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- PDB-7ylq: Crystal structure of Microcystinase C from Sphingomonas sp. ACM-3... -

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Basic information

Entry
Database: PDB / ID: 7ylq
TitleCrystal structure of Microcystinase C from Sphingomonas sp. ACM-3962 at 2.6 A resolution
ComponentsMicrocystinase C
KeywordsHYDROLASE / Microcystinase C / microcystins / degradation mechanism / M81 metallopeptidase family
Function / homology
Function and homology information


metallopeptidase activity / peptidase activity / proteolysis / zinc ion binding / metal ion binding
Similarity search - Function
Microcystin LR degradation protein MlrC / Microcystin LR degradation protein MlrC, C-terminal / Microcystin LR degradation protein MlrC, N-terminal / MlrC C-terminus / Metallopeptidase family M81
Similarity search - Domain/homology
Biological speciesSphingomonas sp. ACM-3962 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.68 Å
AuthorsGuo, X. / Li, Z. / Ding, W. / Yin, P. / Feng, L.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Crystal structure of Microcystin C from Sphingomonas sp. ACM-3962 at 2.6 A resolution
Authors: Guo, X. / Li, Z. / Ding, W. / Yin, P. / Feng, L.
History
DepositionJul 26, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 9, 2023Provider: repository / Type: Initial release
Revision 1.1May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Microcystinase C
B: Microcystinase C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,2456
Polymers111,0082
Non-polymers2364
Water1,62190
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2400 Å2
ΔGint-103 kcal/mol
Surface area37530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)138.430, 138.430, 275.572
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Space group name HallP612(x,y,z+5/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+2/3
#8: -x,-y,z+1/2
#9: y,x,-z+1/3
#10: -y,-x,-z+5/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+1/6

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Components

#1: Protein Microcystinase C / MlrC


Mass: 55504.230 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sphingomonas sp. ACM-3962 (bacteria) / Gene: mlrC / Production host: Escherichia coli (E. coli) / References: UniProt: Q93CA6
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 90 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.59 Å3/Da / Density % sol: 65.77 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: Sodium chloride, BTP, PEG 20,000, CaCl2, EDTA

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Data collection

DiffractionMean temperature: 273 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97918 Å
DetectorType: MAR CCD 130 mm / Detector: CCD / Date: Jan 1, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.68→48.83 Å / Num. obs: 44455 / % possible obs: 99.8 % / Redundancy: 2 % / Biso Wilson estimate: 59.37 Å2 / CC1/2: 0.765 / Rmerge(I) obs: 0.056 / Net I/σ(I): 25.5

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
HKL-2000data scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3iuu

3iuu


Resolution: 2.68→48.83 Å / SU ML: 0.3509 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.4783
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.264 2201 4.95 %
Rwork0.2314 42254 -
obs0.233 44455 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 72.82 Å2
Refinement stepCycle: LAST / Resolution: 2.68→48.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7269 0 4 90 7363
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0117432
X-RAY DIFFRACTIONf_angle_d1.458310068
X-RAY DIFFRACTIONf_chiral_restr0.08921103
X-RAY DIFFRACTIONf_plane_restr0.00771342
X-RAY DIFFRACTIONf_dihedral_angle_d13.17092750
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.68-2.740.38131390.34572525X-RAY DIFFRACTION98.67
2.74-2.80.33181340.31652590X-RAY DIFFRACTION99.85
2.8-2.870.30431280.30182602X-RAY DIFFRACTION99.93
2.87-2.950.30951340.29142605X-RAY DIFFRACTION99.82
2.95-3.040.31861400.30142590X-RAY DIFFRACTION99.93
3.04-3.140.35331400.3012587X-RAY DIFFRACTION99.89
3.14-3.250.39941140.29642633X-RAY DIFFRACTION99.71
3.25-3.380.28761200.26312640X-RAY DIFFRACTION99.96
3.38-3.530.28731530.2522594X-RAY DIFFRACTION100
3.53-3.720.24091680.23042591X-RAY DIFFRACTION99.89
3.72-3.950.2761340.22522654X-RAY DIFFRACTION100
3.95-4.250.20841450.20452632X-RAY DIFFRACTION100
4.25-4.680.2471290.18622678X-RAY DIFFRACTION100
4.68-5.360.22811270.20332702X-RAY DIFFRACTION99.96
5.36-6.750.25631440.23052733X-RAY DIFFRACTION99.93
6.75-48.830.23071520.19162898X-RAY DIFFRACTION99.41
Refinement TLS params.Method: refined / Origin x: -10.7672071271 Å / Origin y: -37.7056005186 Å / Origin z: -27.5744525372 Å
111213212223313233
T0.543413087947 Å2-0.0738636924751 Å20.0226288630214 Å2-0.420766303215 Å20.0583726150296 Å2--0.453023436839 Å2
L1.73944888922 °20.329609225702 °20.312607968172 °2-0.353809327119 °20.0102021130437 °2--0.394855948448 °2
S0.113428663847 Å °-0.246894991418 Å °-0.0156223559629 Å °0.133534947267 Å °-0.00814770919042 Å °0.101058078372 Å °0.0901608412113 Å °-0.158376543623 Å °-0.108334519477 Å °
Refinement TLS groupSelection details: all

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