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- PDB-7mch: Crystal structure of a single-chain E/F type bilin lyase-isomeras... -

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Basic information

Entry
Database: PDB / ID: 7mch
TitleCrystal structure of a single-chain E/F type bilin lyase-isomerase MpeQ in space group C2221
Componentsbilin lyase-isomerase
KeywordsLYASE / bilin lyase-isomerase
Function / homologyE-Z type HEAT repeats / PBS lyase HEAT-like repeat / phycobilisome / Armadillo-like helical / Armadillo-type fold / lyase activity / Putative phycobilin:C-phycoerythrin II lyase
Function and homology information
Biological speciesSynechococcus sp. A15-62 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.95 Å
AuthorsYang, X. / Kumarapperuma, I.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Eye Institute (NIH/NEI)EY024363 United States
CitationJournal: Structure / Year: 2022
Title: Crystal structure and molecular mechanism of an E/F type bilin lyase-isomerase.
Authors: Kumarapperuma, I. / Joseph, K.L. / Wang, C. / Biju, L.M. / Tom, I.P. / Weaver, K.D. / Grebert, T. / Partensky, F. / Schluchter, W.M. / Yang, X.
History
DepositionApr 2, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 24, 2022Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: bilin lyase-isomerase
B: bilin lyase-isomerase


Theoretical massNumber of molelcules
Total (without water)93,3582
Polymers93,3582
Non-polymers00
Water2,378132
1
A: bilin lyase-isomerase


Theoretical massNumber of molelcules
Total (without water)46,6791
Polymers46,6791
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: bilin lyase-isomerase


Theoretical massNumber of molelcules
Total (without water)46,6791
Polymers46,6791
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)136.875, 174.300, 113.857
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain AA-5 - 398
211chain BB-5 - 398

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Components

#1: Protein bilin lyase-isomerase


Mass: 46678.965 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechococcus sp. A15-62 (bacteria) / Strain: A15-62 / Gene: mpeY / Production host: Escherichia coli (E. coli) / References: UniProt: U3MW57
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 132 / 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: 3.67 Å3/Da / Density % sol: 66.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Protein concentration: 5 mg/mL; 2.1 M DL-Malic acid, pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.9787 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 3, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 26064 / % possible obs: 97.4 % / Redundancy: 3.8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.149 / Rpim(I) all: 0.081 / Net I/σ(I): 7
Reflection shellResolution: 2.9→2.95 Å / Num. unique obs: 887 / CC1/2: 0.39

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
HKL-2000data scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.95→19.9 Å / SU ML: 0.46 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 40.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3083 1924 7.65 %
Rwork0.2437 23214 -
obs0.2487 25138 86.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 158.68 Å2 / Biso mean: 50.3991 Å2 / Biso min: 7.93 Å2
Refinement stepCycle: final / Resolution: 2.95→19.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6286 0 0 132 6418
Biso mean---34 -
Num. residues----808
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3748X-RAY DIFFRACTION9.944TORSIONAL
12B3748X-RAY DIFFRACTION9.944TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.95-3.020.4745880.38261100118858
3.02-3.10.38831030.33781250135366
3.11-3.20.43291100.32371334144471
3.2-3.30.40591220.31761460158277
3.3-3.420.39871330.29561586171984
3.42-3.550.33361380.27571678181689
3.55-3.710.28941480.24171790193894
3.71-3.910.29681490.23641792194195
3.91-4.150.37151490.21131796194595
4.15-4.470.26351500.19221809195995
4.47-4.910.26971540.20341852200697
4.91-5.60.29131570.22491906206399
5.61-7.010.31931620.26061926208899
7.01-19.90.2231610.2151935209696

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