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- PDB-4jb1: Crystal structure of P. aeruginosa MurB in complex with NADP+ -

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Basic information

Entry
Database: PDB / ID: 4jb1
TitleCrystal structure of P. aeruginosa MurB in complex with NADP+
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
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 / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / UDP-N-acetylenolpyruvoylglucosamine reductase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsChen, M.W. / Lohkamp, B. / Schnell, R. / Lescar, J. / Schneider, G.
CitationJournal: Plos One / Year: 2013
Title: Substrate Channel Flexibility in Pseudomonas aeruginosa MurB Accommodates Two Distinct Substrates.
Authors: Chen, M.W. / Lohkamp, B. / Schnell, R. / Lescar, J. / Schneider, G.
History
DepositionFeb 19, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 17, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 20, 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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-acetylenolpyruvoylglucosamine reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,8479
Polymers37,7661
Non-polymers2,0828
Water2,900161
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)88.710, 88.710, 100.220
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61

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Components

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


Mass: 37765.938 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PAO1 / Gene: murB, PA2977 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q9HZM7, 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: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE / Nicotinamide adenine dinucleotide phosphate


Mass: 743.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 161 / 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: 3.01 Å3/Da / Density % sol: 59.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 40 mM potassium phosphate, 20% v/v glycerol, 16% w/v PEG 8000 and 2 mM Tris-buffered NADP+ sodium salt, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9334 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 9, 2012
RadiationMonochromator: Diamond (111), Ge(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9334 Å / Relative weight: 1
ReflectionResolution: 2.1→76.825 Å / Num. all: 26203 / Num. obs: 26203 / % possible obs: 100 % / Observed criterion σ(F): 2.9 / Observed criterion σ(I): 2.9 / Redundancy: 7.6 % / Rmerge(I) obs: 0.117 / Net I/σ(I): 13.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique all% possible all
2.1-2.167.60.7172.9165422179100
8.91-50.116.90.04339.9248636299.5

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Processing

Software
NameVersionClassificationNB
Aimless0.1.26data scaling
REFMACrefinement
PDB_EXTRACT3.11data extraction
ADSCQuantumdata collection
MOSFLMdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2MBR
Resolution: 2.1→44.39 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.933 / WRfactor Rfree: 0.2205 / WRfactor Rwork: 0.1672 / Occupancy max: 1 / Occupancy min: 0.33 / FOM work R set: 0.8554 / SU B: 9.345 / SU ML: 0.138 / SU R Cruickshank DPI: 0.1886 / SU Rfree: 0.1766 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.189 / ESU R Free: 0.177 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2363 1325 5.1 %RANDOM
Rwork0.1804 ---
all0.1831 26176 --
obs0.1831 26176 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 112.76 Å2 / Biso mean: 41.8756 Å2 / Biso min: 9 Å2
Baniso -1Baniso -2Baniso -3
1-1.29 Å21.29 Å2-0 Å2
2--1.29 Å2-0 Å2
3----4.18 Å2
Refinement stepCycle: LAST / Resolution: 2.1→44.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2640 0 137 161 2938
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0192937
X-RAY DIFFRACTIONr_bond_other_d0.0020.022826
X-RAY DIFFRACTIONr_angle_refined_deg2.1252.0283998
X-RAY DIFFRACTIONr_angle_other_deg0.936468
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3935358
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.20722.621145
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.61915482
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0791540
X-RAY DIFFRACTIONr_chiral_restr0.110.2434
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0213314
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02702
X-RAY DIFFRACTIONr_mcbond_it1.6211.9111387
X-RAY DIFFRACTIONr_mcbond_other1.6211.911386
X-RAY DIFFRACTIONr_mcangle_it2.4552.8581741
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.32 101 -
Rwork0.272 1840 -
all-1941 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
12.93863.05330.275711.85721.36520.27780.5647-0.27080.56730.415-0.63551.1098-0.154-0.38790.07080.63390.37550.23670.92860.0230.288216.786-20.8824-3.4096
20.55480.5821-0.49930.6567-0.31733.63160.2176-0.02160.0660.18390.00390.0492-0.7997-0.4001-0.22160.24970.07480.06560.13940.01480.09629.4429-18.6394-17.0689
32.265-0.99870.07198.41692.43393.6066-0.0864-0.43720.00220.58720.251-0.0783-0.45620.3894-0.16460.2412-0.1285-0.02990.2379-0.00670.118140.9731-20.7977-11.9066
40.74490.76140.77391.1501-0.13413.80310.0272-0.0031-0.0952-0.03120.0685-0.06640.0642-0.2795-0.09570.064-0.03810.01170.1063-0.00750.079432.4222-28.3533-34.7188
52.9681.2261-1.3880.5555-0.13874.77590.16210.08250.15730.0609-0.0360.06730.1958-1.0059-0.12610.3061-0.1161-0.01080.3818-0.0010.198523.106-35.004-24.1817
612.7375.0341.595220.2813-3.47947.8672-0.25430.1493-0.36960.28070.0877-0.36691.39041.38030.16660.49050.3760.12720.34420.08380.084943.7192-53.3901-16.5015
72.53030.4565-1.13581.0715-0.78772.4418-0.0599-0.037-0.2763-0.0642-0.001-0.01890.6047-0.22380.06090.2186-0.1315-0.01560.13420.01360.057828.6244-44.9432-11.2445
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 29
2X-RAY DIFFRACTION2A30 - 148
3X-RAY DIFFRACTION3A149 - 178
4X-RAY DIFFRACTION4A179 - 212
5X-RAY DIFFRACTION5A213 - 244
6X-RAY DIFFRACTION6A245 - 259
7X-RAY DIFFRACTION7A260 - 339

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