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- PDB-7ulb: recombinant Mambalgin-1 -

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Basic information

Entry
Database: PDB / ID: 7ulb
Titlerecombinant Mambalgin-1
ComponentsMambalgin-1
KeywordsBIOSYNTHETIC PROTEIN / recombinant / alpha neurotoxin / refolded
Function / homologyion channel regulator activity / Snake toxin-like superfamily / toxin activity / extracellular region / Mambalgin-1
Function and homology information
Biological speciesDendroaspis polylepis polylepis (black mamba)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.49 Å
AuthorsXu, J. / Lei, X. / Chen, L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM064642 United States
CitationJournal: To Be Published
Title: Structure of recombinant mambalgin at 2.49 Angstroms resolution.
Authors: Xu, J. / Lei, X. / Chen, L.
History
DepositionApr 4, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 3, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: 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

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Assembly

Deposited unit
A: Mambalgin-1
B: Mambalgin-1
C: Mambalgin-1
D: Mambalgin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,3855
Polymers30,1474
Non-polymers2381
Water57632
1
A: Mambalgin-1


Theoretical massNumber of molelcules
Total (without water)7,5371
Polymers7,5371
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Mambalgin-1


Theoretical massNumber of molelcules
Total (without water)7,5371
Polymers7,5371
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Mambalgin-1


Theoretical massNumber of molelcules
Total (without water)7,5371
Polymers7,5371
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Mambalgin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,7752
Polymers7,5371
Non-polymers2381
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)30.984, 80.753, 54.032
Angle α, β, γ (deg.)90.000, 90.470, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 1 through 13 or resid 15...
d_2ens_1(chain "B" and (resid 1 through 13 or resid 15...
d_3ens_1(chain "C" and (resid 1 through 13 or resid 15...
d_4ens_1(chain "D" and (resid 1 through 13 or resid 15...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1LEUHISA4 - 16
d_12ens_1ASPMETA18 - 19
d_13ens_1PHETHRA21 - 47
d_14ens_1ASNASNA49 - 50
d_15ens_1CYSASNA52 - 59
d_21ens_1LEUHISB4 - 16
d_22ens_1ASPMETB18 - 19
d_23ens_1PHETHRB21 - 47
d_24ens_1ASNASNB49 - 50
d_25ens_1CYSASNB52 - 59
d_31ens_1LEUHISD1 - 13
d_32ens_1ASPMETD15 - 16
d_33ens_1PHETHRD18 - 44
d_34ens_1ASNASND46 - 47
d_35ens_1CYSASND49 - 56
d_41ens_1LEUHISE3 - 15
d_42ens_1ASPMETE17 - 18
d_43ens_1PHETHRE20 - 46
d_44ens_1ASNASNE48 - 49
d_45ens_1CYSASNE51 - 58

NCS oper:
IDCodeMatrixVector
1given(0.450527213891, -0.137498336091, -0.882110785058), (-0.309638175743, -0.950802519347, -0.00993827580315), (-0.83734666039, 0.277612637997, -0.470937143957)-48.8777983698, -23.3973745802, -24.0134095311
2given(-0.662740167259, 0.663523586627, 0.347148269032), (0.619937908738, 0.226097368879, 0.751370061352), (0.420062447753, 0.713173492059, -0.561187232759)-26.5047816977, 6.12071482651, -14.1534913632
3given(-0.78573691386, -0.402985446594, 0.469276285392), (-0.435437610496, -0.178482021925, -0.88234814853), (0.439330842945, -0.89763405555, -0.0352351068425)-36.5725578337, -28.6783061942, -23.7095044256

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Components

#1: Protein
Mambalgin-1 / Mamb-1 / Pi-Dp1


Mass: 7536.727 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dendroaspis polylepis polylepis (black mamba)
Production host: Escherichia coli (E. coli) / References: UniProt: P0DKR6
#2: 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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 32 / Source method: isolated from a natural source / Formula: H2O
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: 2.28 Å3/Da / Density % sol: 46 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop
Details: rec-Mambalgin-1(122 mg/ml in 200 mM NH4Ac (pH 7.0)), 1:1 (v/v) with 0.1 M HEPES, pH 7.0, 32% Jeffamine M600, 0.1 M KSCN, 18 degree centigrade

