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- PDB-8he6: Crystal structure of a fosfomycin and bleomycin resistant protein... -

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Basic information

Entry
Database: PDB / ID: 8he6
TitleCrystal structure of a fosfomycin and bleomycin resistant protein (ALL3014) from Anabaena/Nostoc cyanobacterium at 1.70 A resolution
ComponentsAll3014 protein
KeywordsTRANSFERASE / All3014 protein
Function / homology: / 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 / All3014 protein
Function and homology information
Biological speciesNostoc sp. PCC 7120 = FACHB-418 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsChatterjee, A. / Singh, P.K. / Singh, T.P. / Marina, A. / Sharma, S. / Rai, L.C.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Crystal structure of a fosfomycin and bleomycin resistant protein (ALL3014) from Anabaena/Nostoc cyanobacterium at 1.70 A resolution
Authors: Chatterjee, A. / Singh, P.K. / Singh, T.P. / Marina, A. / Sharma, S. / Rai, L.C.
History
DepositionNov 7, 2022Deposition site: PDBJ / Processing site: PDBJ
SupersessionNov 30, 2022ID: 6IPT
Revision 1.0Nov 30, 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: All3014 protein
B: All3014 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,3804
Polymers27,3162
Non-polymers642
Water4,486249
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2950 Å2
ΔGint-36 kcal/mol
Surface area11750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.462, 109.462, 46.668
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number90
Space group name H-MP4212
Noncrystallographic symmetry (NCS)NCS domain: (Details: Chains A B)

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Components

#1: Protein All3014 protein


Mass: 13658.031 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nostoc sp. PCC 7120 = FACHB-418 (bacteria)
Strain: PCC 7120 / SAG 25.82 / UTEX 2576 / Gene: all3014 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8YSS0
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 249 / 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: 2.55 Å3/Da / Density % sol: 51.9 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 0.2M lithium sulphate, 0.1M sodium acetate, 50 % PEG 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 1.0718 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 21, 2016 / Details: mirror
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0718 Å / Relative weight: 1
ReflectionResolution: 1.7→77.41 Å / Num. obs: 31802 / % possible obs: 95 % / Redundancy: 9.1 % / CC1/2: 0.99 / Rmerge(I) obs: 0.068 / Rsym value: 0.072 / Net I/σ(I): 17.4
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 6 % / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 1753 / CC1/2: 0.62 / % possible all: 85

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
SCALAdata scaling
Auto-Rickshawphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6A4X

6a4x


Resolution: 1.7→48.953 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.952 / SU B: 2.183 / SU ML: 0.07 / Cross valid method: FREE R-VALUE / ESU R: 0.102 / ESU R Free: 0.107
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2173 1466 4.863 %
Rwork0.1715 28679 -
all0.174 --
obs-30145 94.793 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 27.792 Å2
Baniso -1Baniso -2Baniso -3
1--0.005 Å20 Å2-0 Å2
2---0.005 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.7→48.953 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1934 0 2 250 2186
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0132075
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171752
X-RAY DIFFRACTIONr_angle_refined_deg1.5681.6362822
X-RAY DIFFRACTIONr_angle_other_deg1.5041.5744074
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4865258
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.43822.5136
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.29815320
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0151512
X-RAY DIFFRACTIONr_chiral_restr0.0870.2260
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022434
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02494
X-RAY DIFFRACTIONr_nbd_refined0.210.2345
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1880.21533
X-RAY DIFFRACTIONr_nbtor_refined0.1710.2952
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0840.2880
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2020.2187
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0920.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1560.213
X-RAY DIFFRACTIONr_nbd_other0.2050.222
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2340.217
X-RAY DIFFRACTIONr_mcbond_it3.1562.63985
X-RAY DIFFRACTIONr_mcbond_other3.1432.622984
X-RAY DIFFRACTIONr_mcangle_it4.8513.9011234
X-RAY DIFFRACTIONr_mcangle_other4.8553.9091235
X-RAY DIFFRACTIONr_scbond_it3.9373.0651090
X-RAY DIFFRACTIONr_scbond_other3.9283.0591089
X-RAY DIFFRACTIONr_scangle_it6.0734.4111580
X-RAY DIFFRACTIONr_scangle_other6.0694.411580
X-RAY DIFFRACTIONr_lrange_it9.29453.68310238
X-RAY DIFFRACTIONr_lrange_other9.24753.44310130
X-RAY DIFFRACTIONr_ncsr_local_group_10.0880.053895
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.7-1.7440.278920.28517530.28523050.8510.82180.04340.273
1.744-1.7920.248910.27418820.27322410.9010.86588.04110.251
1.792-1.8440.2721020.23119490.23421940.8970.90693.48220.204
1.844-1.90.226910.20220100.20321200.9190.93299.10380.173
1.9-1.9630.216810.19617140.19720670.9220.93986.84080.167
1.963-2.0310.2121120.18518960.18720080.9450.9491000.164
2.031-2.1080.218830.18616370.18819290.9390.94789.16540.165
2.108-2.1940.213920.16517720.16718700.9450.95899.67910.147
2.194-2.2910.264910.16315510.16717840.9250.95792.04040.145
2.291-2.4030.226840.16416250.16717120.9510.95699.82480.146
2.403-2.5320.215690.16215740.16416460.940.95999.81770.146
2.532-2.6860.195840.16114730.16315610.9560.96199.74380.149
2.686-2.870.203760.16213950.16414710.9490.9611000.153
2.87-3.0990.219660.16313000.16613710.9470.96399.63530.159
3.099-3.3940.238570.17212030.17412700.940.95999.21260.172
3.394-3.7920.276440.16610650.1711660.9350.96395.11150.167
3.792-4.3750.156520.1359770.13610340.9760.97699.51640.144
4.375-5.3470.201450.1458280.1488890.9630.97598.20020.159
5.347-7.5170.285370.1946660.1997130.9280.95898.59750.203
7.517-48.9530.146170.24080.1984470.9840.96495.07830.219

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