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- PDB-6a4z: Oxidase ChaP -

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Basic information

Entry
Database: PDB / ID: 6a4z
TitleOxidase ChaP
ComponentsChaP protein
KeywordsBIOSYNTHETIC PROTEIN / VOC family / dioxygenase / dimer / Chartreusin / Oxidative Rearrangement
Function / homology
Function and homology information


lactoylglutathione lyase activity / metal ion binding
Similarity search - Function
Glyoxalase I, conserved site / Glyoxalase I signature 1. / Glyoxalase/fosfomycin resistance/dioxygenase domain / Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily / Vicinal oxygen chelate (VOC) domain / Vicinal oxygen chelate (VOC) domain profile. / Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase
Similarity search - Domain/homology
Biological speciesStreptomyces chartreusis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.7 Å
AuthorsZhang, B. / Ge, H.M.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China21572100, 81522042, 81773591, 81421091, 81500059, 81673333, 21672101, and 21661140001 China
CitationJournal: J. Am. Chem. Soc. / Year: 2018
Title: Molecular Basis for the Final Oxidative Rearrangement Steps in Chartreusin Biosynthesis.
Authors: Wang, Y.S. / Zhang, B. / Zhu, J. / Yang, C.L. / Guo, Y. / Liu, C.L. / Liu, F. / Huang, H. / Zhao, S. / Liang, Y. / Jiao, R.H. / Tan, R.X. / Ge, H.M.
History
DepositionJun 21, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 29, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 19, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ChaP protein
B: ChaP protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,1254
Polymers30,0142
Non-polymers1122
Water4,161231
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3620 Å2
ΔGint-52 kcal/mol
Surface area11900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.830, 47.120, 53.920
Angle α, β, γ (deg.)90.000, 109.600, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain AA1 - 127
211chain BB1 - 127

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Components

#1: Protein ChaP protein / dioxidase ChaP


Mass: 15006.812 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces chartreusis (bacteria) / Gene: chaP / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q4R0L3
#2: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 231 / 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: 2.19 Å3/Da / Density % sol: 43.77 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: MgCl2, Tris-HCl, PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9788 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 20, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9788 Å / Relative weight: 1
ReflectionResolution: 1.7→50.8 Å / Num. obs: 27459 / % possible obs: 97.3 % / Redundancy: 3.8 % / Biso Wilson estimate: 19.04 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.104 / Rpim(I) all: 0.06 / Rrim(I) all: 0.121 / Net I/σ(I): 8.1 / Num. measured all: 104844 / Scaling rejects: 407
Reflection shell

Diffraction-ID: 1 / Redundancy: 3.6 %

Resolution (Å)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.7-1.730.915500213730.640.5381.0681.592.4
8.99-50.80.0767091980.9860.0450.08919.396.6

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
MOSFLMdata reduction
Aimlessdata scaling
AutoSolphasing
RefinementResolution: 1.7→50.796 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.26 / Phase error: 23.27
RfactorNum. reflection% reflection
Rfree0.2069 1265 4.62 %
Rwork0.1791 --
obs0.1803 27356 96.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 123.8 Å2 / Biso mean: 29.5356 Å2 / Biso min: 11.38 Å2
Refinement stepCycle: final / Resolution: 1.7→50.796 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2000 0 2 231 2233
Biso mean--29.92 38.19 -
Num. residues----254
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1125X-RAY DIFFRACTION9.017TORSIONAL
12B1125X-RAY DIFFRACTION9.017TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6985-1.76650.30871250.28672719284492
1.7665-1.84690.27751420.23732888303097
1.8469-1.94430.26111670.20832917308498
1.9443-2.06610.23311390.18362916305598
2.0661-2.22560.20491350.17192918305397
2.2256-2.44960.22661540.17432837299195
2.4496-2.80410.24711280.17882915304397
2.8041-3.53270.16051400.16423000314099
3.5327-50.81830.17631350.16542981311696
Refinement TLS params.Method: refined / Origin x: 37.7112 Å / Origin y: 21.6841 Å / Origin z: 7.523 Å
111213212223313233
T0.1857 Å2-0.0157 Å20.015 Å2-0.1404 Å20.0045 Å2--0.1728 Å2
L1.1666 °2-0.1145 °2-1.0187 °2-0.2394 °2-0.1403 °2--2.1519 °2
S0.103 Å °-0.1414 Å °0.0511 Å °0.1133 Å °0.0181 Å °0.0322 Å °-0.3513 Å °0.0955 Å °-0.0632 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1 - 127
2X-RAY DIFFRACTION1allB1 - 127
3X-RAY DIFFRACTION1allC1 - 2
4X-RAY DIFFRACTION1allS1 - 231

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