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- PDB-7kjh: Plasmodium falciparum protein Pf12p bound to nanobody B9 -

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Basic information

Entry
Database: PDB / ID: 7kjh
TitlePlasmodium falciparum protein Pf12p bound to nanobody B9
Components
  • Nanobody B9
  • Surface protein P12p
KeywordsUNKNOWN FUNCTION / Plasmodium falciparum / 6-cysteine protein / s48/45 domain / nanobody
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 / CITRATE ANION / Surface protein P12p
Function and homology information
Biological speciesVicugna pacos (alpaca)
Plasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsDietrich, M.H. / Tham, W.H.
Funding support Australia, United Kingdom, 2items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)GNT1154937 Australia
Wellcome Trust208693/Z/17/Z United Kingdom
CitationJournal: Biochem.J. / Year: 2021
Title: Nanobody generation and structural characterization of Plasmodium falciparum 6-cysteine protein Pf12p.
Authors: Dietrich, M.H. / Chan, L.J. / Adair, A. / Keremane, S. / Pymm, P. / Lo, A.W. / Cao, Y.C. / Tham, W.H.
History
DepositionOct 26, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 3, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 24, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nanobody B9
C: Surface protein P12p
D: Surface protein P12p
B: Nanobody B9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,76110
Polymers102,5624
Non-polymers1,1996
Water10,683593
1
A: Nanobody B9
C: Surface protein P12p
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,8805
Polymers51,2812
Non-polymers5993
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2470 Å2
ΔGint2 kcal/mol
Surface area17490 Å2
MethodPISA
2
D: Surface protein P12p
B: Nanobody B9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,8805
Polymers51,2812
Non-polymers5993
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3200 Å2
ΔGint1 kcal/mol
Surface area17900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.986, 107.044, 113.999
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 1 through 16 or resid 18...
21(chain B and (resid 1 through 4 or (resid 5...
12(chain C and (resid 24 through 57 or resid 59...
22(chain D and (resid 24 through 31 or (resid 32...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111GLNGLNGLYGLY(chain A and (resid 1 through 16 or resid 18...AA1 - 161 - 16
121LEULEUALAALA(chain A and (resid 1 through 16 or resid 18...AA18 - 7518 - 75
131LYSLYSLYSLYS(chain A and (resid 1 through 16 or resid 18...AA7676
141GLNGLNSERSER(chain A and (resid 1 through 16 or resid 18...AA1 - 1201 - 120
151GLNGLNSERSER(chain A and (resid 1 through 16 or resid 18...AA1 - 1201 - 120
161GLNGLNSERSER(chain A and (resid 1 through 16 or resid 18...AA1 - 1201 - 120
171GLNGLNSERSER(chain A and (resid 1 through 16 or resid 18...AA1 - 1201 - 120
181GLNGLNSERSER(chain A and (resid 1 through 16 or resid 18...AA1 - 1201 - 120
211GLNGLNLEULEU(chain B and (resid 1 through 4 or (resid 5...BD1 - 41 - 4
221GLNGLNGLNGLN(chain B and (resid 1 through 4 or (resid 5...BD55
231GLNGLNHOHHOH(chain B and (resid 1 through 4 or (resid 5...BD - N1 - 4011
241GLNGLNHOHHOH(chain B and (resid 1 through 4 or (resid 5...BD - N1 - 4011
251GLNGLNHOHHOH(chain B and (resid 1 through 4 or (resid 5...BD - N1 - 4011
261GLNGLNHOHHOH(chain B and (resid 1 through 4 or (resid 5...BD - N1 - 4011
112ASNASNASNASN(chain C and (resid 24 through 57 or resid 59...CB24 - 574 - 37
122VALVALPROPRO(chain C and (resid 24 through 57 or resid 59...CB59 - 7739 - 57
132ARGARGLYSLYS(chain C and (resid 24 through 57 or resid 59...CB79 - 8059 - 60
142ASNASNGLYGLY(chain C and (resid 24 through 57 or resid 59...CB82 - 10162 - 81
152SERSERSERSER(chain C and (resid 24 through 57 or resid 59...CB23 - 3413 - 321
162SERSERSERSER(chain C and (resid 24 through 57 or resid 59...CB23 - 3413 - 321
172SERSERSERSER(chain C and (resid 24 through 57 or resid 59...CB23 - 3413 - 321
182SERSERSERSER(chain C and (resid 24 through 57 or resid 59...CB23 - 3413 - 321
192SERSERSERSER(chain C and (resid 24 through 57 or resid 59...CB23 - 3413 - 321
1102SERSERSERSER(chain C and (resid 24 through 57 or resid 59...CB23 - 3413 - 321
1112SERSERSERSER(chain C and (resid 24 through 57 or resid 59...CB23 - 3413 - 321
1122SERSERSERSER(chain C and (resid 24 through 57 or resid 59...CB23 - 3413 - 321
212ASNASNSERSER(chain D and (resid 24 through 31 or (resid 32...DC24 - 314 - 11
222GLUGLUGLUGLU(chain D and (resid 24 through 31 or (resid 32...DC3212
232ASNASNSERSER(chain D and (resid 24 through 31 or (resid 32...DC24 - 3414 - 321
242ASNASNSERSER(chain D and (resid 24 through 31 or (resid 32...DC24 - 3414 - 321
252ASNASNSERSER(chain D and (resid 24 through 31 or (resid 32...DC24 - 3414 - 321
262ASNASNSERSER(chain D and (resid 24 through 31 or (resid 32...DC24 - 3414 - 321

