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- PDB-7wcc: Oxidase ChaP-D49L/Q91C mutant -

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Basic information

Entry
Database: PDB / ID: 7wcc
TitleOxidase ChaP-D49L/Q91C mutant
ComponentsChaP
KeywordsBIOSYNTHETIC PROTEIN / ChaP / Oxidative Rearrangement Steps / Mycobacterium tuberculosis
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: 1.5 Å
AuthorsSun, M.X. / Zheng, W. / Wang, Y.S. / Zhu, J.P. / Tan, R.X.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Oxidase ChaP-D49L/Q91C mutant
Authors: Sun, M.X. / Zheng, W. / Wang, Y.S. / Zhu, J.P. / Tan, R.X.
History
DepositionDec 19, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 24, 2023Provider: repository / Type: Initial release

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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)57,8888
Polymers57,6654
Non-polymers2234
Water10,575587
1
A: ChaP
hetero molecules

C: ChaP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,9444
Polymers28,8322
Non-polymers1122
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_565x,y+1,z1
Buried area3420 Å2
ΔGint-53 kcal/mol
Surface area12200 Å2
MethodPISA
2
B: ChaP
hetero molecules

D: ChaP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,9444
Polymers28,8322
Non-polymers1122
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
Buried area3280 Å2
ΔGint-51 kcal/mol
Surface area12200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.800, 48.480, 143.820
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 14416.248 Da / Num. of mol.: 4 / Mutation: D49L,Y109F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces chartreusis (bacteria) / Gene: chaP, HUT05_05055 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q4R0L3
#2: Chemical
ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 587 / 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: 2.47 Å3/Da / Density % sol: 50.13 %
Crystal growTemperature: 295 K / Method: vapor diffusion
Details: Magnesium chloride hexahydrate, Calcium chloride dihygrate, Tris(base), BICINE, MPD, PEG 1000, PEG 3350

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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: Oct 2, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.5→28.88 Å / Num. obs: 90164 / % possible obs: 99.9 % / Redundancy: 5.9 % / CC1/2: 0.99 / Net I/σ(I): 8.4
Reflection shellResolution: 1.5→1.53 Å / Num. unique obs: 2256 / CC1/2: 0.762

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
Aimless1.19.2_4158data scaling
PDB_EXTRACTdata extraction
MOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6A4Z

6a4z


Resolution: 1.5→28.88 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.61 / Phase error: 22.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2155 2014 2.23 %
Rwork0.1909 --
obs0.1915 90158 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.5→28.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3964 0 4 587 4555
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003
X-RAY DIFFRACTIONf_angle_d0.589
X-RAY DIFFRACTIONf_dihedral_angle_d10.2931504
X-RAY DIFFRACTIONf_chiral_restr0.047561
X-RAY DIFFRACTIONf_plane_restr0.005741
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.540.29741390.25156204X-RAY DIFFRACTION100
1.54-1.580.24141420.23516299X-RAY DIFFRACTION100
1.58-1.630.26511440.22746271X-RAY DIFFRACTION100
1.63-1.680.2361420.21896214X-RAY DIFFRACTION100
1.68-1.740.27291440.22216261X-RAY DIFFRACTION100
1.74-1.810.25161420.21456318X-RAY DIFFRACTION100
1.81-1.890.23031440.20686220X-RAY DIFFRACTION100
1.89-1.990.23241420.19416304X-RAY DIFFRACTION100
1.99-2.110.18111430.19166311X-RAY DIFFRACTION100
2.11-2.280.15711450.17656299X-RAY DIFFRACTION100
2.28-2.510.19941460.20596275X-RAY DIFFRACTION100
2.51-2.870.20921450.19446359X-RAY DIFFRACTION100
2.87-3.610.22561450.18456333X-RAY DIFFRACTION100
3.61-28.880.21441510.17056476X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 4.7703 Å / Origin y: -18.3422 Å / Origin z: 35.8983 Å
111213212223313233
T0.1198 Å2-0.0067 Å20.011 Å2-0.1515 Å20.0256 Å2--0.1524 Å2
L0.0435 °2-0.0252 °20.1097 °2-0.1973 °2-0.0129 °2--0.19 °2
S-0.035 Å °0.0193 Å °0.0055 Å °-0.0021 Å °0.0363 Å °0.0623 Å °0.0193 Å °-0.0008 Å °-0.0071 Å °
Refinement TLS groupSelection details: all

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