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- PDB-9r2r: De novo designed M7 protein fold -

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Basic information

Entry
Database: PDB / ID: 9r2r
TitleDe novo designed M7 protein fold
ComponentsM7r1
KeywordsDE NOVO PROTEIN / dark fold / de novo / unnatural
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.91 Å
AuthorsPacesa, M. / Miao, Y. / Georgeon, S. / Schmidt, J. / Correia, B.E.
Funding support1items
OrganizationGrant numberCountry
Swiss National Science Foundation
Citation
Journal: To Be Published
Title: Reimagine accessibility of protein space with generative model
Authors: Miao, Y. / Pacesa, M. / Georgeon, S. / Schmidt, J. / Lu, T. / Huang, P. / Correia, B.E.
#1: 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
DepositionApr 30, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 14, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: M7r1
C: M7r1
D: M7r1
B: M7r1


Theoretical massNumber of molelcules
Total (without water)69,1394
Polymers69,1394
Non-polymers00
Water1267
1
A: M7r1


Theoretical massNumber of molelcules
Total (without water)17,2851
Polymers17,2851
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: M7r1


Theoretical massNumber of molelcules
Total (without water)17,2851
Polymers17,2851
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
D: M7r1


Theoretical massNumber of molelcules
Total (without water)17,2851
Polymers17,2851
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
B: M7r1


Theoretical massNumber of molelcules
Total (without water)17,2851
Polymers17,2851
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)101.480, 88.580, 65.750
Angle α, β, γ (deg.)90.000, 114.038, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein
M7r1


