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

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Basic information

Entry
Database: PDB / ID: 5xnj
TitleCrystal structure of Microcystis aeruginosa PCC 7806 aspartate/glutamate racemase in complex with L-glutamate
ComponentsMcyF
KeywordsISOMERASE / aspartate/glutamate racemase / McyF / microcystin
Function / homologyamino-acid racemase activity / Asp/Glu racemase / Asp/Glu/hydantoin racemase / Asp/Glu/Hydantoin racemase / GLUTAMIC ACID / McyF
Function and homology information
Biological speciesMicrocystis aeruginosa PCC 7806 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.82 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
Water23413
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 area2900 Å2
ΔGint-11 kcal/mol
Surface area18940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)129.247, 129.247, 44.292
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 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-GLU / GLUTAMIC ACID


Type: L-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.: 13 / 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: 3.66 Å3/Da / Density % sol: 66.35 %
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: 2.82→111.93 Å / Num. obs: 10438 / % possible obs: 99.5 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.026 / Rrim(I) all: 0.072 / Χ2: 1.402 / Net I/σ(I): 11.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.82-2.875.80.4620.9190.2050.5090.84599.8
2.87-2.9260.4730.930.2030.5170.88599.8
2.92-2.986.10.410.9540.1740.4470.90298.3
2.98-3.046.40.3030.9580.1270.330.96899.6
3.04-3.16.30.2710.9710.1140.2951.02499.8
3.1-3.186.20.2360.9760.10.2571.0397.8
3.18-3.266.30.1990.9830.0850.2171.01799.4
3.26-3.346.20.180.9850.0770.1961.18799.6
3.34-3.446.10.1540.9880.0660.1681.27798.3
3.44-3.556.50.1280.9920.0530.1391.32299.8
3.55-3.6860.1040.9930.0450.1141.684100
3.68-3.8360.0970.9960.0420.1061.54399.8
3.83-45.80.0820.9960.0360.091.91299.6
4-4.216.50.0730.9970.030.0791.91199.4
4.21-4.487.10.0620.9980.0240.0661.91299.8
4.48-4.828.10.0560.9980.020.061.962100
4.82-5.318.20.0540.9980.0190.0571.67199.8
5.31-6.078.40.0520.9980.0180.0551.41999.6
6.07-7.657.40.040.9990.0150.0431.27199.8
7.65-507.80.0360.9940.0140.0391.72299.6

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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: 2.82→50 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.94 / SU B: 10.201 / SU ML: 0.192 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.443 / ESU R Free: 0.258
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES
RfactorNum. reflection% reflectionSelection details
Rfree0.2102 525 5 %RANDOM
Rwork0.1867 ---
obs0.1879 9892 99.12 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 135.6 Å2 / Biso mean: 68.508 Å2 / Biso min: 43.82 Å2
Baniso -1Baniso -2Baniso -3
1--0.77 Å2-0.39 Å2-
2---0.77 Å2-0 Å2
3---2.51 Å2
Refinement stepCycle: final / Resolution: 2.82→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1786 0 10 13 1809
Biso mean--82.56 59.76 -
Num. residues----227
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0191827
X-RAY DIFFRACTIONr_bond_other_d0.0020.021801
X-RAY DIFFRACTIONr_angle_refined_deg1.2671.9972472
X-RAY DIFFRACTIONr_angle_other_deg0.88734176
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8165226
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.51125.78976
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.5715343
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.675155
X-RAY DIFFRACTIONr_chiral_restr0.0650.2292
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212011
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02368
LS refinement shellResolution: 2.817→2.89 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.354 40 -
Rwork0.268 699 -
all-739 -
obs--96.1 %

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