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- PDB-7mc4: Crystal structure of a single-chain E/F type bilin lyase-isomeras... -

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Basic information

Entry
Database: PDB / ID: 7mc4
TitleCrystal structure of a single-chain E/F type bilin lyase-isomerase MpeQ
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. P1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 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 1, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 23, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 20, 2022Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first

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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
Water3,783210
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)114.389, 173.213, 83.818
Angle α, β, γ (deg.)90.000, 126.020, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-483-

HOH

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Components

#1: Protein Bilin Lyase-Isomerase / Putative phycoerythrobilin:phycoerythrin II lyase


Mass: 46678.965 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechococcus sp. P1 (bacteria) / Strain: A15-62 / Gene: mpeY / Production host: Escherichia coli (E. coli) / References: UniProt: U3MW57
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 210 / 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: 3.63 Å3/Da / Density % sol: 66.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Protein concentration: 5 mg/mL, 2.1 M DL-Malic acid
Temp details: room temperature

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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: 2.4→56 Å / Num. obs: 51398 / % possible obs: 99.78 % / Redundancy: 3.7 % / Biso Wilson estimate: 28.63 Å2 / CC1/2: 0.977 / Net I/σ(I): 3.4
Reflection shellResolution: 2.4→2.44 Å / Num. unique obs: 2424 / CC1/2: 0.597

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
xia2data scaling
PDB_EXTRACT3.27data extraction
xia2data reduction
SHELXDEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.5→19.999 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 32.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2853 1679 3.87 %
Rwork0.2324 41666 -
obs0.2345 43345 95.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 173.23 Å2 / Biso mean: 44.1166 Å2 / Biso min: 5.42 Å2
Refinement stepCycle: final / Resolution: 2.5→19.999 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6289 0 0 210 6499
Biso mean---38.44 -
Num. residues----808
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0096396
X-RAY DIFFRACTIONf_angle_d1.0138673
X-RAY DIFFRACTIONf_chiral_restr0.0511011
X-RAY DIFFRACTIONf_plane_restr0.0071131
X-RAY DIFFRACTIONf_dihedral_angle_d19.5154015
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.5-2.57340.3591280.2955322189
2.5734-2.65630.36191340.295328991
2.6563-2.7510.35591350.2939333192
2.751-2.86090.36911340.2922338493
2.8609-2.99070.38041400.2867345394
2.9907-3.14780.34571430.262346996
3.1478-3.34420.27321440.2418351697
3.3442-3.6010.28411400.2222353298
3.601-3.96080.25861410.1923357999
3.9608-4.52820.22141460.1819359899
4.5282-5.68320.24221480.2057363199
5.6832-19.90.24471460.2215366399
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.8072-2.7524-3.24841.50021.79342.062-0.4452-0.36530.11390.5920.01210.23170.01330.050.32680.48520.0212-0.05250.3875-0.08080.530627.731374.89637.1986
22.16380.24680.8230.24540.1371.0357-0.10130.040.01110.0288-0.0131-0.0929-0.19520.08340.09990.3101-0.04710.02460.21610.00830.181324.631255.10917.9293
33.09130.67980.42975.03410.03212.47270.1485-0.03470.2921-0.3623-0.0005-0.0705-0.6393-0.0874-0.13180.48620.03490.00950.2082-0.08050.26258.682279.819926.8585
49.01552.71213.42620.80570.98071.2914-0.06220.9022-0.2561-0.2758-0.00870.00260.5120.45080.08780.59990.05230.1880.42920.00360.398726.9529101.390231.9762
51.4145-0.2333-0.71630.15830.10121.31370.03290.09680.1296-0.2034-0.0309-0.15750.06470.1941-0.00850.31520.02520.05760.275-0.01590.194928.4891121.757751.4024
62.3597-0.4009-0.05063.87510.4973.29610.22640.017-0.28140.1862-0.0669-0.15510.6643-0.0265-0.14070.3523-0.0019-0.00970.1532-0.05370.234911.130496.893546.0737
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain A and resi :14A-5 - 397
2X-RAY DIFFRACTION2chain A and resi 15:254A-5 - 397
3X-RAY DIFFRACTION3chain A and resi 285:A-5 - 397
4X-RAY DIFFRACTION4chain B and resi :14B-6 - 398
5X-RAY DIFFRACTION5chain B and resi 15:254B-6 - 398
6X-RAY DIFFRACTION6chain B and resi 285:B-6 - 398

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