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

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Basic information

Entry
Database: PDB / ID: 5xnk
TitleCrystal structure of Microcystis aeruginosa PCC 7806 aspartate racemase in complex with DL-methyl-aspartate
ComponentsMcyF
KeywordsISOMERASE / aspartate racemase / McyF / microcystin
Function / homologyamino-acid racemase activity / Asp/Glu racemase / Asp/Glu/hydantoin racemase / Asp/Glu/Hydantoin racemase / (2S,3S)-3-methyl-aspartic acid / 3-METHYL-BETA-D-ASPARTIC ACID / McyF
Function and homology information
Biological speciesMicrocystis aeruginosa PCC 7806 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å
AuthorsCao, D.D. / Zhou, K. / Jiang, Y.L. / Zhou, C.Z.
CitationJournal: To Be Published
Title: Structure-function Analyses of a Cyanobacterial Aspartate 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)29,5243
Polymers29,2301
Non-polymers2942
Water724
1
A: McyF
hetero molecules

A: McyF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,0486
Polymers58,4592
Non-polymers5894
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+2/31
Buried area2870 Å2
ΔGint-12 kcal/mol
Surface area18930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)129.046, 129.046, 43.898
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: 29229.668 Da / Num. of mol.: 1 / Mutation: C87S
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-2AS / (2S,3S)-3-methyl-aspartic acid


Type: L-peptide linking / Mass: 147.129 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H9NO4
#3: Chemical ChemComp-ACB / 3-METHYL-BETA-D-ASPARTIC ACID / (3S)-3-methyl-D-aspartic acid / D-METHYL ASPARTIC ACID


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


Mass: 18.015 Da / Num. of mol.: 4 / 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: 3.61 Å3/Da / Density meas: 34.76 Mg/m3 / Density % sol: 65.93 %
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: 0.97775 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 24, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97775 Å / Relative weight: 1
ReflectionResolution: 3.4→111.76 Å / Num. obs: 5683 / % possible obs: 96.1 % / Redundancy: 4.8 % / Net I/σ(I): 9.1

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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: 3.4→50 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.924 / SU B: 22.046 / SU ML: 0.338 / Cross valid method: THROUGHOUT / ESU R Free: 0.441 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21735 274 4.8 %RANDOM
Rwork0.17895 ---
obs0.18085 5409 95.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 85.789 Å2
Baniso -1Baniso -2Baniso -3
1--1.6 Å2-0.8 Å2-0 Å2
2---1.6 Å2-0 Å2
3---5.19 Å2
Refinement stepCycle: 1 / Resolution: 3.4→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1786 0 20 4 1810
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0191836
X-RAY DIFFRACTIONr_bond_other_d0.0020.021808
X-RAY DIFFRACTIONr_angle_refined_deg1.1722.0052485
X-RAY DIFFRACTIONr_angle_other_deg0.85134190
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6435226
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.07525.73375
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.14315341
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.421155
X-RAY DIFFRACTIONr_chiral_restr0.0580.2295
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212021
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02370
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_it2.868.445913
X-RAY DIFFRACTIONr_mcbond_other2.868.445913
X-RAY DIFFRACTIONr_mcangle_it4.7512.651136
X-RAY DIFFRACTIONr_mcangle_other4.74912.651136
X-RAY DIFFRACTIONr_scbond_it2.7058.82923
X-RAY DIFFRACTIONr_scbond_other2.7048.82923
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.67913.0841350
X-RAY DIFFRACTIONr_long_range_B_refined8.50965.7451989
X-RAY DIFFRACTIONr_long_range_B_other8.5165.7591989
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.405→3.493 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.318 26 -
Rwork0.255 367 -
obs--94.02 %

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