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- PDB-5xni: Crystal structure of Microcystis aeruginosa PCC 7806 aspartate/gl... -

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Basic information

Entry
Database: PDB / ID: 5xni
TitleCrystal structure of Microcystis aeruginosa PCC 7806 aspartate/glutamate racemase in complex with D-glutamate
ComponentsMcyF
KeywordsISOMERASE / aspartate/glutamate racemase / McyF / microcystin
Function / homologyamino-acid racemase activity / Asp/Glu racemase / Asp/Glu/hydantoin racemase / Asp/Glu/Hydantoin racemase / D-GLUTAMIC ACID / McyF
Function and homology information
Biological speciesMicrocystis aeruginosa PCC 7806 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.22 Å
AuthorsCao, D.D. / Zhou, K. / Jiang, Y.L. / Zhou, C.Z.
CitationJournal: To Be Published
Title: Structure-function Analyses of a Cyanobacterial Aspartate/Glutamate Racemase Reveal Its Catalytic Mechanism and Substrate Specificity
Authors: Cao, D.D. / Zhou, C.Z.
History
DepositionMay 23, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 30, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 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)29,3612
Polymers29,2141
Non-polymers1471
Water1448
1
A: McyF
hetero molecules

A: McyF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,7214
Polymers58,4272
Non-polymers2942
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+1/31
Buried area2850 Å2
ΔGint-9 kcal/mol
Surface area19130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)129.304, 129.304, 43.811
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-DGL / D-GLUTAMIC ACID


Type: D-peptide linking / Mass: 147.129 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H9NO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / 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: 3.62 Å3/Da / Density meas: 34.89 Mg/m3 / Density % sol: 66.01 %
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: BL19U1 / Wavelength: 0.97776 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 20, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97776 Å / Relative weight: 1
ReflectionResolution: 3.22→111.98 Å / Num. obs: 7030 / % possible obs: 100 % / Redundancy: 8.4 % / Net I/σ(I): 21.7

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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: 3.22→50 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.913 / SU B: 18.062 / SU ML: 0.292 / Cross valid method: THROUGHOUT / ESU R Free: 0.409 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24088 309 4.4 %RANDOM
Rwork0.18739 ---
obs0.18966 6704 99.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 82.556 Å2
Baniso -1Baniso -2Baniso -3
1--1.73 Å2-0.86 Å20 Å2
2---1.73 Å2-0 Å2
3---5.61 Å2
Refinement stepCycle: 1 / Resolution: 3.22→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1786 0 10 8 1804
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0191827
X-RAY DIFFRACTIONr_bond_other_d0.0020.021801
X-RAY DIFFRACTIONr_angle_refined_deg1.18422472
X-RAY DIFFRACTIONr_angle_other_deg0.86634176
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6155226
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.81425.73375
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.86215341
X-RAY DIFFRACTIONr_dihedral_angle_4_deg2.544155
X-RAY DIFFRACTIONr_chiral_restr0.0630.2292
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0212011
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_it2.6068.1910
X-RAY DIFFRACTIONr_mcbond_other2.5928.1909
X-RAY DIFFRACTIONr_mcangle_it4.28512.1521134
X-RAY DIFFRACTIONr_mcangle_other4.28812.1531135
X-RAY DIFFRACTIONr_scbond_it2.8688.49917
X-RAY DIFFRACTIONr_scbond_other2.8518.481914
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.89912.5781339
X-RAY DIFFRACTIONr_long_range_B_refined7.20463.1311990
X-RAY DIFFRACTIONr_long_range_B_other7.20463.1441991
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.219→3.303 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.296 21 -
Rwork0.303 498 -
obs--99.43 %

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