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- PDB-8cd8: Ulilysin - C269A with AEBSF complex -

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Open data


ID or keywords:

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Basic information

Entry
Database: PDB / ID: 8cd8
TitleUlilysin - C269A with AEBSF complex
Components
  • GLY-SER-SER
  • Ulilysin
KeywordsHYDROLASE / Inhibitor / complex / protease / serine protease / metalloprotease / metzincin
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases / metallopeptidase activity / proteolysis / metal ion binding
Similarity search - Function
Peptidase M43, pregnancy-associated plasma-A / Pregnancy-associated plasma protein-A / Metallopeptidase, catalytic domain superfamily / Neutral zinc metallopeptidases, zinc-binding region signature.
Similarity search - Domain/homology
4-(2-AMINOETHYL)BENZENESULFONYL FLUORIDE / Ulilysin
Similarity search - Component
Biological speciesMethanosarcina acetivorans C2A (archaea)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsRodriguez-Banqueri, A. / Eckhard, U. / Gomis-Ruth, F.X.
Funding support Spain, 1items
OrganizationGrant numberCountry
Ministerio de Ciencia e Innovacion (MCIN) Spain
Citation
Journal: Dalton Trans / Year: 2023
Title: Structural insights into latency of the metallopeptidase ulilysin (lysargiNase) and its unexpected inhibition by a sulfonyl-fluoride inhibitor of serine peptidases.
Authors: Rodriguez-Banqueri, A. / Moliner-Culubret, M. / Mendes, S.R. / Guevara, T. / Eckhard, U. / Gomis-Ruth, F.X.
#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
DepositionJan 30, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 22, 2023Provider: repository / Type: Initial release
Revision 1.1Mar 29, 2023Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ulilysin
B: GLY-SER-SER
C: Ulilysin
D: GLY-SER-SER
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,24815
Polymers81,3264
Non-polymers92211
Water12,394688
1
A: Ulilysin
B: GLY-SER-SER
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,1047
Polymers40,6632
Non-polymers4415
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Ulilysin
D: GLY-SER-SER
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,1448
Polymers40,6632
Non-polymers4816
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.130, 124.660, 86.900
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 61 through 150 or resid 152 through 999))
d_2ens_1(chain "B" and (resid 61 through 150 or resid 152 through 999))
d_1ens_2chain "C"
d_2ens_2chain "D"

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1ARGTHRA1 - 90
d_12ens_1ASPALAA94 - 264
d_13ens_1CACAB
d_14ens_1CACAC
d_21ens_1ARGTHRG1 - 90
d_22ens_1ASPALAG94 - 264
d_23ens_1CACAH
d_24ens_1CACAI
d_11ens_2GLYSERF1 - 3
d_21ens_2GLYSERL1 - 3

NCS ensembles :
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixVector
1given(-0.999998852252, 0.00150011895311, -0.000212458106001), (-0.00149772943777, -0.999940201183, -0.0108328604284), (-0.000228695980503, -0.0108325297902, 0.999941300275)24.9735291646, 62.2673536227, 0.37315368688
2given(-0.999976297157, -0.00688083527802, -0.000243373326141), (0.00688317488978, -0.999910483148, -0.0114737785851), (-0.000164402359667, -0.0114751818051, 0.999934144419)25.2730068093, 62.0512493582, 0.399276154775

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Components

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Protein / Protein/peptide , 2 types, 4 molecules ACBD

#1: Protein Ulilysin


Mass: 40413.957 Da / Num. of mol.: 2 / Mutation: C269A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanosarcina acetivorans C2A (archaea)
Gene: MA_3214 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q8TL28, Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases
#2: Protein/peptide GLY-SER-SER


Mass: 249.223 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)

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Non-polymers , 5 types, 699 molecules

#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-AES / 4-(2-AMINOETHYL)BENZENESULFONYL FLUORIDE / AEBSF / AEBSF


Mass: 203.234 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10FNO2S / Feature type: SUBJECT OF INVESTIGATION / Comment: protease inhibitor*YM
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 688 / 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

Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 100 mM MES pH 6.5, 200 mM calcium chloride, 18% polyethylene glycol 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97866 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 4, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97866 Å / Relative weight: 1
ReflectionResolution: 1.65→86.9 Å / Num. obs: 66338 / % possible obs: 99.9 % / Redundancy: 6 % / Biso Wilson estimate: 53.7 Å2 / Rrim(I) all: 0.125 / Net I/σ(I): 11.8
Reflection shellResolution: 1.65→1.65 Å / Num. unique obs: 66008 / Rrim(I) all: 0.125 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PHENIX1.18.2_3874refinement
XDSdata reduction
XSCALEdata scaling
PHENIX1.18.2_3874phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.65→62.33 Å / SU ML: 0.2274 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 41.7301
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2429 752 1.14 %
Rwork0.2073 65256 -
obs0.2077 66008 99.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.07 Å2
Refinement stepCycle: LAST / Resolution: 1.65→62.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4114 0 45 688 4847
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064286
X-RAY DIFFRACTIONf_angle_d0.90135844
X-RAY DIFFRACTIONf_chiral_restr0.0598626
X-RAY DIFFRACTIONf_plane_restr0.006776
X-RAY DIFFRACTIONf_dihedral_angle_d24.32361546
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS0.181657867527
ens_2d_2BX-RAY DIFFRACTIONTorsion NCS0.0257292901405
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.780.42931470.358712862X-RAY DIFFRACTION99.24
1.78-1.960.29771530.284912885X-RAY DIFFRACTION99.55
1.96-2.240.26311440.220112987X-RAY DIFFRACTION99.48
2.24-2.820.23741450.209813101X-RAY DIFFRACTION99.77
2.82-62.330.20781630.169813421X-RAY DIFFRACTION99.1
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)
10.290486224703-0.01640157363380.1026111076520.0978681392208-0.02069463726940.522010913643-0.09863796295470.205174950869-0.1650403679320.0610626224485-0.009032632823410.0401938454249-0.3135329144150.0521591755037-0.04151238862520.2159098423230.00319834139674-0.07335923016260.217596525120.01131013204720.26092839952921.57748.887-12.064
20.0724468064698-0.0217581568543-0.05380676007720.01447138456430.004923337691870.0504703292089-0.1550229032610.0640839896390.08449373328320.177978964692-0.0157912282786-0.0666481319185-0.5178432285050.0444923436763-0.001406784806850.388525072357-0.0196054553248-0.09569761735930.189315803530.03601017064210.31723589587920.65356.197-17.679
30.737155605284-0.2086531236320.4829618928250.1119242267490.004203400301830.575049289876-0.0980442752096-0.05140593713680.09252174830910.007694867268210.0333264940184-0.140176871663-0.1656654842130.0121688401328-6.91772750329E-60.2769679378220.0222952366817-0.02064097062570.1769416776250.01075005774340.2280132341417.27147.248-14.546
40.0258657991942-0.0113933868633-0.01653761350780.01290272481170.01104196888410.03214094413270.1909052862290.493358667793-0.248486678863-0.00948811754744-0.113266903871-0.085281847840.235829731150.09275467996934.42472976227E-50.332789932806-0.0002991078771950.006795950219490.308457030107-0.08059546438930.29117018149724.1933.7-24.515
50.134661800146-0.1360864712830.1807658740940.153407683804-0.259991211780.449307218915-0.05666460858060.09542260237920.02195904481570.02153822799350.0094299092598-0.0355709077214-0.119508863294-0.0344831108141-7.25350206415E-60.29906571473-0.03728776846980.00239189865090.2018919316540.03086536482080.22513704687116.54544.382-22.693
60.4040427730250.355359200306-0.08051891539820.562359564821-0.02398436952670.02675728821220.003265518043070.3411598824390.0464959402673-0.0576187916704-0.0306598786790.2487510681310.129881943611-0.2987510830030.04208419795660.414706126257-0.0601404880928-0.05123224281970.355117402392-0.004007328743850.1785179729954.83240.048-37.864
70.0568293169731-0.07675886525290.0127785879770.123754896984-0.07528540611030.1145860879830.0559593374980.09821252087910.0915963330264-0.163719360638-0.0191025828127-0.103290692423-0.075940246823-0.03798455934711.98008376552E-50.28230916484-0.00806532317479-0.002280032775440.2424774301830.05731911227580.22551283383514.28649.806-37.936
80.08058376793040.00137979021414-0.03164814053880.0596523760749-0.01460403896770.0898105903247-0.00202445815329-0.08655583029430.139849009365-0.06171928616940.1350904052310.0627052853396-0.154153612815-0.21857172350.0008519741730330.2225163588850.0985805332919-0.0007138261109480.3290039935880.007357194721770.2706000951.7450.838-18.022