NCS ensembles :
ID
1
2

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Components

#1: Antibody Nanobody B9


Mass: 14033.533 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vicugna pacos (alpaca) / Production host: Escherichia coli (E. coli)
#2: Protein Surface protein P12p /


Mass: 37247.488 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: isolate 3D7 / Gene: PFS12P, PF12P, PFF0620c / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: C6KSX1
#3: Chemical
ChemComp-FLC / CITRATE ANION / Citric acid


Mass: 189.100 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H5O7
#4: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 593 / 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: 2.53 Å3/Da / Density % sol: 51.34 %
Crystal growTemperature: 281 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 20% PEG3000, 0.1 M trisodium citrate-citric acid pH 5.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.953725 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 30, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953725 Å / Relative weight: 1
ReflectionResolution: 2→47.338 Å / Num. obs: 70873 / % possible obs: 100 % / Redundancy: 13.813 % / Biso Wilson estimate: 34.603 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.195 / Rrim(I) all: 0.203 / Χ2: 0.785 / Net I/σ(I): 10.73 / Num. measured all: 978968
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2-2.1214.1261.4341.615962611311113000.7021.48799.9
2.12-2.2714.0040.9462.6914898710639106390.8390.982100
2.27-2.4513.4220.6763.84133359993799360.910.702100
2.45-2.6813.9670.4615.88128291918591850.960.479100
2.68-314.1930.2959.26117872830583050.9840.306100
3-3.4613.410.16415.6698950737973790.9940.171100
3.46-4.2313.8540.09526.4887279630063000.9980.099100
4.23-5.9613.8380.07233.6868514495149510.9990.075100
5.96-47.33812.540.0733.2236090288628780.9990.07399.7

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Processing

Software
NameVersionClassification
PHENIX1.15_3459refinement
XDSdata scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2YMO, 6WAQ

2ymo

6waq


Resolution: 2→47.338 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 21.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2169 2126 3 %
Rwork0.1803 68716 -
obs0.1814 70842 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 123.55 Å2 / Biso mean: 35.9642 Å2 / Biso min: 15.44 Å2
Refinement stepCycle: final / Resolution: 2→47.338 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6019 0 128 593 6740
Biso mean--66.46 41.16 -
Num. residues----767
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086301
X-RAY DIFFRACTIONf_angle_d0.9328551
X-RAY DIFFRACTIONf_dihedral_angle_d6.635037
X-RAY DIFFRACTIONf_chiral_restr0.061928
X-RAY DIFFRACTIONf_plane_restr0.0051110
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A714X-RAY DIFFRACTION11.352TORSIONAL
12B714X-RAY DIFFRACTION11.352TORSIONAL
21C1472X-RAY DIFFRACTION11.352TORSIONAL
22D1472X-RAY DIFFRACTION11.352TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2-2.04650.30651390.27374492
2.0465-2.09770.31761400.24994548
2.0977-2.15440.26781400.23544527
2.1544-2.21780.27231400.21984515
2.2178-2.28940.2271410.20634552
2.2894-2.37120.26781410.21434556
2.3712-2.46620.24121390.20634499
2.4662-2.57840.2571420.2084607
2.5784-2.71430.23681410.19224538
2.7143-2.88440.2221410.18594559
2.8844-3.1070.21911410.18584575
3.107-3.41960.22081430.17064617
3.4196-3.91430.18731430.15664627
3.9143-4.93070.16921440.13384665
4.9307-47.3380.20011510.17764839

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