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- PDB-7u9e: Pfs230 D1 domain in complex with 230AL-26 -

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Basic information

Entry
Database: PDB / ID: 7u9e
TitlePfs230 D1 domain in complex with 230AL-26
Components
  • 230AL-26
  • Gametocyte surface protein P230
  • LMIV230-01
KeywordsCELL INVASION / antibody / Plasmodium falciparum / Pfs230 / transmission blocking
Function / homology6-Cysteine (6-Cys) domain / 6-Cysteine (6-Cys) domain superfamily / Sexual stage antigen s48/45 domain / 6-Cysteine (6-Cys) domain profile. / Sexual stage antigen s48/45 domain / cell surface / plasma membrane / Gametocyte surface protein P230
Function and homology information
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.39 Å
AuthorsTang, W.K. / Tolia, N.H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
Citation
Journal: Immunity / Year: 2023
Title: A human antibody epitope map of Pfs230D1 derived from analysis of individuals vaccinated with a malaria transmission-blocking vaccine.
Authors: Tang, W.K. / Coelho, C.H. / Miura, K. / Nguemwo Tentokam, B.C. / Salinas, N.D. / Narum, D.L. / Healy, S.A. / Sagara, I. / Long, C.A. / Duffy, P.E. / Tolia, N.H.
#1: Journal: Acta Crystallogr., Sect. D: Biol. Crystallogr. / Year: 2019
Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix
Authors: Tang, W.K. / Tolia, N.H.
History
DepositionMar 10, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 15, 2023Provider: repository / Type: Initial release
Revision 1.1Mar 1, 2023Group: 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.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 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

Downloads & links

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Assembly

Deposited unit
A: Gametocyte surface protein P230
B: LMIV230-01
H: 230AL-26


Theoretical massNumber of molelcules
Total (without water)75,2953
Polymers75,2953
Non-polymers00
Water1,09961
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)106.590, 150.940, 103.520
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number21
Space group name H-MC222
Space group name HallC22
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z
#8: -x+1/2,-y+1/2,z

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Components

#1: Protein Gametocyte surface protein P230


Mass: 21468.346 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: isolate 3D7 / Gene: PFS230, PF230, S230, PF3D7_0209000 / Production host: Komagataella pastoris (fungus) / References: UniProt: P68874
#2: Antibody LMIV230-01


Mass: 27470.537 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Antibody 230AL-26


Mass: 26355.865 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 61 / Source method: isolated from a natural source / Formula: H2O

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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: 2.76 Å3/Da / Density % sol: 55.51 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 0.16 M MES, pH 6.5, 1.6 M ammonium sulfate, 10 % dioxane

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 29, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.39→19.81 Å / Num. obs: 31739 / % possible obs: 94.8 % / Redundancy: 3.27 % / Biso Wilson estimate: 56.64 Å2 / CC1/2: 0.99 / Net I/σ(I): 9.76
Reflection shellResolution: 2.39→2.47 Å / Num. unique obs: 6618 / CC1/2: 0.67

