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- PDB-7anu: Crystal structure of Pyrococcus abyssi Pbp11 -

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Basic information

Entry
Database: PDB / ID: 7anu
TitleCrystal structure of Pyrococcus abyssi Pbp11
ComponentsPbp11 protein
KeywordsPROTEIN BINDING / OB-fold / proteasome adaptor / tRNA binding
Function / homologyUncharacterised conserved protein UCP019072 / Elongation factor Tu-type domain / Elongation factor Tu domain 4 / Translation protein, beta-barrel domain superfamily / IMIDAZOLE / NICKEL (II) ION / THIOCYANATE ION / Elongation factor Tu-type domain-containing protein
Function and homology information
Biological speciesPyrococcus abyssi (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.64 Å
AuthorsHogrel, G. / Girard, E. / Franzetti, B.
Funding support France, 1items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-18-CE11-0018-01 France
CitationJournal: Mol.Microbiol. / Year: 2022
Title: Characterization of a small tRNA-binding protein that interacts with the archaeal proteasome complex.
Authors: Hogrel, G. / Marino-Puertas, L. / Laurent, S. / Ibrahim, Z. / Coves, J. / Girard, E. / Gabel, F. / Fenel, D. / Daugeron, M.C. / Clouet-d'Orval, B. / Basta, T. / Flament, D. / Franzetti, B.
History
DepositionOct 12, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 3, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 22, 2022Group: 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jul 20, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Jan 31, 2024Group: 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

Downloads & links

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Assembly

Deposited unit
A: Pbp11 protein
B: Pbp11 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,47212
Polymers20,7332
Non-polymers73910
Water1,838102
1
A: Pbp11 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,8067
Polymers10,3661
Non-polymers4396
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Pbp11 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,6675
Polymers10,3661
Non-polymers3004
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.581, 54.156, 62.551
Angle α, β, γ (deg.)90.000, 95.058, 90.000
Int Tables number5
Space group name H-MI121
Space group name HallC2y(x,y,-x+z)
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z+1/2
#4: -x+1/2,y+1/2,-z+1/2

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Pbp11 protein


Mass: 10366.458 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: The crystal structure corresponds to the truncated form of the protein (Delta-Nter 1-20). Presence of the TAG with linker at position 103
Source: (gene. exp.) Pyrococcus abyssi (strain GE5 / Orsay) (archaea)
Strain: GE5 / Orsay / Gene: PAB1698 / Plasmid: pET30a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9UZY3

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Non-polymers , 5 types, 112 molecules

#2: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H5N2
#5: Chemical ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: CNS
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 102 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.21 Å3/Da / Density % sol: 44.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 200 mM potassium thioycyanate, 25% PEG 3350.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.976 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 12, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.64→42.42 Å / Num. obs: 21583 / % possible obs: 99.2 % / Redundancy: 5.6 % / Biso Wilson estimate: 21.98 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.076 / Rpim(I) all: 0.038 / Net I/σ(I): 10.4
Reflection shellResolution: 1.64→1.73 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.792 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 3058 / CC1/2: 0.848 / Rpim(I) all: 0.404 / % possible all: 97.3

