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- PDB-1jnv: The Conformation of the Epsilon and Gamma Subunits within the E. ... -

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Basic information

Entry
Database: PDB / ID: 1jnv
TitleThe Conformation of the Epsilon and Gamma Subunits within the E. coli F1 ATPase
Components
  • ATP SYNTHASE ALPHA CHAIN
  • ATP SYNTHASE BETA CHAIN
  • ATP SYNTHASE EPSILON CHAIN
  • ATP SYNTHASE GAMMA CHAIN
KeywordsHYDROLASE / F1 ATPase / ATP synthase / bioenergetics
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.4 Å
AuthorsHausrath, A.C. / Capaldi, R.A. / Matthews, B.W.
CitationJournal: J.Biol.Chem. / Year: 2001
Title: The conformation of the epsilon- and gamma-subunits within the Escherichia coli F(1) ATPase.
Authors: Hausrath, A.C. / Capaldi, R.A. / Matthews, B.W.
History
DepositionJul 25, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 21, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 2023Group: Database references / Refinement description / Category: database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ATP SYNTHASE ALPHA CHAIN
B: ATP SYNTHASE ALPHA CHAIN
C: ATP SYNTHASE ALPHA CHAIN
D: ATP SYNTHASE BETA CHAIN
E: ATP SYNTHASE BETA CHAIN
F: ATP SYNTHASE BETA CHAIN
Y: ATP SYNTHASE EPSILON CHAIN
Z: ATP SYNTHASE GAMMA CHAIN


Theoretical massNumber of molelcules
Total (without water)280,9058
Polymers280,9058
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)180.683, 197.517, 237.896
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein ATP SYNTHASE ALPHA CHAIN


Mass: 41889.645 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: atpA / Plasmid: pAN45 / Production host: Escherichia coli (E. coli) / Strain (production host): GO104 / References: EC: 3.6.1.34
#2: Protein ATP SYNTHASE BETA CHAIN


Mass: 39762.000 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: atpD / Plasmid: pAN45 / Production host: Escherichia coli (E. coli) / Strain (production host): GO104 / References: EC: 3.6.1.34
#3: Protein ATP SYNTHASE EPSILON CHAIN


Mass: 11507.176 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: atpC / Plasmid: pAN45 / Production host: Escherichia coli (E. coli) / Strain (production host): GO104 / References: EC: 3.6.1.34
#4: Protein ATP SYNTHASE GAMMA CHAIN