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Processing

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

7jum


Resolution: 2.39→19.81 Å / SU ML: 0.353 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 31.1282
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2686 1587 5 %
Rwork0.2246 30150 -
obs0.2267 31737 95.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 64.81 Å2
Refinement stepCycle: LAST / Resolution: 2.39→19.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4857 0 0 61 4918
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00244958
X-RAY DIFFRACTIONf_angle_d0.55946721
X-RAY DIFFRACTIONf_chiral_restr0.0461747
X-RAY DIFFRACTIONf_plane_restr0.0037858
X-RAY DIFFRACTIONf_dihedral_angle_d14.09521810
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.39-2.470.35461340.35222544X-RAY DIFFRACTION88.97
2.47-2.550.38521470.30592794X-RAY DIFFRACTION98.3
2.55-2.660.36381470.30622782X-RAY DIFFRACTION97.73
2.66-2.780.33111430.31642723X-RAY DIFFRACTION95.25
2.78-2.920.31691470.29082789X-RAY DIFFRACTION98.03
2.92-3.110.32921470.27912802X-RAY DIFFRACTION97.33
3.11-3.340.37111450.28342755X-RAY DIFFRACTION96.09
3.34-3.680.29741450.23832738X-RAY DIFFRACTION94.93
3.68-4.210.21931390.20762643X-RAY DIFFRACTION91
4.21-5.280.20891450.16212766X-RAY DIFFRACTION94.98
5.28-19.810.22141480.17982814X-RAY DIFFRACTION92.77
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)
16.701146100364.095519204713.302012267262.741141078411.582812394162.444325433490.5751991087690.420833559771-1.78133384587-1.03107826816-0.39890746056-0.4599544642151.00222557590.393969712327-0.04138059349810.8865645747430.00876494782392-0.03935127627260.854264336337-0.1631845142360.9342111571362.86551610872-5.223357673189.60828309851
21.66492474197-0.52532490905-0.9401865254822.286498353840.8165096611513.27126237592-0.0390205555138-0.158919062360.06374584324640.3210065847530.102631925119-0.1862173148830.07151750746010.101104368376-0.06454678580560.455857325711-0.0611721348465-0.07358767377290.4755706934310.03786356413620.43746843710316.2585630003-3.4171734235825.344513894
32.71923530992.24951771865-1.603440328716.60800580846-2.876233391015.633520867660.108722147602-0.03653711939130.03831083384840.712406365641-0.313416849748-0.71267265252-0.4808492206620.7301666086660.2187357043130.404459191243-0.0296168239889-0.05467572563370.52444235224-0.05447783821960.68570409584631.58844015119.72827528329.97220410845
43.334989981522.02898810009-1.861790354087.00784792334-3.22535866976.816779410870.0596992372068-0.0605460923830.9554037609920.3889121058010.8000681391881.1079191877-1.03975867959-0.371997008922-0.4012517274020.3859066267640.009208102848940.02272538653920.3764404065540.03198061021530.47324997290821.315066162926.15852965767.43139428513
53.224978120951.56375093206-1.446881313777.61627271234-3.565535776257.40957065126-0.03204301127020.2869164614330.0917103667288-0.9758673359550.06348773584620.1475657209410.387503348688-0.212382225123-0.1548652301610.480092307186-0.00242931816270.007219852080770.45428164461-0.005769848541360.46432406561820.759294971814.20210562332.77318382997
62.946130634881.63464538503-3.168099086233.23057104205-0.4519481817124.050996090620.168894492966-0.2081884299050.101314064249-0.06981185150860.0243364482871-0.468809014879-0.2984457794770.32746990011-0.26707446130.464134020792-0.0252257883039-0.02266271802270.4971392495170.03647804646430.59384910048926.354300515219.73942560768.22550787048
74.16605377832-0.804630491627-1.328655010432.323125399270.4520237365522.745123207840.3671026347150.2593486244070.4480129695030.00595707901112-0.0167699554845-0.0467065179565-0.330383503282-0.147268042144-0.2987302220680.586737535724-0.02069135740840.001785023739730.4442749541080.0945568122270.48886301566214.285730593132.18956644577.50239573503
82.89359004831-1.34927984697-0.8373967214892.374656749671.466746656512.687646579250.0976133434771-0.06177840643310.259030174505-0.01055318567210.024951051733-0.118588803247-0.285769913065-0.125599210914-0.1705865497290.52901694746-0.0510450130950.02236898621280.4678362926740.03161197420280.5488106497639.8312618710829.449264547821.2619443621
