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- PDB-4xbz: Crystal Structure of EvdO1 from Micromonospora carbonacea var. au... -

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Basic information

Entry
Database: PDB / ID: 4xbz
TitleCrystal Structure of EvdO1 from Micromonospora carbonacea var. aurantiaca
ComponentsEvdO1
KeywordsOXIDOREDUCTASE / double stranded beta helix
Function / homologyPhytanoyl-CoA dioxygenase / Phytanoyl-CoA dioxygenase (PhyH) / NICKEL (II) ION / EvdO1
Function and homology information
Biological speciesMicromonospora carbonacea (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsMcCulloch, K.M. / McCranie, E.K. / Sarwar, M. / Mathieu, J.L. / Gitschlag, B.L. / Du, Y. / Bachmann, B.O. / Iverson, T.M.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2015
Title: Oxidative cyclizations in orthosomycin biosynthesis expand the known chemistry of an oxygenase superfamily.
Authors: McCulloch, K.M. / McCranie, E.K. / Smith, J.A. / Sarwar, M. / Mathieu, J.L. / Gitschlag, B.L. / Du, Y. / Bachmann, B.O. / Iverson, T.M.
History
DepositionDec 17, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 5, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 19, 2015Group: Database references
Revision 1.2Sep 30, 2015Group: Database references
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: EvdO1
B: EvdO1
C: EvdO1
D: EvdO1
E: EvdO1
F: EvdO1
G: EvdO1
H: EvdO1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)301,73022
Polymers300,7088
Non-polymers1,02214
Water24,0141333
1
A: EvdO1
B: EvdO1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,4796
Polymers75,1772
Non-polymers3024
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3490 Å2
ΔGint-35 kcal/mol
Surface area25550 Å2
MethodPISA
2
C: EvdO1
D: EvdO1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,3865
Polymers75,1772
Non-polymers2093
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3300 Å2
ΔGint-31 kcal/mol
Surface area26170 Å2
MethodPISA
3
E: EvdO1
F: EvdO1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,3865
Polymers75,1772
Non-polymers2093
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3190 Å2
ΔGint-28 kcal/mol
Surface area25350 Å2
MethodPISA
4
G: EvdO1
H: EvdO1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,4796
Polymers75,1772
Non-polymers3024
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3630 Å2
ΔGint-36 kcal/mol
Surface area25620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.615, 109.432, 146.050
Angle α, β, γ (deg.)90.000, 108.270, 90.000
Int Tables number4
Space group name H-MP1211
DetailsThe biological unit is a dimer. There are 4 biological units in the asymmetric unit (chains A & B, chains C & D, chains E & F, and chains G & H).

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Components

#1: Protein
EvdO1


Mass: 37588.465 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Micromonospora carbonacea (bacteria) / Strain: var. aurantiaca / Gene: evdO1 / Plasmid: pET28a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A0M3KL03*PLUS
#2: Chemical
ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ni
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1333 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsThe authors state that the structure contains four dimers in the ASU and four partially ordered ...The authors state that the structure contains four dimers in the ASU and four partially ordered purification His tags, of which it is unclear what chain the tag belongs to. They are currently modeled as part of the polymer chains.

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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: 2.31 Å3/Da / Density % sol: 46.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.1
Details: 100 mM sodium citrate, 13% PEG8000, crystals soaked with 2 mM NiCl2

