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- PDB-5wxz: Crystal structure of Microcystis aeruginosa PCC 7806 aspartate ra... -

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Basic information

Entry
Database: PDB / ID: 5wxz
TitleCrystal structure of Microcystis aeruginosa PCC 7806 aspartate racemase in complex with D-aspartate
ComponentsMcyF
KeywordsISOMERASE / aspartate racemase / McyF / microcystin
Function / homology: / Asp/Glu racemase / Asp/Glu/hydantoin racemase / Asp/Glu/Hydantoin racemase / D-ASPARTIC ACID / McyF
Function and homology information
Biological speciesMicrocystis aeruginosa PCC 7806 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsCao, D.D. / Zhou, K. / Jiang, Y.L. / Zhou, C.Z.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2019
Title: Structural insights into the catalysis and substrate specificity of cyanobacterial aspartate racemase McyF.
Authors: Cao, D.D. / Zhang, C.P. / Zhou, K. / Jiang, Y.L. / Tan, X.F. / Xie, J. / Ren, Y.M. / Chen, Y. / Zhou, C.Z. / Hou, W.T.
History
DepositionJan 9, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 17, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 31, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: McyF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3472
Polymers29,2141
Non-polymers1331
Water48627
1
A: McyF
hetero molecules

A: McyF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,6934
Polymers58,4272
Non-polymers2662
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_554-x,-x+y,-z-1/31
Buried area2910 Å2
ΔGint-12 kcal/mol
Surface area18460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)129.097, 129.097, 44.641
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein McyF / McyF protein


Mass: 29213.605 Da / Num. of mol.: 1 / Mutation: C87S, C195S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Microcystis aeruginosa PCC 7806 (bacteria)
Gene: mcyF, IPF_371 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9RNB4
#2: Chemical ChemComp-DAS / D-ASPARTIC ACID


Type: D-peptide linking / Mass: 133.103 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H7NO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / 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: 3.83 Å3/Da / Density % sol: 67.85 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 25% (w/v) polyethylene glycol 3350, 0.2 magnesium chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 12, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.8→111.8 Å / Num. obs: 10736 / % possible obs: 99.9 % / Redundancy: 4.8 % / Net I/σ(I): 15.2
Reflection shellResolution: 2.8→2.85 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5WXX

5wxx


Resolution: 2.8→42.257 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.947 / SU B: 10.662 / SU ML: 0.196 / Cross valid method: THROUGHOUT / ESU R: 0.411 / ESU R Free: 0.243 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20246 503 4.7 %RANDOM
Rwork0.18326 ---
obs0.18421 10225 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 60.504 Å2
Baniso -1Baniso -2Baniso -3
1--0.59 Å2-0.3 Å2-0 Å2
2---0.59 Å20 Å2
3---1.92 Å2
Refinement stepCycle: 1 / Resolution: 2.8→42.257 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1786 0 9 27 1822
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0191826
X-RAY DIFFRACTIONr_bond_other_d0.0020.021799
X-RAY DIFFRACTIONr_angle_refined_deg1.26422471
X-RAY DIFFRACTIONr_angle_other_deg0.89534171
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6635226
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.2225.73375
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.12715341
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.988155
X-RAY DIFFRACTIONr_chiral_restr0.0690.2292
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212011
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02368
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_it2.7545.861910
X-RAY DIFFRACTIONr_mcbond_other2.7515.86909
X-RAY DIFFRACTIONr_mcangle_it4.5168.7881134
X-RAY DIFFRACTIONr_mcangle_other4.5148.791135
X-RAY DIFFRACTIONr_scbond_it3.1176.262916
X-RAY DIFFRACTIONr_scbond_other3.1166.259913
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.2299.2251338
X-RAY DIFFRACTIONr_long_range_B_refined7.60945.7121990
X-RAY DIFFRACTIONr_long_range_B_other7.60745.7261991
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.8→2.873 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.4 38 -
Rwork0.311 731 -
obs--99.61 %

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