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- PDB-7o62: Crystal structure of a 2`-deoxyribosyltransferase from the psychr... -

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Basic information

Entry
Database: PDB / ID: 7o62
TitleCrystal structure of a 2`-deoxyribosyltransferase from the psychrophilic bacterium Desulfotalea psychrophila.
ComponentsChains: A,B,C,D
KeywordsTRANSFERASE / Psychrophilic enzyme / tetramer / thermal stability
Function / homology
Function and homology information


deoxyribonucleoside monophosphate catabolic process / 5-hydroxymethyl-dUMP N-hydrolase activity
Similarity search - Function
: / Nucleoside 2-deoxyribosyltransferase / Nucleoside 2-deoxyribosyltransferase / Rossmann fold - #450 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Nucleoside 2-deoxyribosyltransferase
Similarity search - Component
Biological speciesDesulfotalea psychrophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsMancheno, J.M.
CitationJournal: Int.J.Biol.Macromol. / Year: 2021
Title: Biochemical and structural studies of two tetrameric nucleoside 2'-deoxyribosyltransferases from psychrophilic and mesophilic bacteria: Insights into cold-adaptation.
Authors: Fernandez-Lucas, J. / Acebron, I. / Wu, R.Y. / Alfaro, Y. / Acosta, J. / Kaminski, P.A. / Arroyo, M. / Joachimiak, A. / Nocek, B.P. / De la Mata, I. / Mancheno, J.M.
History
DepositionApr 9, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 20, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Chains: A,B,C,D
B: Chains: A,B,C,D
C: Chains: A,B,C,D
D: Chains: A,B,C,D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,4458
Polymers67,0774
Non-polymers3684
Water23413
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9920 Å2
ΔGint-85 kcal/mol
Surface area22350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.165, 86.366, 140.930
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein
Chains: A,B,C,D


Mass: 16769.176 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Desulfotalea psychrophila (strain LSv54 / DSM 12343) (bacteria)
Strain: LSv54 / DSM 12343 / Gene: DP0734 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6AQB0
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 13 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.4 Å3/Da / Density % sol: 48.82 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 20 % PEG 3350, 0.1 M sodium malonate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 12M / Detector: PIXEL / Date: Feb 9, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.4→46.98 Å / Num. obs: 27119 / % possible obs: 99.9 % / Redundancy: 13.2 % / Biso Wilson estimate: 55.36 Å2 / Rpim(I) all: 0.029 / Rrim(I) all: 0.104 / Net I/σ(I): 14.8
Reflection shellResolution: 2.4→2.53 Å / Num. unique obs: 3856 / Rpim(I) all: 0.204 / Rrim(I) all: 0.737 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PHENIX1.19.2_4158refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7M5H

