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- PDB-8a1h: Bacterial 6-4 photolyase from Vibrio cholerase -

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Basic information

Entry
Database: PDB / ID: 8a1h
TitleBacterial 6-4 photolyase from Vibrio cholerase
Components6-4 photolyase (FeS-BCP, CryPro)
KeywordsDNA BINDING PROTEIN / Enzyme / iron-sulfur cluster / DNA-repair / photoreceptor
Function / homologyPhotolyase PhrB-like / Deoxyribodipyrimidine photo-lyase-related protein / Cryptochrome/DNA photolyase, FAD-binding domain-like superfamily / Rossmann-like alpha/beta/alpha sandwich fold / Chem-DLZ / FLAVIN-ADENINE DINUCLEOTIDE / IRON/SULFUR CLUSTER / Cryptochrome/photolyase family protein
Function and homology information
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsEssen, L.-O. / Emmerich, H.J.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)ES152/18 Germany
Citation
Journal: Photochem.Photobiol. / Year: 2023
Title: Structural and Functional Analysis of a Prokaryotic (6-4) Photolyase from the Aquatic Pathogen Vibrio Cholerae † .
Authors: Emmerich, H.J. / Schneider, L. / Essen, L.O.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2012
Title: Towards automated crystallographic structure refinement with phenix.refine.
Authors: Afonine, P.V. / Grosse-Kunstleve, R.W. / Echols, N. / Headd, J.J. / Moriarty, N.W. / Mustyakimov, M. / Terwilliger, T.C. / Urzhumtsev, A. / Zwart, P.H. / Adams, P.D.
#2: Journal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams /
Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.
History
DepositionJun 1, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 8, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 22, 2023Group: Database references / Category: citation / Item: _citation.title
Revision 1.2Oct 4, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 1.3Feb 7, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 6-4 photolyase (FeS-BCP, CryPro)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,23030
Polymers61,6691
Non-polymers3,56129
Water11,205622
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6380 Å2
ΔGint-174 kcal/mol
Surface area20190 Å2
Unit cell
Length a, b, c (Å)199.687, 199.687, 76.996
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number181
Space group name H-MP6422
Space group name HallP642(x,y,z+1/6)
Symmetry operation#1: x,y,z
#2: x-y,x,z+2/3
#3: y,-x+y,z+1/3
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+2/3
#8: -x,-y,z
#9: y,x,-z+1/3
#10: -y,-x,-z+1/3
#11: -x+y,y,-z
#12: x,x-y,-z+2/3
Components on special symmetry positions
IDModelComponents
11A-1074-

HOH

21A-1100-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein 6-4 photolyase (FeS-BCP, CryPro) / Cryptochrome/photolyase family protein


Mass: 61669.031 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Strain: ATCC 39315 / El Tor Inaba N16961 / Gene: VC_A0809 / Plasmid: pET28a
Details (production host): N-terminal fusion to histidine tag
Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Gold / References: UniProt: Q9KLD7

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Non-polymers , 9 types, 651 molecules

#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#3: Chemical ChemComp-DLZ / 1-deoxy-1-(6,7-dimethyl-2,4-dioxo-3,4-dihydropteridin-8(2H)-yl)-D-ribitol / 6,7-dimethyl-8-(1'-D-ribityl) lumazine


Mass: 326.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H18N4O6
#4: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4S4
#5: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#8: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Na
#9: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 622 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.59 Å3/Da / Density % sol: 65.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.1 M Tris pH 8.5, 1.5 ammonium sulfate and 12% (v/v) glycerol, 6.25 mg/ml Vc6-4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.00003 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 26, 2019
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00003 Å / Relative weight: 1
ReflectionResolution: 1.65→34.6 Å / Num. obs: 108011 / % possible obs: 99.97 % / Redundancy: 11 % / Biso Wilson estimate: 19.8 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.06137 / Rpim(I) all: 0.01912 / Rrim(I) all: 0.06433 / Net I/σ(I): 25.34
Reflection shellResolution: 1.65→1.71 Å / Redundancy: 8.7 % / Rmerge(I) obs: 0.7395 / Mean I/σ(I) obs: 2.73 / Num. unique obs: 10661 / CC1/2: 0.844 / CC star: 0.957 / Rpim(I) all: 0.2609 / Rrim(I) all: 0.7853 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487phasing
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4DJA

