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- PDB-7w5e: Oxidase ChaP D49L mutant -

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Basic information

Entry
Database: PDB / ID: 7w5e
TitleOxidase ChaP D49L mutant
ComponentsChaP
KeywordsBIOSYNTHETIC PROTEIN / Chap / Chartreusin Biosynthesis / Oxidative Rearrangement Steps
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 / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsWang, Y. / Zheng, W. / Meng, Z. / Jin, Y. / Zhu, J. / Tan, R.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2022
Title: Alteration of the Catalytic Reaction Trajectory of a Vicinal Oxygen Chelate Enzyme by Directed Evolution.
Authors: Wang, Y.S. / Zheng, W. / Jiang, N. / Jin, Y.X. / Meng, Z.K. / Sun, M.X. / Zong, Y.L. / Xu, T. / Zhu, J. / Tan, R.X.
History
DepositionNov 30, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 26, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ChaP
B: ChaP
C: ChaP
D: ChaP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,62017
Polymers58,8944
Non-polymers72613
Water9,044502
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11760 Å2
ΔGint-229 kcal/mol
Surface area19190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.760, 62.070, 92.020
Angle α, β, γ (deg.)90.000, 91.800, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 1 through 10 or (resid 11...
d_2ens_1(chain "B" and (resid 1 through 10 or (resid 11...
d_3ens_1(chain "C" and (resid 1 through 10 or (resid 11...
d_4ens_1(chain "D" and (resid 1 through 15 or (resid 16...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1METASPA3 - 54
d_12ens_1ASPGLYA60 - 98
d_13ens_1GLYASPA102 - 110
d_14ens_1GLYARGA113 - 121
d_21ens_1METASPB3 - 54
d_22ens_1ASPHISB58 - 93
d_23ens_1GLUGLYB95 - 97
d_24ens_1GLYASPB99 - 107
d_25ens_1GLYARGB110 - 118
d_31ens_1METHISC2 - 89
d_32ens_1GLUGLYC91 - 93
d_33ens_1GLYARGC100 - 117
d_41ens_1METASPD1 - 52
d_42ens_1ASPHISD54 - 89
d_43ens_1GLUGLYD91 - 93
d_44ens_1GLYASPD99 - 107
d_45ens_1GLYARGD110 - 118

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Components

#1: Protein
ChaP / ChaP protein / VOC family protein


Mass: 14723.511 Da / Num. of mol.: 4 / Mutation: D49L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces chartreusis (bacteria) / Gene: chaP, HUT05_05055 / Production host: Escherichia coli (E. coli) / References: UniProt: Q4R0L3
#2: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 502 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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 Å3/Da / Density % sol: 38.39 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 0.01M Zinc sulfate heptahydrate, 0.1M MES monohydrate pH6.5, 25% v/v PEG monomethyl ether 550

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 7, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.59→29.41 Å / Num. obs: 57729 / % possible obs: 94.5 % / Redundancy: 3.2 % / Biso Wilson estimate: 17.02 Å2 / CC1/2: 0.995 / Net I/σ(I): 8
Reflection shellResolution: 1.59→1.62 Å / Rmerge(I) obs: 0.481 / Num. unique obs: 2790 / CC1/2: 0.716

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
Aimlessdata scaling
PDB_EXTRACT3.27data extraction
AUTOMARdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6A4Z

6a4z


Resolution: 1.65→29.41 Å / SU ML: 0.202 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 24.4504
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2381 1787 3.43 %
Rwork0.2043 50277 -
obs0.2055 52064 94.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.85 Å2
Refinement stepCycle: LAST / Resolution: 1.65→29.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3660 0 13 502 4175
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073743
X-RAY DIFFRACTIONf_angle_d1.54975059
X-RAY DIFFRACTIONf_chiral_restr0.061538
X-RAY DIFFRACTIONf_plane_restr0.0138677
X-RAY DIFFRACTIONf_dihedral_angle_d9.0553497
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS0.636573815504
ens_1d_3AX-RAY DIFFRACTIONTorsion NCS1.2597887575
ens_1d_4AX-RAY DIFFRACTIONTorsion NCS1.28647524585
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.690.32661270.27023831X-RAY DIFFRACTION93.61
1.69-1.740.26871430.24953858X-RAY DIFFRACTION95.24
1.74-1.80.28491310.23283759X-RAY DIFFRACTION92.31
1.8-1.870.25361290.21633763X-RAY DIFFRACTION90.91
1.87-1.940.271410.21113908X-RAY DIFFRACTION95.61
1.94-2.030.21591410.21263915X-RAY DIFFRACTION96.05
2.03-2.130.24271370.20653897X-RAY DIFFRACTION94.63
2.14-2.270.24241390.19813722X-RAY DIFFRACTION91.04
2.27-2.440.24291380.20613955X-RAY DIFFRACTION96.85
2.44-2.690.27651390.213939X-RAY DIFFRACTION95.71
2.69-3.080.25211370.213802X-RAY DIFFRACTION92.16
3.08-3.880.22021450.19074001X-RAY DIFFRACTION96.78
3.88-29.410.20211400.1873927X-RAY DIFFRACTION93.19
Refinement TLS params.Method: refined / Origin x: 30.5200531222 Å / Origin y: 21.1835890177 Å / Origin z: 68.7038860825 Å
111213212223313233
T0.0559538023186 Å20.010574761761 Å20.00490297973987 Å2-0.10551370483 Å2-0.0128019839178 Å2--0.125788379905 Å2
L0.286357369095 °20.0524810267278 °2-0.0675383508872 °2-0.772625580757 °2-0.447413644571 °2--1.33445721267 °2
S0.0104556514669 Å °-0.00212789071427 Å °0.0122267292167 Å °-0.0106895907346 Å °0.0422579775172 Å °0.0806234855832 Å °-0.0295558358849 Å °-0.134886515444 Å °0.0266712503144 Å °
Refinement TLS groupSelection details: all

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