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- PDB-7k3z: P. falciparum Cpn60 D474A mutant bound to ATP -

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Basic information

Entry
Database: PDB / ID: 7k3z
TitleP. falciparum Cpn60 D474A mutant bound to ATP
Components60 kDa chaperonin
KeywordsCHAPERONE / malaria / mitochondrial protein
Function / homology
Function and homology information


apicoplast / ATP-dependent protein folding chaperone / unfolded protein binding / protein folding / protein refolding / ATP binding / metal ion binding
Similarity search - Function
GroEL / GroEL / Chaperonin Cpn60/GroEL / GroEL-like equatorial domain superfamily / TCP-1-like chaperonin intermediate domain superfamily / GroEL-like apical domain superfamily / TCP-1/cpn60 chaperonin family / Chaperonin Cpn60/GroEL/TCP-1 family / 3-Layer(bba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / 60 kDa chaperonin
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.69 Å
AuthorsTolia, N.H. / Shi, D. / Nguyen, B.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)1ZIAAI001253 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)1ZIAAI001237 United States
CitationJournal: Sci Rep / Year: 2021
Title: Crystal structure of P. falciparum Cpn60 bound to ATP reveals an open dynamic conformation before substrate binding.
Authors: Nguyen, B. / Ma, R. / Tang, W.K. / Shi, D. / Tolia, N.H.
History
DepositionSep 14, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 21, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 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: 60 kDa chaperonin
B: 60 kDa chaperonin
C: 60 kDa chaperonin
D: 60 kDa chaperonin
E: 60 kDa chaperonin
F: 60 kDa chaperonin
G: 60 kDa chaperonin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)446,65421
Polymers442,9347
Non-polymers3,72014
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area33040 Å2
ΔGint-201 kcal/mol
Surface area169680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)281.498, 281.498, 298.827
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number182
Space group name H-MP6322
Space group name HallP6c2c
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/2
#3: y,-x+y,z+1/2
#4: -y,x-y,z
#5: -x+y,-x,z
#6: x-y,-y,-z
#7: -x,-x+y,-z
#8: -x,-y,z+1/2
#9: y,x,-z
#10: -y,-x,-z+1/2
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41
51
61
71

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYGLYGLUGLU(chain 'A' and (resid 69 through 275 or resid 277...AA69 - 2745 - 210
12ASPASPILEILE(chain 'A' and (resid 69 through 275 or resid 277...AA277 - 293213 - 229
13ILEILEARGARG(chain 'A' and (resid 69 through 275 or resid 277...AA296 - 343232 - 279
14GLYGLYTHRTHR(chain 'A' and (resid 69 through 275 or resid 277...AA348 - 433284 - 369
15TYRTYRHISHIS(chain 'A' and (resid 69 through 275 or resid 277...AA436 - 630372 - 566
16ATPATPATPATP(chain 'A' and (resid 69 through 275 or resid 277...AI702
27GLYGLYGLUGLU(chain 'B' and (resid 69 through 275 or resid 277...BB69 - 2745 - 210
28ASPASPILEILE(chain 'B' and (resid 69 through 275 or resid 277...BB277 - 293213 - 229
29ILEILEARGARG(chain 'B' and (resid 69 through 275 or resid 277...BB296 - 343232 - 279
210GLYGLYTHRTHR(chain 'B' and (resid 69 through 275 or resid 277...BB348 - 433284 - 369
211TYRTYRHISHIS(chain 'B' and (resid 69 through 275 or resid 277...BB436 - 630372 - 566
212ATPATPATPATP(chain 'B' and (resid 69 through 275 or resid 277...BK702
313GLYGLYGLUGLU(chain 'C' and (resid 69 through 275 or resid 277...CC69 - 2745 - 210
314ASPASPILEILE(chain 'C' and (resid 69 through 275 or resid 277...CC277 - 293213 - 229
315ILEILEARGARG(chain 'C' and (resid 69 through 275 or resid 277...CC296 - 343232 - 279
316GLYGLYTHRTHR(chain 'C' and (resid 69 through 275 or resid 277...CC348 - 433284 - 369
317TYRTYRHISHIS(chain 'C' and (resid 69 through 275 or resid 277...CC436 - 630372 - 566
318ATPATPATPATP(chain 'C' and (resid 69 through 275 or resid 277...CM702
419GLYGLYGLUGLU(chain 'D' and (resid 69 through 294 or resid 296...DD69 - 2745 - 210
420ASPASPILEILE(chain 'D' and (resid 69 through 294 or resid 296...DD277 - 293213 - 229
421ILEILEARGARG(chain 'D' and (resid 69 through 294 or resid 296...DD296 - 343232 - 279
422GLYGLYTHRTHR(chain 'D' and (resid 69 through 294 or resid 296...DD348 - 433284 - 369
423TYRTYRHISHIS(chain 'D' and (resid 69 through 294 or resid 296...DD436 - 630372 - 566
424ATPATPATPATP(chain 'D' and (resid 69 through 294 or resid 296...DO702
525GLYGLYGLUGLU(chain 'E' and (resid 69 through 275 or resid 277...EE69 - 2745 - 210
526ASPASPILEILE(chain 'E' and (resid 69 through 275 or resid 277...EE277 - 293213 - 229
527ILEILEARGARG(chain 'E' and (resid 69 through 275 or resid 277...EE296 - 343232 - 279
528GLYGLYTHRTHR(chain 'E' and (resid 69 through 275 or resid 277...EE348 - 433284 - 369
529TYRTYRHISHIS(chain 'E' and (resid 69 through 275 or resid 277...EE436 - 630372 - 566
530ATPATPATPATP(chain 'E' and (resid 69 through 275 or resid 277...EQ702
631GLYGLYGLUGLU(chain 'F' and (resid 69 through 275 or resid 277...FF69 - 2745 - 210
632ASPASPILEILE(chain 'F' and (resid 69 through 275 or resid 277...FF277 - 293213 - 229
633ILEILEARGARG(chain 'F' and (resid 69 through 275 or resid 277...FF296 - 343232 - 279
634GLYGLYTHRTHR(chain 'F' and (resid 69 through 275 or resid 277...FF348 - 433284 - 369
635TYRTYRHISHIS(chain 'F' and (resid 69 through 275 or resid 277...FF436 - 630372 - 566
636ATPATPATPATP(chain 'F' and (resid 69 through 275 or resid 277...FS702
737GLYGLYGLUGLU(chain 'G' and (resid 69 through 275 or resid 277...GG69 - 2745 - 210
738ASPASPILEILE(chain 'G' and (resid 69 through 275 or resid 277...GG277 - 293213 - 229
739ILEILEARGARG(chain 'G' and (resid 69 through 275 or resid 277...GG296 - 343232 - 279
740GLYGLYTHRTHR(chain 'G' and (resid 69 through 275 or resid 277...GG348 - 433284 - 369
741TYRTYRHISHIS(chain 'G' and (resid 69 through 275 or resid 277...GG436 - 630372 - 566
742ATPATPATPATP(chain 'G' and (resid 69 through 275 or resid 277...GU702