7m5h


Resolution: 2.4→44.15 Å / SU ML: 0.3485 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.9593
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2769 1342 5.03 %
Rwork0.2205 25324 -
obs0.2234 26666 98.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 74.22 Å2
Refinement stepCycle: LAST / Resolution: 2.4→44.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4133 0 24 13 4170
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00844214
X-RAY DIFFRACTIONf_angle_d1.00315674
X-RAY DIFFRACTIONf_chiral_restr0.0536633
X-RAY DIFFRACTIONf_plane_restr0.0079743
X-RAY DIFFRACTIONf_dihedral_angle_d7.5045566
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.490.40691100.36252300X-RAY DIFFRACTION90.98
2.49-2.590.36731430.29622379X-RAY DIFFRACTION95.49
2.59-2.70.33971300.27392523X-RAY DIFFRACTION98.73
2.7-2.850.29231340.27212520X-RAY DIFFRACTION99.96
2.85-3.020.3171250.29312551X-RAY DIFFRACTION99.89
3.02-3.260.31691390.26362555X-RAY DIFFRACTION99.96
3.26-3.580.27771260.22372563X-RAY DIFFRACTION100
3.58-4.10.26321580.19832565X-RAY DIFFRACTION100
4.1-5.170.22321350.17742624X-RAY DIFFRACTION100
5.17-44.150.27281420.19772744X-RAY DIFFRACTION99.97
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)
17.79765646271-0.246924573866-5.351835410772.740589447810.188307296313.71129192197-0.292269113734-0.3957168470150.0492604280460.3650442263340.2227895162870.07072181383740.003731464221610.535893207092-0.2559537203180.459060421721-0.0872546999132-0.01386974255810.36777211625-0.01149771618250.574141784828-13.15326778763.57003442348-24.3005190441
22.39510010348-2.736561475680.9367046602466.286489886911.611369315185.22373552186-0.3933573159590.1409394122431.21506046591-1.030704503560.899891607108-1.47276503116-1.483797581311.75147946738-0.7124415017441.01388351756-0.356632020004-0.03466595131760.602619020326-0.01414495178480.935436326911-9.8800592382911.9220961811-29.6707205738
38.55047759053-0.862990615807-1.799568985821.955273216882.525765986517.687021813990.18528846464-1.08171965753-1.10278013890.940663932965-0.236381955818-1.61353971319-0.1966439143190.674953898303-0.2005161596560.617559979379-0.142424505538-0.09602812273190.5274365631850.02426643185560.584320802943-12.90598523897.4511117579-19.3557799997
44.653949887261.19523954397-2.910114636171.71418288648-2.65700797914.440854812140.867010329011-0.4629650111130.91944954306-0.4077676581210.381784427333-1.45729002433-1.184720542471.000879648880.03029303053540.423004799504-0.377278607421-0.0867037993981.22881024246-0.1331226583560.9482341690681.19141263483-0.0808646866089-29.7253549547
53.746638066030.179899250496-3.648923631354.294115754561.765332819518.2099874556-0.110573973113-0.4613397236030.1234345900530.3688695737410.337975617612-0.459429726299-0.0807443353711.244440277720.02870839676310.4659115267070.124339010331-0.06897099703720.7334009242710.02093649257420.700042332099-5.18119140602-8.57716546624-27.6976289265
61.396181937231.16483629284-0.7900999274733.546349828181.391635510317.16125949284-0.0857975392707-0.1638918996110.2804237921820.2430802629930.033227730883-0.0203930533249-0.389556285650.3274885809040.11173446730.414268855722-0.0193550385099-0.009249793198880.3173780236530.02627370220850.509992643803-18.7624537889-1.85195997615-30.1679634071
70.4472574356550.324601583138-1.326616907193.788778266070.810333415754.749694860230.2984922910690.5821954787130.688660736323-0.3324770494170.07444510460071.9830035719-0.830397720167-0.7362109419530.09815433949250.8215926253530.124710697883-0.1297875160980.5248124381930.03020194093130.781421504862-25.27918467494.5056806768-42.4987160603
84.22022559988-1.418864809532.029244019656.03760887863.179783520316.84644685002-0.706268759693-0.4947993978140.4134845568970.1208447343820.1111901902740.280862714937-0.852796248679-0.5226527189350.4677737065110.4882398242230.1030132337960.02719163341310.4177980315950.006807931345820.461616827892-26.38374183685.98074741498-25.4778691148