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 21-ID-F10.979
SYNCHROTRONAPS 21-ID-D21.485
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 4, 2013
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.9791
21.4851
ReflectionRedundancy: 7.7 % / Number: 462649 / Rmerge(I) obs: 0.121 / Χ2: 1.95 / D res high: 2.9 Å / D res low: 50 Å / Num. obs: 60108 / % possible obs: 98.1
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)IDRmerge(I) obsChi squaredRedundancy
7.865010.052.9067.3
6.247.8610.0662.3467.6
5.466.2410.0752.2567.7
4.965.4610.0782.3567.6
4.64.9610.0782.577.7
4.334.610.0842.5857.6
4.114.3310.0922.4887.7
3.944.1110.1032.3617.7
3.783.9410.1162.37.7
3.653.7810.1342.1867.7
3.543.6510.1441.9357.7
3.443.5410.1571.8227.7
3.353.4410.1811.7687.8
3.273.3510.2061.5967.8
3.193.2710.2411.4337.8
3.123.1910.2781.347.8
3.063.1210.2971.37.8
33.0610.3411.1987.8
2.95310.3861.1747.8
2.92.9510.4181.1377.8
ReflectionResolution: 2.3→50 Å / Num. obs: 120971 / % possible obs: 99.5 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.086 / Rpim(I) all: 0.051 / Rrim(I) all: 0.101 / Χ2: 1.019 / Net I/av σ(I): 15.212 / Net I/σ(I): 7.5 / Num. measured all: 456961
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.3-2.343.10.44359730.7880.3010.5380.81499.1
2.34-2.383.30.41459990.8230.2730.4980.84899.2
2.38-2.433.50.36360210.8850.230.4310.84399.2
2.43-2.483.80.33360200.9220.1980.3880.8699.3
2.48-2.533.90.30459780.9350.1780.3520.84799.4
2.53-2.593.90.26360090.9480.1540.3050.86699.4
2.59-2.663.90.2260390.970.1290.2560.86899.5
2.66-2.733.90.21660290.9620.1260.250.92199.5
2.73-2.813.90.17260630.9750.1010.1990.89899.5
2.81-2.93.90.14960070.980.0870.1730.93199.6
2.9-33.90.1360070.9830.0760.1511.00799.7
3-3.123.90.11560600.9870.0670.1331.10799.7
3.12-3.263.90.10560670.9860.0620.1221.2399.7
3.26-3.443.90.08860740.9880.0520.1021.39199.7
3.44-3.653.90.07360890.9910.0430.0851.31399.8
3.65-3.933.90.06260390.9930.0360.0711.28799.8
3.93-4.333.90.05460980.9950.0320.0631.23899.8
4.33-4.953.90.05360820.9950.0310.0621.34399.8
4.95-6.243.90.0561120.9940.030.0581.10499.8
6.24-503.70.03662050.9980.0210.0420.51399.3

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Processing

Software
NameVersionClassification
HKL-2000data reduction
PHENIXrefinement
PDB_EXTRACT3.15data extraction
HKL-2000data scaling
PHENIXAutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.3→46.316 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2372 6079 5.03 %
Rwork0.183 114814 -
obs0.1857 120893 99.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 84.93 Å2 / Biso mean: 35.2407 Å2 / Biso min: 16.41 Å2
Refinement stepCycle: final / Resolution: 2.3→46.316 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19105 0 44 1333 20482
Biso mean--44.25 38.45 -
Num. residues----2396
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00819634
X-RAY DIFFRACTIONf_angle_d1.07126778
X-RAY DIFFRACTIONf_chiral_restr0.0412889
X-RAY DIFFRACTIONf_plane_restr0.0063528
X-RAY DIFFRACTIONf_dihedral_angle_d14.5797220
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2993-2.32550.32161590.23273699385895
2.3255-2.35280.31472250.23463805403099
2.3528-2.38150.29162310.22493732396399
2.3815-2.41170.32812060.22263839404599
2.4117-2.44340.28541900.21843777396799
2.4434-2.47690.27992150.21493806402199
2.4769-2.51220.27462040.21013808401299
2.5122-2.54970.29392250.20953814403999
2.5497-2.58960.30111800.20753745392599
2.5896-2.6320.31572070.21323868407599
2.632-2.67740.27351990.20013800399999
2.6774-2.72610.29152050.205638134018100
2.7261-2.77850.27631950.204338134008100
2.7785-2.83520.29891830.203438454028100
2.8352-2.89690.27362020.205238604062100
2.8969-2.96420.25722130.200838214034100
2.9642-3.03840.27351840.206538544038100
3.0384-3.12050.29211960.20837993995100
3.1205-3.21230.26112360.204738074043100
3.2123-3.31590.24022070.194338474054100
3.3159-3.43440.25081680.181838774045100
3.4344-3.57190.23772240.177338194043100
3.5719-3.73440.21451820.165238434025100
3.7344-3.93120.19072020.158138694071100
3.9312-4.17730.18252040.150338674071100
4.1773-4.49960.18592230.149238054028100
4.4996-4.9520.18622090.143438914100100
4.952-5.66740.17572020.160338694071100
5.6674-7.13610.24591960.180739004096100
7.1361-46.32510.19922070.17833922412999

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