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- PDB-3bzm: Crystal Structure of Open form of Menaquinone-Specific Isochorism... -

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Basic information

Entry
Database: PDB / ID: 3bzm
TitleCrystal Structure of Open form of Menaquinone-Specific Isochorismate Synthase, MenF
ComponentsMenaquinone-specific isochorismate synthase
KeywordsISOMERASE / chorismate / isochorismate / menaquinone / Menaquinone biosynthesis
Function / homology
Function and homology information


isochorismate synthase / isochorismate synthase activity / menaquinone biosynthetic process / magnesium ion binding
Similarity search - Function
Isochorismate synthase MenF / Isochorismate synthase MenF-like / Isochorismate synthase / Anthranilate synthase / Anthranilate synthase / ADC synthase / Chorismate-utilising enzyme, C-terminal / chorismate binding enzyme / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
CITRIC ACID / Isochorismate synthase MenF
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.95 Å
AuthorsParsons, J.F. / Shi, K.M. / Ladner, J.E.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2008
Title: Structure of isochorismate synthase in complex with magnesium.
Authors: Parsons, J.F. / Shi, K.M. / Ladner, J.E.
History
DepositionJan 18, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 20, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 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

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Assembly

Deposited unit
A: Menaquinone-specific isochorismate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,0162
Polymers48,8231
Non-polymers1921
Water1,820101
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)72.370, 72.370, 164.010
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Menaquinone-specific isochorismate synthase / Isochorismate mutase


Mass: 48823.422 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: menF, yfbA / Plasmid: Pet15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P38051, isochorismate synthase
#2: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 101 / 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: 2.54 Å3/Da / Density % sol: 51.56 %
Crystal growTemperature: 298 K / Method: sitting drop vapor diffusion / pH: 8
Details: well solution: 0.2M sodium citrate, 6% glycerol, 8% PEG 3350, 5mM chorismic acid. protein solution: 50mM Tris, 5 mM magnesium chloride, 1 mM DTT, pH 7.6, 20 mg/mL. Drops were equal volumes ...Details: well solution: 0.2M sodium citrate, 6% glycerol, 8% PEG 3350, 5mM chorismic acid. protein solution: 50mM Tris, 5 mM magnesium chloride, 1 mM DTT, pH 7.6, 20 mg/mL. Drops were equal volumes well and protein., sitting drop vapor diffusion, temperature 298K

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Data collection

DiffractionMean temperature: 105 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jan 1, 2007
RadiationMonochromator: MSC Blue Confocal Optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.95→19.67 Å / Num. obs: 36355 / % possible obs: 98.1 % / Redundancy: 7.97 % / Rmerge(I) obs: 0.064 / Χ2: 1 / Net I/σ(I): 14.7 / Scaling rejects: 2189
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allΧ2% possible all
1.95-2.024.610.4742.61429430840.9584.8
2.02-2.15.810.3893.52068135450.9697.4
2.1-2.28.320.3284.53046536560.9199.5
2.2-2.318.640.3114.13145636241.0699.6
2.31-2.468.690.197.43206236790.9199.8
2.46-2.658.710.1449.83191736540.8999.9
2.65-2.918.750.10813.13261037130.87100
2.91-3.338.750.07819.73268637230.89100
3.33-4.198.690.05928.43291337621.07100
4.19-19.678.030.04342.83271439151.4899.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3 Å9.99 Å
Translation3 Å9.99 Å

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Processing

Software
NameVersionClassificationNB
d*TREKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.004data extraction
CrystalCleardata collection
d*TREKdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→19.67 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.916 / SU B: 6.357 / SU ML: 0.178 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.208 / ESU R Free: 0.2 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.308 1804 5 %RANDOM
Rwork0.245 ---
obs0.248 35738 96.43 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 48.543 Å2
Baniso -1Baniso -2Baniso -3
1-1.09 Å20.54 Å20 Å2
2--1.09 Å20 Å2
3----1.63 Å2
Refinement stepCycle: LAST / Resolution: 1.95→19.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3432 0 13 101 3546
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0223521
X-RAY DIFFRACTIONr_angle_refined_deg1.9751.9534787
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5755434
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.79223.6175
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.58815599
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8751534
X-RAY DIFFRACTIONr_chiral_restr0.1490.2529
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022711
X-RAY DIFFRACTIONr_nbd_refined0.2290.21566
X-RAY DIFFRACTIONr_nbtor_refined0.3110.22297
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1730.2190
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2220.233
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1330.27
X-RAY DIFFRACTIONr_mcbond_it1.1081.52232
X-RAY DIFFRACTIONr_mcangle_it1.79423457
X-RAY DIFFRACTIONr_scbond_it2.67931495
X-RAY DIFFRACTIONr_scangle_it3.7854.51327
LS refinement shellResolution: 1.95→2.054 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.398 217 -
Rwork0.349 4358 -
all-4575 -
obs--86.63 %

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