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1XE1

1xe1


Resolution: 1.64→42.42 Å / SU ML: 0.2471 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 27.7162
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2222 1075 5 %
Rwork0.1935 20444 -
obs0.1949 21519 98.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.33 Å2
Refinement stepCycle: LAST / Resolution: 1.64→42.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1344 0 54 102 1500
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01161417
X-RAY DIFFRACTIONf_angle_d1.21571873
X-RAY DIFFRACTIONf_chiral_restr0.0825221
X-RAY DIFFRACTIONf_plane_restr0.0076226
X-RAY DIFFRACTIONf_dihedral_angle_d13.8703542
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.64-1.720.42511270.34552441X-RAY DIFFRACTION95.64
1.72-1.810.31931340.26132554X-RAY DIFFRACTION99.08
1.81-1.920.25961340.21922551X-RAY DIFFRACTION99.15
1.92-2.070.25481370.20092578X-RAY DIFFRACTION99.67
2.07-2.280.21341340.18312547X-RAY DIFFRACTION99.37
2.28-2.610.21791360.18922573X-RAY DIFFRACTION99.56
2.61-3.290.21091360.1992587X-RAY DIFFRACTION99.42
3.29-42.420.19321370.16982613X-RAY DIFFRACTION98.6
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)
17.28552667006-3.8027166813-1.075567646165.982605603793.046796557082.239147490380.127152593360.391475825765-0.542107933913-0.0471780243969-0.4303541466480.6524598098610.0153228925783-0.1271033109360.3856119365090.223607814111-0.01081751566610.005486280559740.1690599997930.05393261663530.1650473126219.9298412903714.667329878912.8895578859
24.2579480755-5.06038798458-1.826139644776.028743503561.841047337665.673035658280.08421547564030.251715400671-0.168427096745-0.27362501711-0.1797556189950.295369808243-0.126539591643-0.0496883302340.1939432631340.2067758664070.00406077593133-0.02692702556870.218741261476-0.0149194284970.18434408882611.404647808310.991197821513.5381746372
33.214498888611.719756117260.4021583577455.522646922394.944752726394.900247852960.0233982135718-0.209677848241-1.052469377720.5655443620150.0741604424712-0.5702775332530.4084155813370.243083168409-7.73921276355E-50.2335681230120.0018520237597-0.0252141141970.2366038721260.003156928209710.22757089622320.75365542316.7786067430619.4365967918
47.26282668845-0.1607588902480.5652307665066.36876721232-3.22273707196.212485413150.3911592706541.072450028870.899717160854-0.923621369068-0.603167446622-0.4814059771190.4825143188860.9141488528150.106150149070.3308236679850.07426105212590.03315228700390.40531790070.1317313694520.41305956338223.001330589117.01526531069.37211540453
59.616216531216.50326328817-5.295113727248.98669880963-3.022783806663.74266986833-0.00912470700202-0.1211861950920.7825900712730.222786831320.02616259365920.3729995855460.008086549755240.0374951388339-0.2046507935880.2158710186360.0443737718509-0.009831257530750.250437156166-0.03495479071460.30122570842617.069221961615.254192561718.906649094
65.03314970821-3.66657653426-2.518226341747.682439728673.56408549559.09405025009-0.159022803635-0.0477229212261-0.5362682677230.3154479639560.06010537096840.86218750485-0.0557541826871-0.5549395991770.1290683039180.2156122483230.03062128870090.08535458087130.2282867150480.07732532853710.31412006940310.59914703024.3472288546421.1587780915
75.82224802755.39659920473-0.1581376747035.456757694770.9425608256958.785266068940.23975436022-0.8309549729790.0983757932020.753506146098-0.2751360489460.5992205557820.00139538963443-0.1705844170690.1233396551250.1994973763680.03886325432670.003633425515450.2439321231910.0002631356755280.29553784760911.499364740412.335200184517.5723670662
89.496106428814.757785818772.101505912458.414435096545.586277775128.98213823485-0.007355079194850.4269557867330.751317235201-0.354023682791-0.00605611576505-0.0949306763023-0.4809407474480.269169264580.02112349494880.2804309103490.0564298099148-0.002127151678360.2511628592080.0678866241170.40248036480614.567873594819.332936492810.4567300937
92.21493315359-1.162543491962.28960394826.18331272642-1.785606027152.549172407980.2825659510660.910256363583-0.139536680014-0.484731087485-0.133812015761-0.4780353617320.1353967083811.00693870993-0.06878225582210.253383526740.01684818499770.02659127665370.3749628008320.03367366868960.15494585123421.278294440311.17069215639.42600842952
104.48396756397-2.18455809575.598082065275.68176025686-2.312254215317.02567683610.447011256907-1.29775155609-0.633573380721.12397818783-0.245012252971-0.4553842381750.6921270935-0.455840563238-0.4118074216460.394648289543-0.0928755395067-0.07409386500070.4821153782660.1115711427040.42254264825630.84058737597.4178032040125.3867983308
112.000007920739.574492766513.06986794447.037106690550.3549846238639.204785322731.01439720390.284407543146-0.0728391018332-0.801207745434-0.132601643377-0.9684974596450.3359451718380.2778143332590.3326995857260.5840499223040.1859785281870.2739726047230.3159506269680.1791465801510.67999226199131.69632065930.44204788444233.6366015029
