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- PDB-6n04: The X-ray crystal structure of AbsH3, an FAD dependent reductase ... -

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Basic information

Entry
Database: PDB / ID: 6n04
TitleThe X-ray crystal structure of AbsH3, an FAD dependent reductase from the Abyssomicin biosynthesis pathway in Streptomyces
ComponentsAbsH3
KeywordsBIOSYNTHETIC PROTEIN / Oxidoreductase / Biosynthesis / Abyssomicin / Structural Genomics / PSI-Biology / Protein Structure Initiative / Enzyme Discovery for Natural Product Biosynthesis / NatPro
Function / homologyFlavin-dependent monooxygenase TetX / Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With NADH or NADPH as one donor, and incorporation of one atom of oxygen into the other donor / FAD-binding domain / FAD binding domain / FAD binding / FAD/NAD(P)-binding domain superfamily / FLAVIN-ADENINE DINUCLEOTIDE / Flavin-dependent monooxygenase
Function and homology information
Biological speciesStreptomyces sp. LC-6-2 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.998 Å
AuthorsClinger, J.A. / Wang, X. / Cai, W. / Miller, M.D. / Van Lanen, S.G. / Thorson, J.S. / Phillips Jr., G.N. / Enzyme Discovery for Natural Product Biosynthesis (NatPro)
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 CA217255-01A1 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM115261-02 United States
CitationJournal: Proteins / Year: 2020
Title: The crystal structure of AbsH3: A putative flavin adenine dinucleotide-dependent reductase in the abyssomicin biosynthesis pathway.
Authors: Clinger, J.A. / Wang, X. / Cai, W. / Zhu, Y. / Miller, M.D. / Zhan, C.G. / Van Lanen, S.G. / Thorson, J.S. / Phillips Jr., G.N.
History
DepositionNov 6, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 13, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Feb 23, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 11, 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

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Assembly

Deposited unit
A: AbsH3
B: AbsH3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,8236
Polymers92,1812
Non-polymers1,6424
Water15,763875
1
A: AbsH3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,9123
Polymers46,0911
Non-polymers8212
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: AbsH3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,9123
Polymers46,0911
Non-polymers8212
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)53.316, 109.491, 143.637
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 39 through 76 or resid 80...
21(chain B and (resid 39 through 104 or resid 111...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 39 through 76 or resid 80...A39 - 76
121(chain A and (resid 39 through 76 or resid 80...A80 - 121
131(chain A and (resid 39 through 76 or resid 80...A123 - 154
141(chain A and (resid 39 through 76 or resid 80...A156 - 227
151(chain A and (resid 39 through 76 or resid 80...A229 - 238
161(chain A and (resid 39 through 76 or resid 80...A240 - 312
171(chain A and (resid 39 through 76 or resid 80...A314 - 322
181(chain A and (resid 39 through 76 or resid 80...A324 - 3395
191(chain A and (resid 39 through 76 or resid 80...A397395
1101(chain A and (resid 39 through 76 or resid 80...A397 - 417
1111(chain A and (resid 39 through 76 or resid 80...A500
211(chain B and (resid 39 through 104 or resid 111...B39 - 104
221(chain B and (resid 39 through 104 or resid 111...B111 - 121
231(chain B and (resid 39 through 104 or resid 111...B123 - 154
241(chain B and (resid 39 through 104 or resid 111...B156 - 227
251(chain B and (resid 39 through 104 or resid 111...B229 - 238
261(chain B and (resid 39 through 104 or resid 111...B240 - 312
271(chain B and (resid 39 through 104 or resid 111...B314 - 322
281(chain B and (resid 39 through 104 or resid 111...B324 - 388
291(chain B and (resid 39 through 104 or resid 111...B390 - 395
2101(chain B and (resid 39 through 104 or resid 111...B397 - 417
2111(chain B and (resid 39 through 104 or resid 111...B500

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Components

#1: Protein AbsH3


Mass: 46090.672 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces sp. LC-6-2 (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1V0QH64
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 875 / 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: 2.6 Å3/Da / Density % sol: 52.65 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: 1:1 10mg/mL AbsH3, 200mM sodium chrloide, 20mM HEPES pH 7.5 and 22% PEG3350, 20mM Magnesium chloride, 100mM HEPES pH 7.4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9793 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Feb 18, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.998→38.195 Å / Num. obs: 53265 / % possible obs: 92 % / Redundancy: 7.13 % / Biso Wilson estimate: 36.506 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.124 / Rrim(I) all: 0.133 / Χ2: 1.044 / Net I/σ(I): 12.07
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.998-2.126.9760.9332.1990820.7511.00898.4
2.12-2.277.1870.6822.9956030.8730.73564.7
2.27-2.457.2370.4884.3868030.9360.52683.9
2.45-2.687.4070.2887.3174800.9710.3199.9
2.68-2.997.3750.18411.2167940.9860.198100
2.99-3.457.2130.10718.2660030.9940.11599.9
3.45-4.236.6510.07625.4251280.9950.08399.3
4.23-5.957.0530.05431.9340420.9980.05899.9
5.95-38.1956.650.03632.9323300.9990.03997.6

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation7.49 Å47.94 Å
Translation7.49 Å47.94 Å

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Processing

Software
NameVersionClassificationNB
PHENIX(1.14_3260)refinement
XDSdata reduction
XSCALEdata scaling
PHASER2.6.0phasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3V3N

3v3n


Resolution: 1.998→38.195 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.32
RfactorNum. reflection% reflection
Rfree0.2365 2023 3.8 %
Rwork0.1832 --
obs0.1852 53222 91.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 130.06 Å2 / Biso mean: 34.7097 Å2 / Biso min: 14.67 Å2
Refinement stepCycle: final / Resolution: 1.998→38.195 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5465 0 108 891 6464
Biso mean--25.7 42.99 -
Num. residues----731
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3248X-RAY DIFFRACTION7.791TORSIONAL
12B3248X-RAY DIFFRACTION7.791TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9982-2.04810.31881480.27973778392696
2.0481-2.10350.28371550.24839104065100
2.1035-2.16540.26571540.231839014055100
2.1654-2.23530.3391000.25332516261697
2.2353-2.31520.3053470.24841168121593
2.3152-2.40790.28231530.230139114064100
2.4079-2.51740.26781560.213839474103100
2.5174-2.65010.24021560.200339554111100
2.6501-2.81610.26321570.198739684125100
2.8161-3.03350.26591560.197439524108100
3.0335-3.33860.24331560.179840014157100
3.3386-3.82130.23581590.16273982414199
3.8213-4.81290.16711610.138340374198100
4.8129-38.20240.22151650.16074173433899

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