92.93550320561-1.36396145682-0.9389907461773.956801460191.067948662453.458068105110.3337916212420.1087590750580.649898265281-0.625169754557-0.364105196866-0.08627744843-0.454299516893-0.105858861084-0.1950038260310.555117868122-0.03504120304460.02133941474870.5448734975530.02403150020650.55976719346311.611491456530.667893247813.4566989247
103.50682574941-0.3605909131110.6716154103164.19699103238-0.713430642922.941174232880.0302969981326-0.1609188487630.0987283180491-0.001462230614230.03861103824190.180248275292-0.0126008624674-0.152599852921-0.01191909790880.467585452901-0.0665812976810.02073289855850.4472559042920.02693379962020.341888813913.30004508564-28.046193982339.591156506
114.4446676542-1.717919349441.152867624367.11844585673-0.2623290062932.62197147416-0.01416387089570.538535354725-0.0413509079851-0.2234206113380.08465525452120.03134364520590.02475821911410.0589362418241-0.07272126098810.598398666127-0.0652242957638-0.007272212374790.5593594766990.0358691696160.4919259679270.628736650609-30.965015700733.1572874912
123.55135896525-0.5085246297630.5231695818625.0956975734-0.946715049292.391981733580.08279075383530.359420898067-0.760057574931-0.232433691695-0.1448231482850.2233781904450.328705993629-0.0967155286467-0.1021070736740.626949922258-0.01466754713430.04379914500070.5585320042320.02642511673270.641524011930.649311071951-36.909460654938.7237353826
132.412876234560.280953450121-0.0187628825622.64617632883-0.3956761500662.561743893610.00213119027486-0.0588504708821-0.3062876263720.1365934841510.0791539787928-0.02045552214670.213900207594-0.164464947285-0.05076664845520.599798086782-0.00866943068655-0.03253425205570.577125309066-0.002645052263170.55018952477411.1420979694-29.942856772543.4665543222
143.06629228213-0.0266098374073-0.02216445754692.92738653488-0.8650628708013.236316715740.0377109999879-0.341690916171-0.05286252792810.377879161791-0.046197585849-0.477344998757-0.136735311290.283741987020.02271400905940.604489498671-0.0543599379184-0.06168364588190.6186422296650.01553420721940.67042476856624.6636627417-25.435344159444.6102377118
153.70545409450.0792231521088-0.2751052175722.43594942954-0.9697139746413.016369966270.278796208104-0.7643184066380.5654039289930.2730973297110.0436417297576-0.610251191113-0.2693160537950.391308348962-0.04322898931210.684401682703-0.0988036244708-0.06426649561320.6952975892490.0348693168840.76520617260926.0343530885-17.368066955543.4677557251
162.7028504467-0.3593076012960.2905838139162.631606029-0.9287698881043.584882944580.171725488928-0.375889370333-0.2059163196450.4069989638480.153762702007-0.654755082357-0.44468071390.696808500448-0.01980280590320.575112059438-0.0386212782544-0.03711857463190.6702967513670.03437724542030.64926755032122.250152031-27.614963010745.0507452283
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 553 through 562 )AA553 - 5621 - 10
22chain 'A' and (resid 563 through 732 )AA563 - 73211 - 180
33chain 'B' and (resid 1 through 32 )BB1 - 321 - 32
44chain 'B' and (resid 33 through 45 )BB33 - 4533 - 45
55chain 'B' and (resid 46 through 67 )BB46 - 6746 - 67
66chain 'B' and (resid 68 through 111 )BB68 - 11168 - 111
77chain 'B' and (resid 112 through 156 )BB112 - 156112 - 132
88chain 'B' and (resid 157 through 233 )BB157 - 233133 - 209
99chain 'B' and (resid 234 through 251 )BB234 - 251210 - 227
1010chain 'H' and (resid 1 through 60 )HC1 - 601 - 60
1111chain 'H' and (resid 61 through 76 )HC61 - 7661 - 76
1212chain 'H' and (resid 77 through 91 )HC77 - 9177 - 91
1313chain 'H' and (resid 92 through 145 )HC92 - 14592 - 124
1414chain 'H' and (resid 146 through 186 )HC146 - 186125 - 165
1515chain 'H' and (resid 187 through 213 )HC187 - 213166 - 192
1616chain 'H' and (resid 214 through 247 )HC214 - 247193 - 226

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