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- PDB-6dqw: Flavobacterium johnsoniae class Id ribonucleotide reductase alpha... -

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Basic information

Entry
Database: PDB / ID: 6dqw
TitleFlavobacterium johnsoniae class Id ribonucleotide reductase alpha subuint
ComponentsRibonucleoside-diphosphate reductase, alpha chainRibonucleotide reductase
KeywordsOXIDOREDUCTASE / Ribonucleotide Reductase / alpha subunit / nucleotide metabolism
Function / homologyRibonucleotide reductase alpha chain / Ribonucleoside-diphosphate reductase large subunit / Ribonucleotide reductase large subunit, C-terminal / Ribonucleotide reductase, barrel domain / ribonucleoside-diphosphate reductase / ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor / DNA replication / Ribonucleoside-diphosphate reductase, alpha chain
Function and homology information
Biological speciesFlavobacterium johnsoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsMaggiolo, A.O. / Boal, A.K.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM119707 United States
CitationJournal: Biochemistry / Year: 2019
Title: Structures of Class Id Ribonucleotide Reductase Catalytic Subunits Reveal a Minimal Architecture for Deoxynucleotide Biosynthesis.
Authors: Rose, H.R. / Maggiolo, A.O. / McBride, M.J. / Palowitch, G.M. / Pandelia, M.E. / Davis, K.M. / Yennawar, N.H. / Boal, A.K.
History
DepositionJun 11, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 17, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 24, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ribonucleoside-diphosphate reductase, alpha chain
B: Ribonucleoside-diphosphate reductase, alpha chain
C: Ribonucleoside-diphosphate reductase, alpha chain
D: Ribonucleoside-diphosphate reductase, alpha chain


Theoretical massNumber of molelcules
Total (without water)263,6154
Polymers263,6154
Non-polymers00
Water2,414134
1
A: Ribonucleoside-diphosphate reductase, alpha chain
B: Ribonucleoside-diphosphate reductase, alpha chain


Theoretical massNumber of molelcules
Total (without water)131,8082
Polymers131,8082
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1800 Å2
ΔGint-17 kcal/mol
Surface area38320 Å2
MethodPISA
2
C: Ribonucleoside-diphosphate reductase, alpha chain
D: Ribonucleoside-diphosphate reductase, alpha chain


Theoretical massNumber of molelcules
Total (without water)131,8082
Polymers131,8082
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1830 Å2
ΔGint-18 kcal/mol
Surface area34510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)161.031, 161.031, 187.733
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61

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Components

#1: Protein
Ribonucleoside-diphosphate reductase, alpha chain / Ribonucleotide reductase


Mass: 65903.852 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Flavobacterium johnsoniae (strain ATCC 17061 / DSM 2064 / UW101) (bacteria)
Strain: ATCC 17061 / DSM 2064 / UW101 / Gene: Fjoh_4065 / Plasmid: pE-SUMO / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: A5FCJ4, ribonucleoside-diphosphate reductase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 134 / 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: 2.76 Å3/Da / Density % sol: 55.37 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.25 M magnesium chloride, 0.1 M Tris pH 7.0, 10% (w/v) PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Oct 12, 2015
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 85045 / % possible obs: 100 % / Redundancy: 11.6 % / Rmerge(I) obs: 0.1 / Rpim(I) all: 0.031 / Rrim(I) all: 0.104 / Χ2: 0.969 / Net I/σ(I): 8
Reflection shell

Diffraction-ID: 1 / % possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2
2.6-2.6411.60.90542600.8560.2760.9460.94
2.64-2.6911.60.76942600.8810.2350.8040.968
2.69-2.7411.70.68441950.9090.2090.7150.944
2.74-2.811.70.55542350.9360.1690.580.925
2.8-2.8611.70.46642450.9540.1420.4870.935
2.86-2.9311.70.38142510.9640.1160.3980.935
2.93-311.70.33642150.9710.1020.3510.936
3-3.0811.70.27742490.9810.0840.2890.922
3.08-3.1711.70.22342700.9860.0680.2330.92
3.17-3.2811.70.17542230.9910.0530.1830.917
3.28-3.3911.70.1442480.9940.0430.1460.917
3.39-3.5311.70.10842460.9960.0330.1130.928
3.53-3.6911.70.0842420.9970.0240.0830.911
3.69-3.8811.70.06542440.9980.020.0680.866
3.88-4.1311.70.05142650.9990.0160.0530.843
4.13-4.4511.70.04842490.9990.0150.0510.971
4.45-4.8911.60.05242640.9980.0160.0541.37
4.89-5.611.50.05642700.9980.0170.0581.538
5.6-7.0511.60.04742780.9980.0140.0491.034
7.05-5011.30.02643360.9990.0080.0270.655

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Processing

Software
NameVersionClassification
HKL-2000data scaling
REFMAC5.8.0222refinement
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2WGH

2wgh


Resolution: 2.6→46.53 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.902 / SU B: 20.649 / SU ML: 0.208 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.485 / ESU R Free: 0.289
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2508 4248 5 %RANDOM
Rwork0.2062 ---
obs0.2084 80627 99.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 119.2 Å2 / Biso mean: 45.607 Å2 / Biso min: 11.56 Å2
Baniso -1Baniso -2Baniso -3
1--0.12 Å2-0.06 Å20 Å2
2---0.12 Å20 Å2
3---0.38 Å2
Refinement stepCycle: final / Resolution: 2.6→46.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15184 0 0 134 15318
Biso mean---30.43 -
Num. residues----1900
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.01415476
X-RAY DIFFRACTIONr_bond_other_d0.0010.01714102
X-RAY DIFFRACTIONr_angle_refined_deg1.0371.64820811
X-RAY DIFFRACTIONr_angle_other_deg0.7831.63533072
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3951871
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.51123.371798
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.836152878
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3431577
X-RAY DIFFRACTIONr_chiral_restr0.0510.21998
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0217075
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022869
LS refinement shellResolution: 2.596→2.663 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.324 332 -
Rwork0.263 5923 -
all-6255 -
obs--99.21 %
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)
10.267-0.04-0.04550.58370.03080.3665-0.02420.0001-0.04870.03550.01440.0194-0.0152-0.01140.00990.1010.0122-0.00670.06380.01390.031205.157111.32975.2759
20.44270.0348-0.13850.2652-0.10540.40710.01570.07250.024100.0297-0.02630.0468-0.0871-0.04540.07830.0346-0.00150.13850.03030.0152166.3445.5302-16.7766
31.28970.10780.13340.4725-0.16750.254-0.07390.05110.16510.0229-0.02230.04340.03760.0480.09620.0602-0.0456-0.00140.0840.05260.0809243.614454.2613-11.511
41.52060.0310.3020.6450.0030.6394-0.2116-0.24190.4064-0.00360.1545-0.0991-0.0024-0.04240.05710.03360.0424-0.07140.1263-0.16920.2522203.156483.41883.9925
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A19 - 547
2X-RAY DIFFRACTION2B19 - 546
3X-RAY DIFFRACTION3C20 - 545
4X-RAY DIFFRACTION4D22 - 543

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