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- PDB-3pqb: The crystal structure of pregilvocarcin in complex with GilR, an ... -

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Basic information

Entry
Database: PDB / ID: 3pqb
TitleThe crystal structure of pregilvocarcin in complex with GilR, an oxidoreductase that catalyzes the terminal step of gilvocarcin biosynthesis
ComponentsPutative oxidoreductase
KeywordsOXIDOREDUCTASE / FAD binding protein / covalently bound FAD
Function / homology
Function and homology information


FAD binding / oxidoreductase activity
Similarity search - Function
Vanillyl-alcohol Oxidase; Chain A, domain 3 - #20 / Oxygen oxidoreductase covalent FAD-binding site / Berberine/berberine-like / Berberine and berberine like / Oxygen oxidoreductases covalent FAD-binding site. / Vanillyl-alcohol Oxidase; Chain A, domain 3 / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 3 - #10 / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 3 / FAD linked oxidase, N-terminal / FAD binding domain ...Vanillyl-alcohol Oxidase; Chain A, domain 3 - #20 / Oxygen oxidoreductase covalent FAD-binding site / Berberine/berberine-like / Berberine and berberine like / Oxygen oxidoreductases covalent FAD-binding site. / Vanillyl-alcohol Oxidase; Chain A, domain 3 / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 3 - #10 / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 3 / FAD linked oxidase, N-terminal / FAD binding domain / FAD-binding domain, PCMH-type / PCMH-type FAD-binding domain profile. / FAD-binding, type PCMH, subdomain 2 / FAD-binding, type PCMH-like superfamily / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / Chem-VGP / Putative oxidoreductase
Similarity search - Component
Biological speciesStreptomyces griseoflavus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.324 Å
AuthorsNoinaj, N. / Bosserman, M.A. / Schickli, M.A. / Kharel, M.K. / Rohr, J. / Buchanan, S.K.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: The Crystal Structure and Mechanism of an Unusual Oxidoreductase, GilR, Involved in Gilvocarcin V Biosynthesis.
Authors: Noinaj, N. / Bosserman, M.A. / Schickli, M.A. / Piszczek, G. / Kharel, M.K. / Pahari, P. / Buchanan, S.K. / Rohr, J.
History
DepositionNov 25, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 11, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 3, 2011Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative oxidoreductase
B: Putative oxidoreductase
C: Putative oxidoreductase
D: Putative oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)222,77912
Polymers217,6504
Non-polymers5,1288
Water9,944552
1
A: Putative oxidoreductase
D: Putative oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,3896
Polymers108,8252
Non-polymers2,5644
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5780 Å2
ΔGint-30 kcal/mol
Surface area32250 Å2
MethodPISA
2
B: Putative oxidoreductase
C: Putative oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,3896
Polymers108,8252
Non-polymers2,5644
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5780 Å2
ΔGint-30 kcal/mol
Surface area32180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.003, 115.973, 291.405
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain A and (resseq 7:498 )
211chain B and (resseq 7:498 )
311chain C and (resseq 7:498 )
411chain D and (resseq 7:498 )

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Components

#1: Protein
Putative oxidoreductase /


Mass: 54412.594 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces griseoflavus (bacteria) / Gene: gilR / Production host: Escherichia coli (E. coli) / References: UniProt: Q7X2G7
#2: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical
ChemComp-VGP / (1R)-1,4-anhydro-6-deoxy-1-[(6R)-8-ethenyl-1,6-dihydroxy-10,12-dimethoxy-6H-dibenzo[c,h]chromen-4-yl]-D-galactitol / pregilvocarcin V


Mass: 496.506 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H28O9
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 552 / 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: 2.64 Å3/Da / Density % sol: 53.4 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 100 mM Tris 8.5, 200 mM MgCl2, 20% PEG 8000, 5-15% glycerol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.9796 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD
RadiationMonochromator: Si 220 (Rosenbaum-Rock double-crystal monochromator)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 2.3→45.7 Å / Num. all: 98696 / Num. obs: 98524 / Observed criterion σ(F): 1 / Observed criterion σ(I): 1

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
PHENIX(phenix.refine: dev_501)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.324→19.985 Å / SU ML: 0.32 / σ(F): 0.14 / Phase error: 19.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.205 4922 5 %Random
Rwork0.1724 ---
obs0.1741 98524 98.47 %-
all-98696 --
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 28.579 Å2 / ksol: 0.328 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--4.2405 Å20 Å20 Å2
2--2.0306 Å20 Å2
3---4.6878 Å2
Refinement stepCycle: LAST / Resolution: 2.324→19.985 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14914 0 356 552 15822
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01315729
X-RAY DIFFRACTIONf_angle_d1.30321484
X-RAY DIFFRACTIONf_dihedral_angle_d18.6825535
X-RAY DIFFRACTIONf_chiral_restr0.0962276
X-RAY DIFFRACTIONf_plane_restr0.0062789
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A3713X-RAY DIFFRACTIONPOSITIONAL
12B3713X-RAY DIFFRACTIONPOSITIONAL0.234
13C3715X-RAY DIFFRACTIONPOSITIONAL0.272
14D3707X-RAY DIFFRACTIONPOSITIONAL0.305
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.324-2.4070.31434350.26978213X-RAY DIFFRACTION88
2.407-2.50320.30984570.24589391X-RAY DIFFRACTION100
2.5032-2.61690.29584800.23749425X-RAY DIFFRACTION100
2.6169-2.75450.27875440.21989313X-RAY DIFFRACTION100
2.7545-2.92660.25554900.20919414X-RAY DIFFRACTION100
2.9266-3.15170.22185090.1819381X-RAY DIFFRACTION99
3.1517-3.46740.21165200.17559398X-RAY DIFFRACTION99
3.4674-3.96580.17425070.15059534X-RAY DIFFRACTION100
3.9658-4.98360.14364910.11639606X-RAY DIFFRACTION100
4.9836-19.98540.15944890.15519927X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.56730.1868-0.11541.1325-0.34141.5871-0.0943-0.04170.04140.0796-0.012-0.04580.0431-0.0750.08810.14550.00580.0313-0.03290.0167-0.024310.177710.39664.5941
20.70880.0212-0.37990.831-0.27631.57740.11410.11080.1022-0.044-0.0491-0.01620.0047-0.1853-0.07020.13770.02090.04120.09550.0390.04316.5655-5.640877.557
30.7741-0.0467-0.08240.7654-0.01761.07450.1157-0.05010.08910.0919-0.08220.0149-0.12960.2734-0.03630.121-0.11530.06120.1142-0.05080.032730.4001-0.7962103.865
41.26950.1674-0.08141.0716-0.27591.2038-0.0758-0.0833-0.0253-0.0606-0.0638-0.14340.09940.12870.12560.23820.11790.02550.10830.05090.031415.2331-13.080631.5474
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B
3X-RAY DIFFRACTION3chain C
4X-RAY DIFFRACTION4chain D

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