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Components

#1: Protein
60 kDa chaperonin


Mass: 63276.266 Da / Num. of mol.: 7 / Mutation: D474A, N283Q, N125Q, N145Q, N381Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (isolate 3D7) (eukaryote)
Strain: isolate 3D7 / Gene: PF3D7_1232100 / Plasmid: pET28AKS / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): Rosetta / References: UniProt: Q8I0V3
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
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

CrystalDensity Matthews: 3.9 Å3/Da / Density % sol: 68.5 % / Description: hexagonal prism
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.4
Details: 100 mM phosphate citrate buffer pH 4.4, 13% Isopropanol, and 0.21 mM of Lithium Sulfate

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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: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Feb 25, 2020
Details: Si 111. Rosenbaum-Rock double-crystal monochromator: liquid nitrogen cooled; sagitally focusing 2nd crystal, Rosenbaum-Rock vertical focusing mirror
RadiationMonochromator: double crystal - liquid nitrogen cooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.69→63 Å / Num. obs: 75184 / % possible obs: 98.8 % / Observed criterion σ(I): 0 / Redundancy: 9.1 % / Biso Wilson estimate: 117.85 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.133 / Net I/σ(I): 12.93
Reflection shellResolution: 3.69→3.79 Å / Mean I/σ(I) obs: 1.7 / Num. unique obs: 5368 / CC1/2: 0.607 / Rrim(I) all: 1.5 / % possible all: 98.3

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
XDSVersion Jan. 31, 2020data reduction
XDSVersion Jan. 31, 2020data scaling
PHENIX1.14_3260phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4V4O