94.11063464293-0.209287772534-0.9307364475449.98596013293-0.6385031594330.8975391936820.2386126904530.452843235132-0.0552119165946-0.358341584267-0.1835967651250.326658963660.515005161209-0.348634282266-0.1385704915610.436828726159-0.0960001462636-0.01225999081960.440359907849-0.04007984257420.49619228303-22.8181791955-20.3814055109-47.5620192582
105.31120779245-4.29116799289-2.186482843558.008898180910.1271963560696.4649270523-0.1952707576840.3698248584750.3277529920790.436881490261-0.09348002737810.3909195581850.576436874152-0.1665226655910.3007657253880.434704218563-0.123959993309-0.007724944371790.4909416442870.1099713193230.641656306669-25.49069412-24.5406235865-44.6989285265
118.528392438584.384865255376.025491589094.586153683033.749109457524.43851777999-1.089344172982.38617128488-0.292705331595-3.6843998780.547780815846-0.656753927051-1.027567441210.3220877461820.5403041418771.40814842706-0.200664053960.4585987636760.7789441654660.1693704079330.991224139203-35.7164870204-10.0554032059-45.3873966083
128.93813365336-4.607223245032.323886520097.51276001948-1.007963654888.26111060255-0.356448731982-0.2941934622310.311542659662-0.4783098149190.02977538567741.58531212545-0.615925636448-0.6944657206940.2401589223370.434584829162-0.0711632225279-0.01388249968520.475873466516-0.00253297205970.848169944796-31.9249780817-11.3069110288-35.2630313486
135.610775261970.18514961278-4.168611655956.245497937821.556878823548.143950008530.04567340372070.322640307351-0.1860576648970.476625137451-0.03522480583560.119939369110.2727666419830.0250511416970.002041272781910.28532002112-0.0345777609348-0.0006353203822150.3086455356750.03607074385450.438633792642-17.3427923872-14.5375884348-37.9317410196
141.41566058668-0.1554168583933.42118480630.203625809802-0.9029126740659.607452174190.000770138369699-0.6746973917870.1475546979460.242321314708-0.543463882975-0.457638731146-1.525654793331.599378419740.178238446210.427065529087-0.2289173403180.1050145834441.08218926562-0.01692717200210.862347643574-6.49706034383-7.85795747723-46.4306880226
151.67923027058-0.832740536690.6073293009597.016493671950.5664108421436.939904922-0.1225542466280.01507379126-1.19252477552-0.110596364260.569691301655-0.7492174381230.3861159279220.974696673553-0.43615122430.3918820420950.132776859308-0.03145720859970.6448436940340.01088315536680.933983661422-9.55100050574-22.8156314461-40.5365113072
163.92061634876-1.526696872143.797751674181.25368831763-2.165048498258.276402959730.2714104394720.302601536913-0.206858623362-0.461249637806-0.193859509917-0.2441591612310.2486533309862.6641479920.5479413977180.726114186471-0.01114759989150.07095477398150.3944363881840.05156032057960.475558965724-16.9355081825-1.47696214027-77.6805088211
179.410388759671.299406480840.7251629569023.516787173080.7189221794082.713586880990.2409719992430.588377559269-0.582833842629-0.827363817402-0.083883542842-0.5180450594890.7315398529460.824256380252-0.3155593774940.5258896207410.02838052463780.07657715437520.4797420617570.0425963599220.691274596827-14.1823497467-9.31338142734-67.3915609917
183.42524888287-0.4777221153721.645576985062.71210487751.490781084782.509160348440.2309645484680.5496877241990.245130832787-0.442409471873-0.0722861369415-0.658041826363-1.262305201150.730102335573-0.04053999981520.780860212115-0.1918078146330.107279169790.4687038859120.07498956363730.525364947574-11.1292534613.45391013506-66.1862650342
195.329119331710.516723664366-0.06687255159414.38309709696-1.026822183829.049608535770.05290565194160.574071518032-0.0472913788635-0.0192691710490.4561662028980.299763913455-1.81193149688-1.60429833573-0.1800597630310.5488117036260.1352578258560.04391698930290.6455570633040.04074889407490.60371416153-27.16407885612.724471731-64.5593453633
