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- PDB-3gse: Crystal structure of menaquinone-specific isochorismate synthase ... -

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Basic information

Entry
Database: PDB / ID: 3gse
TitleCrystal structure of menaquinone-specific isochorismate synthase from Yersinia pestis CO92
ComponentsMenaquinone-specific isochorismate synthase
KeywordsISOMERASE / menaquinone-specific isochorismate synthase / menF / Yersinia pestis CO92 / YPO2528 / CSGID / Structural Genomics / Center for Structural Genomics of Infectious Diseases
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
Isochorismate synthase MenF / Isochorismate synthase MenF
Similarity search - Component
Biological speciesYersinia pestis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.28 Å
AuthorsNocek, B. / Gu, M. / Papazisi, L. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: Crystal structure of menaquinone-specific isochorismate synthase from Yersinia pestis CO92
Authors: Nocek, B. / Gu, M. / Papazisi, L. / Anderson, W.F. / Joachimiak, A.
History
DepositionMar 26, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 5, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Sep 6, 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_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: Menaquinone-specific isochorismate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,6124
Polymers51,3241
Non-polymers2883
Water2,954164
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)84.190, 76.997, 70.414
Angle α, β, γ (deg.)90.00, 90.39, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Menaquinone-specific isochorismate synthase


Mass: 51324.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia pestis (bacteria) / Strain: CO92 / Gene: menF, YPO2528 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)magic
References: UniProt: Q0WDZ8, UniProt: Q8D0S5*PLUS, isochorismate synthase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 164 / 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: 2.22 Å3/Da / Density % sol: 44.68 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 1.6 M Ammonium sulfate 10% dioxane, 0.1 M MES, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9794 Å
DetectorType: SBC-3 / Detector: CCD / Date: Dec 18, 2008 / Details: mirrors
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.28→30 Å / Num. all: 20472 / Num. obs: 20090 / % possible obs: 98.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 2.9 % / Rmerge(I) obs: 0.035 / Net I/σ(I): 21.7
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.119 / Mean I/σ(I) obs: 12 / % possible all: 99.4

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
MOLREPphasing
REFMAC5.5.0054refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3BZN

3bzn


Resolution: 2.28→30 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.913 / SU B: 14.411 / SU ML: 0.165 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.386 / ESU R Free: 0.254 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2519 1029 5.1 %RANDOM
Rwork0.19299 ---
obs0.19604 19054 97.12 %-
all-19709 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.69 Å2
Baniso -1Baniso -2Baniso -3
1-3.89 Å20 Å23.22 Å2
2---1.64 Å20 Å2
3----2.21 Å2
Refinement stepCycle: LAST / Resolution: 2.28→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3370 0 15 164 3549
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0213446
X-RAY DIFFRACTIONr_bond_other_d0.0010.022358
X-RAY DIFFRACTIONr_angle_refined_deg1.4771.9544666
X-RAY DIFFRACTIONr_angle_other_deg0.87435703
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9925421
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.77123.6175
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.77915589
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.1531534
X-RAY DIFFRACTIONr_chiral_restr0.0860.2516
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213845
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02714
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6431.52115
X-RAY DIFFRACTIONr_mcbond_other0.1481.5855
X-RAY DIFFRACTIONr_mcangle_it1.21923379
X-RAY DIFFRACTIONr_scbond_it2.17331331
X-RAY DIFFRACTIONr_scangle_it3.3624.51287
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.276→2.335 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.335 59 -
Rwork0.189 1211 -
obs--85.81 %
Refinement TLS params.

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.7306-0.34480.30860.9548-0.61651.9721-0.0229-0.0855-0.00720.114-0.0050.0589-0.0076-0.00090.02790.0749-0.00640.00330.056-0.01530.0771-18.949-3.53930.7009
20.8658-0.2220.31570.6636-0.66762.48880.0194-0.0465-0.0589-0.05450.03270.10670.1017-0.2411-0.05210.0913-0.02050.0150.0712-0.01360.1332-22.3316-6.734-1.4253
32.47550.40823.3730.15040.09788.4829-0.15050.1617-0.029-0.0210.0711-0.04890.18470.34380.07930.23580.06220.01140.1697-0.07450.1268-9.0889-12.2593-29.8512
40.94860.10910.26941.40390.20512.61870.02860.12350.0085-0.2441-0.1230.02610.1940.05680.09450.11030.06320.02650.07-0.01110.0626-14.6828-4.9172-25.3969
52.81110.1397-1.71650.828-0.21311.5130.06750.1250.1022-0.10060.01330.0008-0.00640.0251-0.08090.06050.01280.00150.0580.00170.0596-15.241314.9887-26.2096
64.2689-0.5309-1.92851.2654-0.14251.8429-0.01070.0328-0.0016-0.04930.03610.081-0.0704-0.0316-0.02540.09090.00360.01380.06640.02020.0621-19.047415.7265-23.3637
71.6604-1.2259-1.65624.59241.90654.59940.04910.2779-0.012-0.159-0.10090.30550.007-0.55280.05180.04670.0126-0.04820.14210.00410.086-31.03068.6466-18.1518
83.27230.4363-1.49499.5753-2.94818.1383-0.06550.17980.2365-0.0628-0.15810.438-0.1027-0.74250.22370.13220.0507-0.10450.2962-0.05660.179-29.3668-1.4571-34.8496
91.3821-0.8761-1.37962.4092.03973.8557-0.0760.0433-0.0152-0.00190.1025-0.04070.27930.053-0.02650.08350.0041-0.01070.0601-0.00960.0852-19.0204-3.3825-19.3347
101.5916-0.55633.04410.7926-1.94967.722-0.23060.5199-0.04910.00410.1024-0.0423-0.69830.93340.12820.6021-0.18060.00330.48310.03720.3316-10.1093-2.3254-37.0729
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 88
2X-RAY DIFFRACTION2A89 - 168
3X-RAY DIFFRACTION3A169 - 193
4X-RAY DIFFRACTION4A194 - 256
5X-RAY DIFFRACTION5A257 - 310
6X-RAY DIFFRACTION6A311 - 341
7X-RAY DIFFRACTION7A342 - 364
8X-RAY DIFFRACTION8A365 - 381
9X-RAY DIFFRACTION9A382 - 421
10X-RAY DIFFRACTION10A422 - 447

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