Mass: 17284.799 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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 % sol: 36.98 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1 M MES 6.5, 0.2 M KSCN, 15% w/v PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.96546 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 17, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96546 Å / Relative weight: 1
ReflectionResolution: 2.91→60.05 Å / Num. obs: 10973 / % possible obs: 93.8 % / Redundancy: 3.3 % / Biso Wilson estimate: 71.85 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.088 / Net I/σ(I): 9.5
Reflection shellResolution: 2.91→2.965 Å / Redundancy: 3.5 % / Rmerge(I) obs: 1.028 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 562 / CC1/2: 0.495 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
autoPROCdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.91→60.05 Å / SU ML: 0.4397 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 35.7093
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3022 512 4.68 %
Rwork0.2482 10429 -
obs0.2508 10941 93.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 97.17 Å2
Refinement stepCycle: LAST / Resolution: 2.91→60.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4450 0 0 7 4457
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00194524
X-RAY DIFFRACTIONf_angle_d0.41746087
X-RAY DIFFRACTIONf_chiral_restr0.0354651
X-RAY DIFFRACTIONf_plane_restr0.0034782
X-RAY DIFFRACTIONf_dihedral_angle_d12.63261750
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.91-3.210.37911200.31082765X-RAY DIFFRACTION99.72
3.21-3.650.35581090.28032383X-RAY DIFFRACTION88.9
3.68-4.620.30821420.2312508X-RAY DIFFRACTION92.53
4.63-60.050.26331410.23272773X-RAY DIFFRACTION98.21
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)
16.241311495390.0485778774694-0.0002140771137595.293741735790.1409209009393.87611193510.3755797790621.516240848020.331356094043-1.137914722560.6746667831161.07529351425-0.191450555288-0.328927843047-0.4976971950270.551309049723-0.0349286004732-0.1906572604330.6194676190460.05799348176740.6115363730088.959402445715.64530454185-1.14537966363
29.01907059282.030426126191.730675762344.301530702653.787803387235.477180215240.4678404798252.43146678934-0.233278391919-0.218374580746-0.3665102648560.198502589654-0.262626786732-0.02109120783791.144004202781.035336970790.0475869295729-0.2427820099331.24816276435-0.1098672284560.52173513887512.8680225174-0.220075462978-10.4943289695
33.388022142121.20201689303-0.7608497491210.7327266422850.9914209968665.47103162714-0.708659758898-0.326558493623-0.889448390657-1.285768789220.2618013551320.2408178248220.957696973791.361970025890.7523465004581.329073039460.292056068770.0223521988150.7053929639130.1202289748931.7120782595132.81947212463.76985995674-6.48731917723
43.46153144562-1.391588662430.2487005414661.897942873540.4532891960241.848695769330.08805034018920.611410532094-0.718886932427-0.800636059693-0.275674351910.2043992789170.3580967796770.3472847467320.03279434131470.4402590860460.0269451674184-0.1228922973310.6675549720680.1000718115480.50485905067119.3956728166-0.5498605068522.021546401
58.450538647511.471357922541.794189898131.536302225280.1331847458785.421947270530.656663719716-1.538039124270.06017573750130.5738697275040.1781955187490.199041073073-0.386541336889-0.8224512676711.680355109280.461813526520.0351697755985-0.1474678249320.367818464546-0.06164990889370.44742023765712.97315009573.8547408995510.1614739393
64.56055015378-4.259172953990.2018140478834.036715986090.14357366575.69570932238-0.0206683520449-0.6569277811781.92190005196-0.3551022841720.238438004311-1.44974259253-0.9816833462911.06899803743-0.2465123445010.716704265061-0.0203354919627-0.1118984804050.666005879866-0.1442329027860.97948929674528.073503181521.402577719531.6736195917
79.98702197106-2.18923365306-4.447138178132.525593916180.02449037367952.427475526691.85897164232-0.1087988947570.4565649611570.9759818921161.30932927306-1.468821985040.5361137493960.3893366229590.9305564975211.56245947174-0.210676319174-0.009925621406561.00986076849-0.173363326070.66101584777924.371405277623.230870699644.1180707999
82.048055091920.4968088098840.9407810760516.097999107713.156569014663.57639540573-0.0830270396372-0.6646622522180.9076891128792.018821060760.490510560384-0.3467693493740.627727754280.3253295795861.250953716031.349543655320.6945654049990.2299045222191.40052309925-0.4400808501771.2745725759313.656141491431.643911826234.0441319686
94.467540554532.82359751903-4.500692891031.94126627661-2.754941247874.583595194081.30079295585-0.6209038795271.166091980.3588430087420.7261772752811.29966278108-0.5772820345840.00401130046481-0.392212349311.712797277350.198640052226-0.06305253435381.75573415983-0.00628947618161.4542342972710.66969595332.6464657318.834110497
105.71916258025-2.374447836972.413780906354.448498184261.083254681645.81048011511-0.101683117752-1.6075682797-0.6031784079150.5316514123520.9871679266740.0298451821083-0.41910267471-0.9870854316374.376821137870.6384312668620.360465819176-0.193205977811.38295577043-0.1619349258040.72786607943914.201924486616.354877361932.7130585655