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jul 31, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.439→80.94 Å / Num. obs: 8923 / % possible obs: 94.7 % / Redundancy: 5.8 % / Biso Wilson estimate: 55.19 Å2 / Rrim(I) all: 0.07 / Net I/σ(I): 19.58
Reflection shellResolution: 2.49→2.579 Å / Rmerge(I) obs: 0.04624 / Num. unique obs: 880 / CC1/2: 0.978

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
PHENIXmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5DU1

5du1


Resolution: 2.49→25.42 Å / SU ML: 0.4152 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 31.4832
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2666 901 10.1 %
Rwork0.2174 8016 -
obs0.2225 8917 94.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 72.89 Å2
Refinement stepCycle: LAST / Resolution: 2.49→25.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1845 0 15 32 1892
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00841888
X-RAY DIFFRACTIONf_angle_d1.16512520
X-RAY DIFFRACTIONf_chiral_restr0.0575267
X-RAY DIFFRACTIONf_plane_restr0.0073324
X-RAY DIFFRACTIONf_dihedral_angle_d17.8918725
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS0.732152486933
ens_1d_3AX-RAY DIFFRACTIONTorsion NCS1.03967443867
ens_1d_4AX-RAY DIFFRACTIONTorsion NCS0.907176899059
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.49-2.640.37071460.3321289X-RAY DIFFRACTION93.12
2.64-2.850.40581560.331379X-RAY DIFFRACTION96.42
2.85-3.130.31431500.28841349X-RAY DIFFRACTION96.71
3.13-3.580.31281520.22851347X-RAY DIFFRACTION96.59
3.59-4.510.2121480.18551316X-RAY DIFFRACTION93.01
4.51-25.420.22451490.17411336X-RAY DIFFRACTION93.28
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)
14.836533926784.992157040236.353253685785.291453456986.013046043228.01777284314-0.7672669417650.836773800284-0.0290345411712-2.116804400810.513608633892-0.565278887963-1.102377791911.0415697780.2013542063890.688808090562-0.1006889278610.13475686150.573004630747-0.07839116266150.512013825562-11.473083865-15.6307500045-36.1947467202
26.75656315412-2.08636389222-0.3048524553533.249879652581.478773118466.07194642670.1919938552470.527642534288-0.3611256629890.441912921096-1.61857178791.225833919512.3664046304-2.158180769121.067642932860.762846089999-0.2035764241250.1213068426690.678760129122-0.08097769900690.597484106929-16.139571327-18.6138134469-29.3655396489
32.22647497844-0.624440076422-0.2086903603397.6385455606-5.349368386669.64294550114-0.811598660332-0.4004869510161.043481144280.4079996993020.4840274388120.125040444945-1.31734813587-0.565830941550.9246394179330.484232681446-0.0158592933375-0.0226023050880.465981514461-0.1261104436910.592810917702-8.52821101665-3.40515326566-12.4624066747
46.14775866092-2.26745325173-2.392099044276.889697192914.580030535133.56451739530.1049368801790.00913001769822-0.8927729528340.886197656322-0.6697267532631.432483800940.411793107592-1.885681669080.5737098684530.712477222248-0.07222131669230.1560646141580.735160273735-0.08416945380950.696784661561-17.3867489593-13.5176222236-23.2801812518
52.397966013981.208947863791.182569210743.425544186212.989074758416.087207774340.2342473310810.6675922460180.779743333301-0.962637577415-1.616591203310.467083016524-1.09556833862-1.344137767851.277819234420.7254227895570.222974066014-0.1456589581891.05473946668-0.1268120494960.618590629496-19.437061906-12.3469525193-32.3176455477
62.934321513974.531241438842.184593285319.693633808323.955966418863.533624136690.6880610476-1.34793051057-0.516673945056-0.327492003453-0.360108682497-1.196564734950.0305485778443-0.29926711722-0.04100767712710.4774971173140.199440655382-0.1050562819811.01634547737-0.3246189320890.800886659733-19.6699775672-2.442849594480.471767680006