202.329751888942.12646062456-0.9683454696977.73071555-4.164352534722.24109959289-0.191643012388-0.2058645802980.245290985310.405214013566-0.143357673583-0.572134897903-1.35594945270.753360971306-0.1019022731041.59585562265-0.369939028182-0.07154312156570.6452315485930.01430829238970.903834844066-10.458716908420.4958857388-51.9130464155
216.67276759783-2.287449870214.110972543722.3054889983-0.8458315890932.75102345590.0658256068954-0.005004251987591.890552954320.486556151475-0.205103185425-0.201509871596-1.729493437821.560685314630.3553745731221.8883189915-0.5921866711270.1329678163770.932545825539-0.1393955463840.908778478012-8.3648855370123.5595027881-46.154259093
223.359945294320.847530216005-1.963265124284.71063718545-0.07523113685261.95389473618-0.3068022494060.7020391907062.482912183460.6224670638390.4399224520221.38607607592-2.456524324050.9374834268790.01512766714531.93061678299-0.2510221757910.1159396040250.805364312771-0.03659456149911.15443432565-20.170245104922.0485362573-51.4796769124
234.739294114241.93966451473.727313113795.327353035653.400899880223.76094962869-1.12527775039-0.4365251455570.778666085506-1.62955526186-0.4298092170741.12784864074-1.08345880424-1.184590349061.272748879141.633389607020.0696789481302-0.0002440597299560.892274695427-0.07242185236480.846601467792-21.363881917119.7988661933-61.0343867371
242.279284147081.65775175195-1.435131869731.41912628435-1.10734195440.8955607852220.175437841019-0.08869681680090.735065002261-0.7020725386410.0578699649173-0.417261111556-1.756447074871.639787488210.08451259862861.43821691269-0.5809909049030.1595888236240.5967802610020.1277787046030.677822502805-8.1493919450314.1763615158-57.7484835547
257.78827123465-0.03029716664342.700737538143.096329445181.519199618278.215403814530.108167779025-0.375514518074-0.391266282889-0.677258375206-0.327517271978-1.21219564110.2959454163921.618973857560.1444853817381.00631376403-0.3506898789960.09354560811470.835166254937-0.004133047079670.796825724608-3.322060966032.10665992538-48.9839033617
264.300118048381.887309068241.766848781266.29502308273.111691794992.31427670548-0.7860595469210.5491954378740.656086311856-1.121704869340.306804535446-0.781367780197-0.0493438962960.6457730787590.4040784862720.768798700782-0.438342195170.06158322126250.9935616732270.05289164570681.020929213152.9469590514315.3653330498-54.4288992459
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 10 through 23 )AA10 - 231 - 14
22chain 'A' and (resid 24 through 37 )AA24 - 3715 - 28
33chain 'A' and (resid 38 through 45 )AA38 - 4529 - 36
44chain 'A' and (resid 46 through 62 )AA46 - 6237 - 44
55chain 'A' and (resid 63 through 80 )AA63 - 8045 - 62
66chain 'A' and (resid 81 through 114 )AA81 - 11463 - 96
77chain 'A' and (resid 115 through 127 )AA115 - 12797 - 109
88chain 'A' and (resid 128 through 153 )AA128 - 153110 - 135
99chain 'B' and (resid 10 through 37 )BB10 - 371 - 28
1010chain 'B' and (resid 38 through 48 )BB38 - 4829 - 39
1111chain 'B' and (resid 49 through 62 )BB49 - 6240 - 47
1212chain 'B' and (resid 63 through 80 )BB63 - 8048 - 65
1313chain 'B' and (resid 81 through 114 )BB81 - 11466 - 99
1414chain 'B' and (resid 115 through 127 )BB115 - 127100 - 112
1515chain 'B' and (resid 128 through 152 )BB128 - 152113 - 137
1616chain 'C' and (resid 10 through 18 )CC10 - 181 - 9
1717chain 'C' and (resid 19 through 62 )CC19 - 6210 - 42
1818chain 'C' and (resid 63 through 114 )CC63 - 11443 - 94
1919chain 'C' and (resid 115 through 153 )CC115 - 15395 - 133
2020chain 'D' and (resid 12 through 23 )DD12 - 231 - 12
2121chain 'D' and (resid 24 through 45 )DD24 - 4513 - 34
2222chain 'D' and (resid 46 through 64 )DD46 - 6435 - 39
2323chain 'D' and (resid 65 through 79 )DD65 - 7940 - 54
2424chain 'D' and (resid 80 through 114 )DD80 - 11455 - 89
2525chain 'D' and (resid 115 through 127 )DD115 - 12790 - 102
2626chain 'D' and (resid 128 through 151 )DD128 - 151103 - 126

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Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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