4v4o


Resolution: 3.69→51.99 Å / SU ML: 0.5109 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.0503 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2765 1684 2.27 %
Rwork0.2268 72393 -
obs0.2279 74077 98.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 163.47 Å2
Refinement stepCycle: LAST / Resolution: 3.69→51.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms30714 0 224 0 30938
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002831259
X-RAY DIFFRACTIONf_angle_d0.803442168
X-RAY DIFFRACTIONf_chiral_restr0.04714984
X-RAY DIFFRACTIONf_plane_restr0.00519287
X-RAY DIFFRACTIONf_dihedral_angle_d5.279619407
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.69-3.80.33371370.27695919X-RAY DIFFRACTION98.44
3.8-3.920.33411390.27625967X-RAY DIFFRACTION99.35
3.92-4.060.32541400.25176002X-RAY DIFFRACTION99.39
4.06-4.230.25971370.22945974X-RAY DIFFRACTION99.3
4.23-4.420.25361390.20435993X-RAY DIFFRACTION99.24
4.42-4.650.30991390.19416013X-RAY DIFFRACTION99.07
4.65-4.940.24461400.1996017X-RAY DIFFRACTION98.97
4.94-5.320.29941410.22146009X-RAY DIFFRACTION98.89
5.32-5.860.30271400.25396056X-RAY DIFFRACTION98.76
5.86-6.70.35291430.27736067X-RAY DIFFRACTION98.67
6.7-8.440.27141420.24646108X-RAY DIFFRACTION98.22
8.44-51.990.23511470.20046268X-RAY DIFFRACTION96.1
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)
14.5167119209-2.90295258877-0.8968881702583.280370141870.4694254108641.75438422379-0.0223399154887-0.02089357827560.527617725829-0.07354974656430.0966657138589-0.845149765704-0.4873160870770.45205141942-0.1152331171090.84965451278-0.292000543831-0.07790054889020.879890297462-0.0733883881320.88769243212691.0603408066-67.2971497216.0822826494
26.533163425472.39489065695-5.664855282878.76682090996-1.549907337727.47544912595-0.0959899665545-0.2948856859960.4459221715780.807298196830.333119940975-0.289614271308-0.811539286471-0.0898329039708-0.2288798310031.024545165440.00118764896956-0.3345608383660.9496953460760.01449346334550.9437115668780.589544097-54.980976420139.8508400831
34.4196777307-0.2836826470450.9759125996189.39859115234-2.535479854774.036083943610.07270746419320.325459636970.10919272844-0.493204957386-0.3968895916890.0721408993698-0.1270158920140.02988846476140.3081881781760.9985160909910.0986020170404-0.1279005979551.10525489568-0.1293575699190.57932026947596.9476185727-65.389428589360.9662961913
46.674940689680.5236212557930.1430288562231.9930784231-0.1645314273151.99782331102-0.0332696426785-0.1820986459580.8485833262680.1655819560410.072912566544-0.00414132122105-0.544836283145-0.17450342133-0.03708344483330.9397431196350.0555436489174-0.04772990494810.721139384074-0.1108126356920.65984482058349.8911539476-57.328283977415.7953381211
53.898767655521.39034667265-0.3570024345394.98103975934-4.148824473424.020936805860.268411611942-1.030645997160.2230113420320.915395172676-0.5780174472280.535732838722-0.0749320407642-0.8776780741090.3485597806921.613277092560.113429312164-0.01701892722521.70061728927-0.3298328613121.1096328534433.7740458214-57.954136082239.5540866092
67.98006803539-1.93075442992-3.140325522237.734262347891.807051812271.94080054966-0.0234363044625-1.376198314890.8225990374451.475194667450.264989991423-0.612262320096-0.08328214614820.967661300524-0.2577580395461.68700834217-0.04215702102580.0008124196806262.27862872064-0.2323687293391.1346900820251.8054190115-52.079084621861.0444423979
72.054981269591.23716246924-0.05364713628716.682377260360.089145558180.903471050524-0.107458321611-0.3579476058460.3828585757820.2194471217660.06528210570380.717925480172-0.0754022839124-0.4435199245360.04848035200290.6895052346750.05408932959490.07091445956571.24031488819-0.04319972003270.71188200660316.8231676978-83.62306296615.4565705086
84.27379541558-0.4003556312873.026886725086.93466853571-4.812139817285.0086741873-0.0356046346639-1.25476982113-0.3665744838940.9834449820820.1051618418320.02392190822-0.30665050373-0.790870036186-0.2336892735631.20332679032-0.1126323653240.2970240978811.73189738079-0.03838766192971.024314937747.49158416666-96.789249464339.1238116196
96.249713390195.464674250764.114776095939.299079119230.1085350813495.497764640051.25160204464-2.912994243232.146873482382.23062891947-1.560567360151.85002555617-1.64420028234-0.1699853449440.3514128583432.83103217344-0.4400905123110.633559729892.44955403993-0.3923308744141.6693237986813.7831885287-78.815535606360.4971051728