118.855478918256.43690255241-4.780088692176.55372929975-6.556886774499.406771573040.210904620631-0.9703862590771.909161450351.730989348110.6011421611551.36640210448-1.764715028090.237452865482.572081815040.9561366733770.11123564619-0.1244672921010.709550131113-0.3920189863870.85242451985319.982147100923.897181332331.9007742989
125.67849737912-1.148288531341.706528797524.9991131994-1.660548359475.11686159118-0.0111381053829-0.517253896517-0.8221441405870.4039930847560.1193981927310.2540462456060.470343068673-1.07356771713-0.6603104780210.3162913002260.221025225420.04897285162680.36632646143-0.156327860680.53813800464820.202923777311.87623734825.7203687343
134.89457944252-1.56937105063-2.094494431712.814650960661.917014376837.339340409610.170058765489-1.30976791744-2.043922791730.743769576255-1.358244832210.7625074714860.816544327307-2.13169760670.00660100530760.968535157629-0.168950329061-0.1957041740721.72697994763-0.09836843541551.06880324318-1.528850796989.909602562414.3944701382
142.69757798711.615408230171.427334960625.11494684126-0.2585124144241.316686651620.4425007494090.774570164038-0.205627124965-1.56641772248-1.531758803780.260420418245-0.4238104924270.289382521748-0.0239001707920.9542891252750.4162627452910.02766511184221.329845362780.03598232913090.805042629994-2.5835844152118.227063378715.5563659762
153.389636767463.25125038903-2.569222037635.253125641170.5792332429856.35760253797-0.698521365096-0.4475851055330.4859440747031.216055053520.3837760849861.594134126660.539417004209-0.2856026417032.216256706961.317920969720.7424998964190.2775155196321.3317763053-0.4368063830381.39177816638-5.8633771610520.742090316328.955297199
166.354645216242.29440666574-1.438914675354.55369660272-0.5134935430824.90235109652-0.0883098304111-1.1675636388-0.244310795699-0.312280673575-0.831694245840.136570428443-0.375065826707-1.0031405971-1.311625411560.3657672430340.32340778934-0.0046606310080.756088908404-0.2397392442630.6444380907465.6245949378217.306969881226.1643366666
178.58047425352-0.709453025348-1.235582138516.21259752985-0.1906397421797.57533421961-0.3300533345580.07225328560440.741043302271-1.14285775483-0.3823806891310.0854630324861-0.681134115281-0.4708058234850.1133194667680.532313448470.118736662508-0.2066367985360.523065930214-0.1419389833070.5202803100388.519002198917.334949317714.2008142671
183.91946868321-0.3397434590640.9979298309997.91647982337-0.09414779212095.51895496652-0.070932629535-0.283772622885-0.3355236011141.481091696160.383181056926-1.201382909580.4034451915940.886839910038-0.222456394180.473816725582-0.0391860736282-0.1455717043140.4685046051020.00815645853860.45809984999436.92947218462.6679817572419.7555664352
190.7361481050631.446639926591.589740537474.926335136361.840905155784.35635595918-0.7117232234551.61984306324-1.567084357-1.519764452040.68505493266-1.33610781874-0.3136027179071.1834686197-1.901694463491.158079317140.189925909210.2614299463191.3915133643-0.5847500521240.96314879771738.2309024503-8.1322808828.16984391585
204.32690938198-4.70862814993-4.151747784318.323255205721.3993127316.996590693010.950577211720.006740257599710.463418962363-0.8135204920880.838870411071-0.8811779556711.66370376428-1.548159063581.822358856260.879441344219-0.271776921185-0.4006363666191.06111958450.4810305710151.1847676709619.194547198-16.89946176786.45578536951
211.307518917790.404768824619-0.656471104742.066054745620.6137300078150.669208414172-0.2769269493310.5190606575320.127302668147-1.35835126672-0.4034242281590.1760058169310.237156321811-0.108876835949-0.4979898268580.619806495281-0.106651360389-0.05267979641330.7878391371620.2648067908570.5448448035431.56497811677.712793563124.97210149098
226.665345411822.924624862391.418340509085.33340548871-0.1772576297354.86833318418-0.05608672552520.58070321256-0.0908372529338-0.225912848852-0.0667154503828-0.101317635774-0.2462796604610.07306681164940.1462222171470.2851137984680.0108239361559-0.05341885276730.487818865802-0.1433992067170.2938854840428.8249337964.5717390200613.8682117181
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 32 )AA1 - 321 - 32
22chain 'A' and (resid 33 through 55 )AA33 - 5533 - 50
33chain 'A' and (resid 56 through 73 )AA56 - 7351 - 65
44chain 'A' and (resid 74 through 116 )AA74 - 11666 - 108
55chain 'A' and (resid 117 through 144 )AA117 - 144109 - 136
66chain 'C' and (resid 1 through 42 )CB1 - 421 - 42
77chain 'C' and (resid 43 through 48 )CB43 - 4843 - 48
88chain 'C' and (resid 49 through 65 )CB49 - 6549 - 65
99chain 'C' and (resid 66 through 76 )CB66 - 7666 - 70
1010chain 'C' and (resid 77 through 101 )CB77 - 10171 - 91
1111chain 'C' and (resid 108 through 116 )CB108 - 11692 - 100
1212chain 'C' and (resid 117 through 144 )CB117 - 144101 - 128
1313chain 'D' and (resid 1 through 18 )DC1 - 181 - 18
1414chain 'D' and (resid 19 through 36 )DC19 - 3619 - 36
1515chain 'D' and (resid 37 through 65 )DC37 - 6537 - 60
1616chain 'D' and (resid 66 through 109 )DC66 - 10961 - 89
1717chain 'D' and (resid 110 through 144 )DC110 - 14490 - 124
1818chain 'B' and (resid 4 through 42 )BD4 - 421 - 39
1919chain 'B' and (resid 43 through 66 )BD43 - 6640 - 63
2020chain 'B' and (resid 67 through 75 )BD67 - 7564 - 72
2121chain 'B' and (resid 76 through 92 )BD76 - 9273 - 84
2222chain 'B' and (resid 93 through 144 )BD93 - 14485 - 136

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