4dja


Resolution: 1.65→34.59 Å / SU ML: 0.112 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 12.1127
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Details: with hydrogens and TLS refinement
RfactorNum. reflection% reflection
Rfree0.1362 4130 2 %
Rwork0.119 202552 -
obs0.1194 103341 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.36 Å2
Refinement stepCycle: LAST / Resolution: 1.65→34.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4181 0 207 622 5010
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01694626
X-RAY DIFFRACTIONf_angle_d1.36516314
X-RAY DIFFRACTIONf_chiral_restr0.0893648
X-RAY DIFFRACTIONf_plane_restr0.0162794
X-RAY DIFFRACTIONf_dihedral_angle_d15.04451691
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.670.28481650.20356736X-RAY DIFFRACTION100
1.67-1.690.21051350.18566744X-RAY DIFFRACTION100
1.69-1.710.15341270.16366776X-RAY DIFFRACTION100
1.71-1.730.13631250.14566722X-RAY DIFFRACTION100
1.73-1.750.16831670.14156806X-RAY DIFFRACTION100
1.75-1.780.15171430.1296664X-RAY DIFFRACTION100
1.78-1.80.14971500.12986762X-RAY DIFFRACTION100
1.8-1.830.15361210.1226823X-RAY DIFFRACTION100
1.83-1.860.1621450.12216679X-RAY DIFFRACTION100
1.86-1.890.13431120.11896763X-RAY DIFFRACTION100
1.89-1.920.14781250.12116821X-RAY DIFFRACTION100
1.92-1.960.11021220.116726X-RAY DIFFRACTION100
1.96-1.990.14531260.11346765X-RAY DIFFRACTION100
1.99-2.030.13111380.10226776X-RAY DIFFRACTION100
2.03-2.080.13341200.10116772X-RAY DIFFRACTION100
2.08-2.130.11631320.10046723X-RAY DIFFRACTION100
2.13-2.180.1351440.10226740X-RAY DIFFRACTION99.99
2.18-2.240.12631410.10386755X-RAY DIFFRACTION100
2.24-2.310.11471620.10726723X-RAY DIFFRACTION100
2.31-2.380.12021500.09936756X-RAY DIFFRACTION100
2.38-2.460.12991410.10726754X-RAY DIFFRACTION100
2.46-2.560.15771440.10466736X-RAY DIFFRACTION100
2.56-2.680.15261400.10756759X-RAY DIFFRACTION100
2.68-2.820.10821580.10426701X-RAY DIFFRACTION100
2.82-30.11921180.10966773X-RAY DIFFRACTION100
3-3.230.10871390.10676752X-RAY DIFFRACTION100
3.23-3.550.13321260.11336772X-RAY DIFFRACTION100
3.55-4.070.11851440.10346765X-RAY DIFFRACTION99.99
4.07-5.120.13291550.11656726X-RAY DIFFRACTION100
5.12-34.590.20031150.19146782X-RAY DIFFRACTION99.84
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)
12.145494130750.1642931007550.1115768696821.38441744910.004616942782641.36559258492-0.0861738312009-0.0149923039390.158103230478-0.01884484195120.0269026860262-0.09838654157-0.2082661964960.2635978455760.07708736886220.19151640751-0.06125374447260.0008646237348340.1495378392370.004016941034450.150388294665-57.388529362140.6908633295-1.52933910018
20.702559044765-0.08479538802410.07428186241990.5293115035720.1703945422560.988039084842-0.1178398416230.07551470161820.193941047012-0.1550224678030.0556682350224-0.0839260461368-0.2940214064710.2310976058430.03168755841140.227756934221-0.0856973869462-0.008850730077480.1648686986650.02493430320190.201287329569-57.756238090642.1557863333-4.69652973516
31.114273771090.733816024573-0.2483046342332.69208503625-0.4414556806571.19993713228-0.03328670412210.167461772622-0.0747487059531-0.3868095720360.00318132211034-0.1913634377640.0920879408840.05465699204790.03483646622410.2278221978390.008232926117940.04558719295350.127274893261-0.01483383406140.169658203903-64.405128498910.0462430024-11.8672344771
40.8181324543740.3490143470910.156811334830.933200449544-0.02152190905080.582137437346-0.044714101836-0.04749763895330.0632260042728-0.00236048767485-0.007051471613070.0990512764685-0.062828056009-0.09054155548650.04484520164520.1577564725640.00249380307895-0.00571353536790.135466758445-0.01282096062960.151157469043-79.849655879527.52309550113.06171493724
52.723749753440.6752774575410.8353047860223.147450680260.3950548585182.44802860590.0261694328472-0.0836712306579-0.1108751328010.149122013761-0.00974227397442-0.01466106621170.1230876456070.00901933677355-0.001829263227460.1739468670270.01040232894740.0187862115910.106433496465-0.0005407435849450.158968440229-69.911948422711.47069139762.13173327732
61.496441935990.0595461087653-0.2384852084610.560615568802-0.07944933567160.935097343491-0.05924116704730.1738052890550.104571309871-0.1867502437670.04739575809360.0559180258887-0.032316085097-0.1426149152690.007602014575370.216810567772-0.0323904983079-0.02349693756520.1593540489670.01439101405350.15310280457-81.673779056428.3694373429-15.8980707679
71.662746385520.230134964104-0.3041140955740.741467647552-0.06037940134820.647938867175-0.08843598340590.175512477249-0.0149909620635-0.1485789289010.03844450199520.0304045319531-0.000105453570885-0.09230069630060.05336172140230.211120778968-0.0273460484275-0.01071383508460.1716974471420.004598482188080.148007520417-80.446914261824.5816575342-14.6801443892
80.6275531811820.2329423801890.2810709689931.898632300770.3657415849992.43792112125-0.1233834385340.509359116458-0.0342583745776-0.440344375170.1289324987750.2047957381940.011764665421-0.3389666130260.02413618144670.253239990668-0.0702789826576-0.07190511570990.357764718495-0.006374197903410.186609134098-98.437768208120.6044341306-20.9600488514
94.296618394021.31980420440.2367310675162.999815047250.691577431253.209178913-0.2567593437010.74993859423-0.780701997559-0.6806986367140.3020980376940.08584944261190.449781017437-0.131941824136-0.06717412908260.501897648522-0.136575299352-0.08053069604380.478774756546-0.03655421008010.324016399504-94.186087857517.3988256812-29.2177990999
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A

IDRefine TLS-IDSelection detailsLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 21 through 65 )A21 - 651 - 45
22chain 'A' and (resid 66 through 155 )A66 - 15546 - 135
33chain 'A' and (resid 156 through 202 )A156 - 202136 - 182
44chain 'A' and (resid 203 through 303 )A203 - 303183 - 283
55chain 'A' and (resid 304 through 335 )A304 - 335284 - 315
66chain 'A' and (resid 336 through 410 )A336 - 410316 - 390
77chain 'A' and (resid 411 through 467)A - B411 - 467391
88chain 'A' and (resid 468 through 493)A - D468 - 493448
99chain 'A' and (resid 494 through 536 )A494 - 536474 - 516

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