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- PDB-1hsk: CRYSTAL STRUCTURE OF S. AUREUS MURB -

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Basic information

Entry
Database: PDB / ID: 1hsk
TitleCRYSTAL STRUCTURE OF S. AUREUS MURB
ComponentsUDP-N-ACETYLENOLPYRUVOYLGLUCOSAMINE 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 / regulation of cell shape / cell cycle / cell division / 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
FLAVIN-ADENINE DINUCLEOTIDE / UDP-N-acetylenolpyruvoylglucosamine reductase
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å
AuthorsBenson, T.E. / Harris, M.S. / Choi, G.H. / Cialdella, J.I. / Herberg, J.T. / Martin Jr., J.P. / Baldwin, E.T.
CitationJournal: Biochemistry / Year: 2001
Title: A structural variation for MurB: X-ray crystal structure of Staphylococcus aureus UDP-N-acetylenolpyruvylglucosamine reductase (MurB).
Authors: Benson, T.E. / Harris, M.S. / Choi, G.H. / Cialdella, J.I. / Herberg, J.T. / Martin Jr., J.P. / Baldwin, E.T.
History
DepositionDec 27, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 14, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 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 / 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
Remark 999SEQUENCE Using blast, an appropriate match was not found for the sequence of the protein at the ...SEQUENCE Using blast, an appropriate match was not found for the sequence of the protein at the time the entry was processed.

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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)36,8042
Polymers36,0191
Non-polymers7861
Water3,837213
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)178.990, 178.990, 178.990
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number199
Space group name H-MI213
Components on special symmetry positions
IDModelComponents
11A-505-

HOH

21A-513-

HOH

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Components

#1: Protein UDP-N-ACETYLENOLPYRUVOYLGLUCOSAMINE REDUCTASE / UDP-N-ACETYLMURAMATE DEHYDROGENASE


Mass: 36018.730 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P61431, EC: 1.1.1.158
#2: 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
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 213 / 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

Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: PEG 8000, cacodylic acid, ammonium sulfate, DMSO, 2-mercaptoethanol with EP-UDPGlcNAc , pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal grow
*PLUS
pH: 7.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 mMHEPES1drop
25 mM2-mercaptoethanol1drop
320 mg/mlprotein1drop
49.75 %PEG80001reservoir
50.1 Mcacodylic acid1reservoir
60.55 Mammonium sulfate1reservoir
720 %DMSO1reservoir
85 mM2-mercaptoethanol1reservoir
91 mMEP-UD-PGlcNAc substrate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1.0332, 0.97939, 0.97928
DetectorType: SIEMENS / Detector: CCD / Date: Jun 12, 1998
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.03321
20.979391
30.979281
ReflectionResolution: 2.3→10 Å / Num. all: 42374 / Num. obs: 39984 / % possible obs: 94.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.3 % / Biso Wilson estimate: 18.2 Å2 / Rmerge(I) obs: 0.075 / Net I/σ(I): 14.8
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 6 % / Rmerge(I) obs: 0.297 / % possible all: 51.8
Reflection
*PLUS
Num. measured all: 252156

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Processing

Software
NameVersionClassification
MLPHAREphasing
X-PLOR98refinement
SAINTdata reduction
SAINTdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.3→10 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.223 3249 9.8 %RANDOM
Rwork0.201 ---
all0.203 42374 --
obs0.201 33156 79.4 %-
Displacement parametersBiso mean: 28.9 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.24 Å0.23 Å
Refinement stepCycle: LAST / Resolution: 2.3→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2345 0 53 213 2611
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_deg1.4
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.65
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.111.5
X-RAY DIFFRACTIONx_mcangle_it1.842
X-RAY DIFFRACTIONx_scbond_it2.322
X-RAY DIFFRACTIONx_scangle_it3.662.5
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.254 405 9.9 %
Rwork0.233 3671 -
obs--59.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMTOPHCSDX.PRO
X-RAY DIFFRACTION3PARAM19.SOL
X-RAY DIFFRACTION2TOPH19.SOL
Software
*PLUS
Name: X-PLOR(ONLINE) / Version: 98 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 28.9 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_angle_deg1.4
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.65
X-RAY DIFFRACTIONx_mcbond_it1.5
X-RAY DIFFRACTIONx_scbond_it2
X-RAY DIFFRACTIONx_mcangle_it2
X-RAY DIFFRACTIONx_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.254 / % reflection Rfree: 9.9 % / Rfactor Rwork: 0.233

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