90.1086681331170.0418049239216-0.002246054515530.0160463643356-0.0007966670486820.001059374894880.0763208455690.00862096807753-0.0584463879463-0.0109512730160.0586082545464-0.06120808902940.0504389522104-0.0114982489895-9.90637176027E-50.8177620014710.09271297983940.03952142054420.4778066479330.1249309436390.4817749477613.53438.172-25.724
100.143622452660.145289457698-0.02616806053190.164782091803-0.0792538922850.273591572024-0.08896382451860.1421677730590.08531892415220.0658352538909-0.01000804277240.02727586703270.273391669748-0.115947684214-0.0004245191564920.285749622984-0.001124366033090.01569410940850.236416346017-0.03280676101740.2474621843873.46913.468-12.224
110.219103168409-0.11443406414-0.04774389357560.144834502123-0.148921675440.367489706051-0.1722346555030.130782180702-0.0626761076269-0.0445643251963-0.003928153485640.0096697742060.519214827836-0.201912949371-0.03105193255980.347413192495-0.1194256772550.0731389913110.235093330959-0.05781146096530.2829430855374.3796.227-17.891
120.726741899494-0.104109573063-0.4865583491350.0647831163494-0.06581260218680.635266283089-0.135588169541-0.00136833362218-0.08099705673-0.01682379386410.02977234740770.1106849122960.180030240831-0.07870372152240.003356264174280.220403394486-0.03680246237710.009697877599030.19162992692-0.01764064044680.2318262267057.77915.17-14.696
130.030316264032-0.01473567657350.01311809284640.0113466245935-0.005867983838730.03063279215050.1146215405320.4913174901020.0866571754388-0.0689530621192-0.1144239532920.0725003730995-0.157341234244-0.142834682730.0001077682027360.320690970365-0.007715580233590.03279588542050.3578824702210.07562568503490.2564873692070.85828.769-24.541
140.172230398896-0.0102885893419-0.1577380099410.09790824549970.07996817189640.310200599102-0.04565451984230.220979745554-0.0671751469131-0.0848292358881-0.0157799853032-0.1216439196170.105242128488-0.120986639215-0.158116130626-0.00675099291165-0.137587981010.0103861614030.302625741632-0.1029929501250.2544075606574.60218.19-20.002
150.115834079358-0.153288284014-0.07301661882970.2172084416810.1371659065520.129230629786-0.01063736997330.132874317908-0.0377016000068-0.0837876198615-0.006800496263580.001936936109-0.07461206291890.0926705135782-0.00023570202730.200613208106-0.07513479113320.04679414272140.283298387025-0.02254338658660.20192911322216.96320.224-32.128
160.354118688092-0.204695450862-0.2477325848120.3398916096670.08412695765390.1881173004060.01179284340360.114473446058-0.159077714143-0.128080580944-0.0651634818326-0.02335253687640.161647108803-0.0180485635776.61337603633E-50.273161363693-0.03541640286850.03708308479140.284758007653-0.04865132220540.22188494165214.81612.461-31.706
170.1455774429830.06392162205930.004035230647960.0280283004070.001662236369760.001394723153590.05343256345520.01425968987110.0651392826326-0.02763028661420.03692406893670.0433029271935-0.0387155145433-0.002594409326160.0001165223770.74438000004-0.003669917148170.02719652308510.495166752124-0.03685720912780.42787832275411.48424.271-25.763
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 61:83 )A61 - 83
2X-RAY DIFFRACTION2( CHAIN A AND RESID 84:99 )A84 - 99
3X-RAY DIFFRACTION3( CHAIN A AND RESID 100:176 )A100 - 176
4X-RAY DIFFRACTION4( CHAIN A AND RESID 177:188 )A177 - 188
5X-RAY DIFFRACTION5( CHAIN A AND RESID 189:243 )A189 - 243
6X-RAY DIFFRACTION6( CHAIN A AND RESID 244:263 )A244 - 263
7X-RAY DIFFRACTION7( CHAIN A AND RESID 264:302 )A264 - 302
8X-RAY DIFFRACTION8( CHAIN A AND RESID 303:322 )A303 - 322
9X-RAY DIFFRACTION9( CHAIN B AND RESID 401:403 )B401 - 403
10X-RAY DIFFRACTION10( CHAIN C AND RESID 61:83 )C61 - 83
11X-RAY DIFFRACTION11( CHAIN C AND RESID 84:99 )C84 - 99
12X-RAY DIFFRACTION12( CHAIN C AND RESID 100:176 )C100 - 176
13X-RAY DIFFRACTION13( CHAIN C AND RESID 177:188 )C177 - 188
14X-RAY DIFFRACTION14( CHAIN C AND RESID 189:223 )C189 - 223
15X-RAY DIFFRACTION15( CHAIN C AND RESID 224:263 )C224 - 263
16X-RAY DIFFRACTION16( CHAIN C AND RESID 264:322 )C264 - 322
17X-RAY DIFFRACTION17( CHAIN D AND RESID 401:403 )D401 - 403

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  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

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