185265
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.87822.73795
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.55115374
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.1251524
X-RAY DIFFRACTIONr_chiral_restr0.1030.2326
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021648
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2130.21148
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3080.21493
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1630.2348
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1910.263
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1860.261
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0631.51342
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.69622090
X-RAY DIFFRACTIONr_scbond_it2.59431029
X-RAY DIFFRACTIONr_scangle_it3.7884.5907
X-RAY DIFFRACTIONr_rigid_bond_restr1.9832371
X-RAY DIFFRACTIONr_sphericity_free3.2353407
X-RAY DIFFRACTIONr_sphericity_bonded2.87432163
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.238 78 -
Rwork0.184 1916 -
obs--88.58 %

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