71.353735405050.1952670030160.5866873133499.143727585656.823561141026.15466346462-0.996913049343-0.2255270561520.679609211105-1.995083246871.05774033289-0.215619943719-1.498344327390.973909156802-0.1926714694230.6673888258190.118227567982-0.1972619163470.974550648786-0.4029961578061.11536371139-21.5799606959-0.222387488187-3.41856302377
84.597060796065.144988565874.199048143695.412214405744.51241157983.821649453240.827105815742-1.848143285671.21436967440.669700690814-1.294945198791.250658202741.180564194520.5362846704230.7808873506040.6603728114870.137564007542-0.14812407520.858854085986-0.2780773492650.713798583577-32.283893226-5.89901636492-1.95234898188
96.43543422321-6.35950448703-0.7616765553247.73623116263.270261596634.68480969636-0.0288388494059-1.190247014410.254484832018-0.108466789751-0.2316622620860.270645196242.123035011790.6679932033930.7096868602330.52974436475-0.02811484779470.008093295188320.4018020175490.0651016331170.669081816899-41.2680273413-17.4795777831-12.1582865576
103.135645771270.8193747298770.2221780355628.620891708473.989384152662.890143154980.0217947916801-1.285423901961.035873673311.745182697910.5441945373030.7902387449680.151176118814-0.252051694979-0.1044724529110.5582224961110.1520061995840.03466865640350.957424875392-0.2891845998330.783043298063-34.2114679309-4.81036670677-2.21601345203
118.050381936773.214643842874.531748193186.08390789273-0.1774295977453.230978527621.79684905503-0.97756350382-0.4412553741081.79914664828-1.48823801833-0.5887705521522.175913235070.233820612723-0.3485495531360.853121508560.384486158786-0.3821624412431.48849786996-0.1820173693060.622486354561-27.2361418526-6.063568810533.75704230619
125.602616921192.439119294983.793382296353.08681946064.3423221186.305892763561.18640180189-1.162137924980.125605786526-3.76571818856-0.908702483279-1.799821140940.88250344018-1.671333007090.8046940234761.399013504650.03006794041-0.0575319996180.7188355256870.4125861676410.698585215447-40.0559873156-31.5244194659-10.2655546836
136.89675227216-0.624679161698-3.822009419576.99364915192-3.388306913694.150648833030.0751521529848-1.51586079664-0.3448337766440.9798880762380.09002144943850.8313069908450.720455418130.277003327647-0.114931256580.9583733636310.147954809164-0.1240256060010.6482956732470.1175793633340.516139275684-42.1979238155-27.5705285505-7.66497826922
141.98523538824-9.90745440998-3.579847705438.364309592982.010188870334.01506462335-5.206240190570.652678884791-1.939036741630.2829535436981.331766991881.19497329969-1.8070154638-2.301556877352.642534309443.00062799047-0.430338441969-0.07618156002331.50532224250.1036591597320.543647418592-44.6372130064-35.0243990706-19.3983414128
154.82557616326-1.46278980438-0.8231283495754.342969340653.346301615365.82084335158-0.623315834679-0.853104828505-0.158149886460.0111183173711.16931522553-1.889845862221.233439404291.6934218646-0.4954938052830.7835511748240.1495921911020.08339645117920.46584427026-0.0283654802850.53377700952-30.0187726605-17.3182622891-14.4874948544
165.318777064615.077224885660.5494562969064.920931103110.2660796053212.20824389538-0.386375340104-0.0988825735748-1.38325233275-1.501871457480.557889162055-1.676728036772.024296433490.692844577236-0.4642334879030.951649910920.159985086687-0.04065273239590.651333294842-0.01144990368160.607672268625-36.0555807094-23.2187373034-14.5850410951
177.214287372812.498880569397.93572225483.352183657972.095287400119.15591578007-0.03626482221610.89721384101-2.43629244182-1.418729460821.93779073367-1.200280471251.669947135211.561384386281.033706912021.653853119910.002332829413980.3249406420820.807195432658-0.2483382319490.928579416518-28.8137741071-27.3290639003-21.5648345194
180.489922611089-0.1058178566860.01382748183092.93672605569-0.5510702568640.663302612229-1.16703301306-1.25026060637-0.877096319336-1.449444418340.684248783874-1.952870995410.4641215052170.5507060022221.038646098062.508981855050.4606843355810.6620820020620.3013585183130.5994770012491.0247726601-32.3088928161-32.0809886823-13.4725681801
