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- PDB-2mbr: MURB WILD TYPE, COMPLEX WITH ENOLPYRUVYL-UDP-N-ACETYLGLUCOSAMINE -

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Basic information

Entry
Database: PDB / ID: 2mbr
TitleMURB WILD TYPE, COMPLEX WITH ENOLPYRUVYL-UDP-N-ACETYLGLUCOSAMINE
ComponentsURIDINE DIPHOSPHO-N-ACETYLENOLPYRUVYLGLUCOSAMINE REDUCTASE
KeywordsOXIDOREDUCTASE / PEPTIDOGLYCAN SYNTHESIS / CELL WALL / CELL DIVISION / NADP / FLAVOPROTEIN / FAD
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 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-EPU / FLAVIN-ADENINE DINUCLEOTIDE / UDP-N-acetylenolpyruvoylglucosamine reductase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.8 Å
AuthorsBenson, T.E. / Walsh, C.T. / Hogle, J.M.
Citation
Journal: Biochemistry / Year: 1997
Title: X-ray crystal structures of the S229A mutant and wild-type MurB in the presence of the substrate enolpyruvyl-UDP-N-acetylglucosamine at 1.8-A resolution.
Authors: Benson, T.E. / Walsh, C.T. / Hogle, J.M.
#1: Journal: Nat.Struct.Biol. / Year: 1995
Title: An Enzyme-Substrate Complex Involved in Bacterial Cell Wall Biosynthesis
Authors: Benson, T.E. / Filman, D.J. / Walsh, C.T. / Hogle, J.M.
#2: Journal: Int.Immunol. / Year: 1994
Title: Crystallization and Preliminary X-Ray Crystallographic Studies of Udp-N-Acetyl Enolpyruvylglucosamine Reductase
Authors: Benson, T.E. / Walsh, C.T. / Hogle, J.M.
#3: Journal: Biochemistry / Year: 1993
Title: Overexpression, Purification, and Mechanistic Study of Udp-N-Acetylenolpyruvylglucosamine Reductase
Authors: Benson, T.E. / Marquardt, J.L. / Marquardt, A.C. / Etzkorn, F.A. / Walsh, C.T.
History
DepositionNov 8, 1996Processing site: BNL
SupersessionApr 1, 1997ID: 1MBR
Revision 1.0Apr 1, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 21, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _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: URIDINE DIPHOSPHO-N-ACETYLENOLPYRUVYLGLUCOSAMINE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,1103
Polymers37,6471
Non-polymers1,4632
Water4,270237
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.300, 49.300, 262.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein URIDINE DIPHOSPHO-N-ACETYLENOLPYRUVYLGLUCOSAMINE REDUCTASE / MURB


Mass: 37646.613 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-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.: 237 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.12 Å3/Da / Density % sol: 41.91 %
Crystal growpH: 8 / Details: pH 8.0
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
215-18 %PEG80001reservoir
3100 mMHEPES1reservoir
4200 mMcalcium acetate1reservoir
57 mMEP-UDP-GlcNAc1reservoir

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C
RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.8→20 Å / Num. obs: 28829 / % possible obs: 91.6 %
Reflection
*PLUS
Redundancy: 7.5 % / Rmerge(I) obs: 0.042
Reflection shell
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 1.88 Å / % possible obs: 77.3 % / Redundancy: 6.4 % / Num. unique obs: 2962 / Rmerge(I) obs: 0.157 / Mean I/σ(I) obs: 12.3

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 1.8→20 Å / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.256 --
Rwork0.203 --
obs0.203 28770 91.6 %
Refinement stepCycle: LAST / Resolution: 1.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2653 0 98 237 2988
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
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_deg1.56
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_improper_angle_deg / Dev ideal: 1.35

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