122.221335016851.843896319680.3323639295142.77294957487-0.1416675578915.621203322650.377690892914-0.9384730766940.183540824160.538540187492-0.443076989430.03109895299540.05947337051640.5964299920840.05351242877640.241265117279-0.05194419543720.006176025436370.296936570725-0.03018895158060.205504919431-10.14181212121.925537469823.0278705269
138.544734974912.489563013950.8632944778685.04492053824.906970648125.549704775570.1391165183390.2051159687940.493818309209-0.886783393107-0.5141170887070.748652676276-1.05429630417-0.5183884102710.2991018292620.2666134350440.0389321360431-0.03962281189630.2167677000550.01846317150070.198460328919-21.55138507811.124316670515.2838121234
143.516434409282.843924665772.29580304325.195103760851.391806659224.60457756608-0.10696408107-0.1550754900370.2830292236470.344521731498-0.00136758943050.319251958736-0.142628570450.3206389585730.2628718971640.180317201765-0.01964429016730.01793351198940.213250704039-0.01526046135580.178064556063-15.457401245719.058211166217.583997902
152.61076242578-1.77258350373-0.5633158975929.990980139498.151376720349.84064442524-0.05217972166890.2087641022620.797417733116-0.377066985897-0.200468921776-0.201230336477-0.4233080646880.0005528677839150.2030582418760.1937349214960.001367022444130.005588605904270.2841272806180.05304909705520.278803313714-5.9325327522323.091927767411.8924686746
161.920460371471.20275933131-1.487207554422.298781903820.5796135169472.631507843160.0563108683917-0.701247766424-0.7587489924010.5811128107880.0166060694705-0.3956209138320.04676937931320.6727550999850.01969837274020.2569324271170.0338713892484-0.02247613734320.3090310393280.1327587109840.377660323811-4.1256200793613.035582080322.1600400572
174.54674958754-4.507343683985.163855434325.3587349701-3.790038198968.262662634290.240123279590.0344008561905-0.744449472566-0.281759316429-0.07683403781490.1516612280150.3662472222650.0367031397708-0.2646546404630.18642274414-0.03190787922270.02953581512230.1900570478880.009860206444710.232203626185-9.6446772811914.618238529312.6647760328
187.646770496194.574119149333.98166103638.336148324375.41376145447.43113878727-0.1830518302930.5822472502110.184546372216-0.4710547788660.008366386981710.9026001416790.1187736044450.059643298110.1123554234510.282167863358-0.00229918096245-0.08824088056670.3000033622390.02463431483420.286389786528-15.916692654125.38520685719.40139213251
192.462247898471.28901581174-0.5654905662184.167939331022.751828896946.66289142120.1066781635520.364168927354-0.157922647073-0.736852678168-0.2771779495090.870770430875-0.118812277107-0.214033107103-0.02665472518720.193513768089-0.0005945912730580.01950589172710.2234899060930.01037817869150.200317707467-15.243577336517.614023184813.6385647417
206.42643313574-0.4175207728011.371194093883.757220826982.284259708973.184554532970.356798012827-0.282936172979-0.5240426918140.1377020206080.00546187212667-0.7557582025160.138716332410.167295714567-0.159533048890.249300735263-0.03167924561330.02134273514710.2011641320650.02864735905240.363877299213-12.336325185710.720698793521.1770348369
219.833212951832.92010314779-8.06146968344.30668353723-1.749034225939.075230326720.0398660855305-0.230367381195-0.127603331127-0.169621076968-0.138754954106-0.108178211002-0.3266610250530.3129686219550.151368753270.214618427975-0.00613353085248-0.06544120218810.2638340465760.001857535803740.338189240449-2.0654686374720.477117264414.97413337
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 21 through 34 )AA21 - 341 - 14
22chain 'A' and (resid 35 through 44 )AA35 - 4415 - 24
33chain 'A' and (resid 45 through 51 )AA45 - 5125 - 31
44chain 'A' and (resid 52 through 57 )AA52 - 5732 - 40
55chain 'A' and (resid 58 through 66 )AA58 - 6641 - 49
66chain 'A' and (resid 67 through 79 )AA67 - 7950 - 62
77chain 'A' and (resid 80 through 85 )AA80 - 8563 - 68
88chain 'A' and (resid 86 through 95 )AA86 - 9569 - 78
99chain 'A' and (resid 96 through 100 )AA96 - 10079 - 83
1010chain 'A' and (resid 101 through 107 )AA101 - 10784 - 90
1111chain 'A' and (resid 108 through 108 )AB1081
1212chain 'B' and (resid 21 through 26 )BI21 - 261 - 6
1313chain 'B' and (resid 27 through 34 )BI27 - 347 - 14
1414chain 'B' and (resid 35 through 44 )BI35 - 4415 - 24
1515chain 'B' and (resid 45 through 51 )BI45 - 5125 - 31
1616chain 'B' and (resid 52 through 57 )BI52 - 5732 - 37
1717chain 'B' and (resid 58 through 66 )BI58 - 6638 - 46
1818chain 'B' and (resid 67 through 79 )BI67 - 7947 - 59
1919chain 'B' and (resid 80 through 85 )BI80 - 8560 - 65
2020chain 'B' and (resid 86 through 95 )BI86 - 9566 - 75
2121chain 'B' and (resid 96 through 106 )BI96 - 10676 - 86

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