192.13471860581-1.33587801364-2.197448284468.823609417843.57715650842.69514180346-0.847051665666-0.3369767794611.326194273890.6517798684010.8542612796921.40404143091-2.04021665280.141268998624-0.05577241916261.18037004992-0.0667811919935-0.2296372913380.461800534429-0.0458251439070.752191451558-38.226875209910.4825354938-13.860785514
208.51217152376-5.68409625294-1.282747111827.954717195730.01512311456510.944718266955-1.34512898883-3.128233518040.7398479945440.7943389966620.944444050324-0.482043672275-1.985925857721.548979376740.1653877504841.396803117790.00886462528715-0.6250777439811.05080031165-0.2297434895521.32389016737-29.761727831413.0128481075-6.63386620379
213.783623566044.632918155925.627713934246.197700727727.197533807748.61943384007-0.319009274730.4598697854510.617977716681-2.46984940435-0.590560858122-1.78533214503-2.699653530141.743994013140.6507800483220.827413923017-0.31407032815-0.01337970495530.8297184979880.02610913251290.579563091994-30.34311148622.93936063872-18.5148761205
228.73478481385-0.2580949510753.137784720143.067785381424.252768426958.63403256380.298981029913-0.0448995959284-0.778549729328-1.492569281341.54812190699-0.2471122464690.09784684157591.96106375118-1.298215195450.5135343970230.02358746945970.06840608440930.632268433117-0.04882642127510.518735000472-34.7690535706-13.3595040285-24.2445035743
235.150701930832.667075861093.702507382128.298529829034.576501984053.56509203075-0.56719577258-0.2123717190472.099164554460.192907507059-0.369544059229-0.158194153242-0.659779119808-0.1910324098090.7127541447090.574777881723-0.0475019608859-0.07656323513370.48335772234-0.1585185859340.642872319608-33.42855250991.03355091828-15.9342388208
249.85367842071-2.1855837051-4.547920654373.87789837075-2.839527614156.35747368665-0.2082786904090.06220521978191.16633093750.397929602191.16802874273-0.567036326834-0.505937597166-0.280601850169-0.7370322236320.72201460377-0.1955624069840.1638711620470.970203243075-0.3057265193721.19109945357-23.81192849842.79093295795-20.0578085428
251.163790788892.730218548661.053386276749.05663028729-1.339589930038.1098551801-0.7607345541330.764290365106-0.632024903853-0.908487018041.16000001733-0.80631133536-2.047411792240.680723599188-0.2689107497991.07904929581-0.380263031789-0.1313122264080.845879169142-0.06747333480410.766607715917-32.191940236110.0059433362-20.4451613104
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid -2 through 11 )AA-2 - 111 - 14
22chain 'A' and (resid 12 through 24 )AA12 - 2415 - 27
33chain 'A' and (resid 25 through 31 )AA25 - 3128 - 34
44chain 'A' and (resid 32 through 46 )AA32 - 4635 - 49
55chain 'A' and (resid 47 through 56 )AA47 - 5650 - 59
66chain 'B' and (resid -2 through 5 )BB-2 - 51 - 8
77chain 'B' and (resid 6 through 17 )BB6 - 179 - 20
88chain 'B' and (resid 18 through 24 )BB18 - 2421 - 27
99chain 'B' and (resid 25 through 31 )BB25 - 3128 - 34
1010chain 'B' and (resid 32 through 46 )BB32 - 4635 - 49
1111chain 'B' and (resid 47 through 57 )BB47 - 5750 - 60
1212chain 'C' and (resid 1 through 5 )CD1 - 51 - 5
1313chain 'C' and (resid 6 through 11 )CD6 - 116 - 11
1414chain 'C' and (resid 12 through 17 )CD12 - 1712 - 17
1515chain 'C' and (resid 18 through 31 )CD18 - 3118 - 31
1616chain 'C' and (resid 32 through 38 )CD32 - 3832 - 38
1717chain 'C' and (resid 39 through 45 )CD39 - 4539 - 45
1818chain 'C' and (resid 46 through 56 )CD46 - 5646 - 56
1919chain 'D' and (resid -1 through 11 )DE-1 - 111 - 13
2020chain 'D' and (resid 12 through 17 )DE12 - 1714 - 19
2121chain 'D' and (resid 18 through 24 )DE18 - 2420 - 26
2222chain 'D' and (resid 25 through 31 )DE25 - 3127 - 33
2323chain 'D' and (resid 32 through 38 )DE32 - 3834 - 40
2424chain 'D' and (resid 39 through 46 )DE39 - 4641 - 48
2525chain 'D' and (resid 47 through 57 )DE47 - 5749 - 59

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