Mass: 24442.998 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: atpG / Plasmid: pAN45 / Production host: Escherichia coli (E. coli) / Strain (production host): GO104 / References: EC: 3.6.1.34
Sequence detailsTHIS COMPOSITE MODEL WAS CONSTRUCTED BY PLACING COORDINATES FROM PDB ENTRIES 1BMF AND 1FSO INTO A ...THIS COMPOSITE MODEL WAS CONSTRUCTED BY PLACING COORDINATES FROM PDB ENTRIES 1BMF AND 1FSO INTO A LOW-RESOLUTION MAP. ONLY BACKBONE ATOMS HAVE BEEN MODELLED. IT IS NOT POSSIBLE TO UNAMBIGUOUSLY DETERMINE THE SEQUENCE REGISTER FROM THE CRYSTALLOGRAPHIC DATA, AND SO THE SECONDARY STRUCTURE STRUCTURE ASSIGNMENTS MAY BE INACCURATE. EVERY AMINO ACID IS LABELLED UNK. THE RESIDUE NUMBERING FOR CHAINS A-F DERIVES FROM PDB ENTRY 1BMF. THE RESIDUE NUMBERING FOR CHAINS Y AND Z DERIVES FROM PDB ENTRY 1FS0. THE SEQUENCE FOR THE ALPHA CHAIN IS: MQLNSTEISE LIKQRIAQFN VVSEAHNEGT IVSVSDGVIR IHGLADCMQG EMISLPGNRY AIALNLERDS VGAVVMGPYA DLAEGMKVKC TGRILEVPVG RGLLGRVVNT LGAPIDGKGP LDHDGFSAVE AIAPGVIERQ SVDQPVQTGY KAVDSMIPIG RGQRELIIGD RQTGKTALAI DAIINQRDSG IKCIYVAIGQ KASTISNVVR KLEEHGALAN TIVVVATASE SAALQYLAPY AGCAMGEYFR DRGEDALIIY DDLSKQAVAY RQISLLLRRP PGREAFPGDV FYLHSRLLER AARVNAEYVE AFTKGEVKGK TGSLTALPII ETQAGDVSAF VPTNVISITD GQIFLETNLF NAGIRPAVNP GISVSRVGGA AQTKIMKKLS GGIRTALAQY RELAAFSQFA SDLDDATRKQ LDHGQKVTEL LKQKQYAPMS VAQQSLVLFA AERGYLADVE LSKIGSFEAA LLAYVDRDHA PLMQEINQTG GYNDEIEGKL KGILDSFKAT QSW THE SEQUENCE FOR THE BETA CHAIN IS: MATGKIVQVI GAVVDVEFPQ DAVPRVYDAL EVQNGNERLVL EVQQQLGGGI VRTIAMGSSD GLRRGLDVKD LEHPIEVPVGK ATLGRIMNVL GEPVDMKGEI GEEERWAIHR AAPSYEELSNS QELLETGIKV IDLMCPFAKG GKVGLFGGAG VGKTVNMMELI RNIAIEHSGY SVFAGVGERT REGNDFYHEM TDSNVIDKVSL VYGQMNEPPG NRLRVALTGL TMAEKFRDEG RDVLLFVDNIY RYTLAGTEVS ALLGRMPSAV GYQPTLAEEM GVLQERITSTK TGSITSVQAV YVPADDLTDP SPATTFAHLD ATVVLSRQIAS LGIYPAVDPL DSTSRQLDPL VVGQEHYDTA RGVQSILQRYQ ELKDIIAILG MDELSEEDKL VVARARKIQR FLSQPFFVAEV FTGSPGKYVS LKDTIRGFKG IMEGEYDHLP EQAFYMVGSIE EAVEKAKK THE SEQUENCE FOR THE EPSILON CHAIN IS: MAMTYHLDVV SAEQQMFSGL VEKIQVTGSE GELGIYPGHA PLLTAIKPGM IRIVKQHGHE EFIYLSGGIL EVQPGNVTVL ADTAIRGQDL DEARAMEAKR KAEEHISSSH GDVDYAQASA ELAKAIAQLR VIELTKKAM THE SEQUENCE FOR THE GAMMA CHAIN IS: MAGAKEIRSK IASVQNTQKI TKAMEMVAAS KMRKSQDRMA ASRPYAETMR KVIGHLAHGN LEYKHPYLED RDVKRVGYLV VSTDRGLCGG LNINLFKKLL AEMKTWTDKG VQCDLAMIGS KGVSFFNSVG GNVVAQVTGM GDNPSLSELI GPVKVMLQAY DEGRLDKLYI VSNKFINTMS QVPTISQLLP LPASDDDDLK HKSWDYLYEP DPKALLDTLL RRYVESQVYQ GVVENLASEQ AARMVAMKAA TDNGGSLIKE LQLVYNKARQ ASITQELTEI VSGAAAV

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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: 2.9 Å3/Da / Density % sol: 60 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: TRIS, PEG 8000, GLYCEROL, NACL, MGSO4, LISO4, NAN3, EDTA, AMP-PNP, ATP, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Temperature: 25 ℃
Details: Hausrath, A.C., (1999) Proc.Natl.Acad.Sci.U.S.J., 96, 13697.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
2110 mMTris-HCl1drop
310 %glycerol1drop
4100 mM1dropNaCl
510 mM1dropMgSO4
640 mM1dropLi2SO4
70.05 %1dropNaN3
80.1 MEDTA1drop
95 mMadenylylimidodiphosphate1drop
100.1 MATP1drop
118.0 %PEG80001drop
1235 %satammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.98 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 4.4→25 Å / Num. all: 27196 / Num. obs: 17529 / % possible obs: 64 % / Redundancy: 5.1 % / Rmerge(I) obs: 0.122 / Net I/σ(I): 3.7
Reflection shellResolution: 4.4→4.44 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.358 / Mean I/σ(I) obs: 2.1 / % possible all: 53.6

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Processing

Software
NameVersionClassification
AMoREphasing
TNTrefinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry 1bmf,1fs0

1bmf

1fs0


Resolution: 4.4→25 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: TNT PROTGEO 1.0
RfactorNum. reflection% reflection
Rwork0.416 --
all0.416 17529 -
obs-17529 64.5 %
Refinement stepCycle: LAST / Resolution: 4.4→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13072 0 0 0 13072
Software
*PLUS
Name: TNT / Classification: refinement
Refinement
*PLUS
Highest resolution: 4.4 Å / σ(F): 0 / Rfactor all: 0.416
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDType
X-RAY DIFFRACTIONt_bond_d
X-RAY DIFFRACTIONt_angle_d
X-RAY DIFFRACTIONt_angle_deg
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_improper_angle_d
X-RAY DIFFRACTIONt_mcbond_it
X-RAY DIFFRACTIONt_scbond_it
X-RAY DIFFRACTIONt_mcangle_it
X-RAY DIFFRACTIONt_scangle_it

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