100.550855958384-1.82401608373-0.006050159027636.46614788069-0.4476967257541.53902205718-0.0212214086844-0.113800860665-0.165908407704-0.01117344009130.2123096142840.8210525757540.253983293938-0.51399014604-0.1605933807040.72518840011-0.2380857501940.0407484268491.22051410190.1343250740240.89095173523416.7039773655-126.02525334815.1978297257
112.06729475369-2.047999933928.982680797296.91636536865-0.4836945363816.64017609313-0.0940251813271-0.351316939967-0.1972924905750.391074814952-0.115768998103-0.1664008170590.5873062051570.7835358215310.11246875231.14915488579-0.09980130365690.333312758981.727760768210.1993667856411.0834859585720.897051889-141.7136564738.9759229394
123.25839578932-2.227296381670.3375272962738.783236963922.621193444845.30783177847-0.04025108385220.138072981274-0.1569151836130.1357219300450.07615414802410.418804108031-0.03591058193950.3032374547910.01761150696571.30530758259-0.1536532473120.1204660891741.636690938660.2400168570270.86365467461510.5859365901-125.34215687959.9217825095
135.97260684763-3.446658690150.06385579257552.202267090410.02106866429831.889274666440.282987876711-0.148060722597-1.16385330002-0.04982796858650.02759172866970.467901285460.646290742767-0.489742393884-0.2935579342330.943445598751-0.268295083867-0.08915946415780.8795736192310.1994639858091.241334667949.7116948757-152.53820866515.5216131768
146.72766519851-2.364156755853.335652016456.206944330135.121050258289.3497574494-0.107242621461-0.2969753139020.292325457703-0.01437013859580.6285701154460.664984195843-0.08494812810020.827711404826-0.3219202011070.992668319048-0.1533581864890.09575023421.176152144790.3032814224831.3457803373964.845124726-158.56354494339.2873635413
156.91724081667-2.35926201407-3.564445580098.253347440140.8463206778244.20102257850.0895864376761-0.1506628950110.1469301039940.6534730288280.0110812227537-0.2438225246530.0260477863453-0.769084696009-0.09222935739111.41050079278-0.068857976092-0.1471505618631.674039178070.1899075534480.8539419224245.847339052-156.23054373960.435715049
166.882399434432.062189718170.1579170451494.296086972860.173050139992.493487154930.1137065361080.111007461493-0.8989176637780.1696592655450.185430113306-0.5516675005020.5885321286420.234242925624-0.2758115203670.810340676229-0.0107742489168-0.1625936641840.7767764107420.003127428326620.99351336910590.9801732049-143.4273102515.7176567281
176.828859628762.46427617597-2.963568447359.210355703685.81449247276.878991337190.25605795592-0.828927414728-0.1471106736951.90553752111-0.510590855155-0.6789978650720.3254602618931.520738022380.2026112752481.51756486142-0.0871231265817-0.3394476625771.443187412880.2541161034391.11093200761104.97131011-135.98351186639.5326507563
183.891747092044.41529714744-2.44457369556.93325865272-0.5523923573942.371620275370.300622173477-1.14626284006-0.9121561935651.481980710450.0529054306957-0.2080855532690.910342434616-0.612105733634-0.3089823372312.41155564045-0.349668420602-0.3125692303932.231979737310.1578377289881.4360111309891.3636434418-149.26204507260.7273408198
192.21767510153-0.598377884355-0.4956634137725.566678513080.01747352628981.366701158110.03515306281890.113718401945-0.442978203702-0.01481531016860.118965096607-0.5834224689560.01342650497790.34322588406-0.1678390694620.691721579593-0.104440315686-0.09729843525221.02889782719-0.105919981890.873189344258109.390794055-105.3231788515.9593086053
208.619018995320.2074798798-6.008225129236.544023921663.2579075656.064921421630.08055507105540.159347672138-0.600395570610.516866902494-0.171695652409-0.51316345872-0.7031499322140.186267523034-0.0368200392691.062067136540.00133001700031-0.3346349167631.1434969981-0.01003911372680.886966336685112.255116699-89.944341899739.9849149457
214.108335842123.94757737068-3.504010751488.85306894922-2.238744855464.94632425791-0.159041090668-0.1564539032540.0272257465965-0.776774828194-0.1197590933930.6592994424320.124176425432-0.3020192538250.2782311284421.030486963010.146876009726-0.218671676771.23615592427-0.2214746188440.835159558338112.351285624-109.03072846761.4415464895
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and (resid 68:203 or resid 486:631)
2X-RAY DIFFRACTION2chain A and (resid 204:255 or resid 452:485)
3X-RAY DIFFRACTION3chain A and resid 256:451
4X-RAY DIFFRACTION4chain B and (resid 69:203 or resid 486:631)
5X-RAY DIFFRACTION5chain B and (resid 204:255 or resid 452:485)
6X-RAY DIFFRACTION6chain B and resid 256:451
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