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- PDB-1gmj: The structure of bovine IF1, the regulatory subunit of mitochondr... -

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Basic information

Entry
Database: PDB / ID: 1gmj
TitleThe structure of bovine IF1, the regulatory subunit of mitochondrial F-ATPase
ComponentsATPASE INHIBITOR
KeywordsATPASE INHIBITOR / BOVINE F1-ATPASE INHIBITOR PROTEIN / COILED-COIL STRUCTURE / P DEPENDENT OLIGOMERIZATION / ATP HYDROLYSIS
Function / homology
Function and homology information


angiostatin binding / ATPase inhibitor activity / negative regulation of hydrolase activity / heme biosynthetic process / : / negative regulation of endothelial cell proliferation / erythrocyte differentiation / ATPase binding / protein homotetramerization / calmodulin binding ...angiostatin binding / ATPase inhibitor activity / negative regulation of hydrolase activity / heme biosynthetic process / : / negative regulation of endothelial cell proliferation / erythrocyte differentiation / ATPase binding / protein homotetramerization / calmodulin binding / structural molecule activity / cell surface / protein homodimerization activity / protein-containing complex / mitochondrion / identical protein binding
Similarity search - Function
Single helix bin / Mitochondrial ATPase inhibitor / Mitochondrial ATPase inhibitor, IATP / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
ATPase inhibitor, mitochondrial
Similarity search - Component
Biological speciesBOS TAURUS (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.2 Å
AuthorsCabezon, E. / Runswick, M.J. / Leslie, A.G.W. / Walker, J.E.
Citation
Journal: Embo J. / Year: 2001
Title: The Structure of Bovine If(1), the Regulatory Subunit of Mitochondrial F-ATPase.
Authors: Cabezon, E. / Runswick, M.J. / Leslie, A.G.W. / Walker, J.E.
#1: Journal: J.Biol.Chem. / Year: 2000
Title: Modulation of the Oligomerization State of Bovine F1-ATPase Inhibitor Protein, If1, by Ph
Authors: Cabezon, E. / Butler, P.J.G. / Runswick, M.J. / Walker, J.E.
#2: Journal: J.Biol.Chem. / Year: 2000
Title: Dimerization of Bovine F1-ATPase by Binding the Inhibitor Protein, If1
Authors: Cabezon, E. / Arechaga, I. / Butler, P.J.G. / Walker, J.E.
History
DepositionSep 14, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 1, 2002Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 24, 2018Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name ..._entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_variant
Revision 1.4May 15, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.method / _exptl_crystal_grow.temp
Revision 1.5May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ATPASE INHIBITOR
B: ATPASE INHIBITOR
C: ATPASE INHIBITOR
D: ATPASE INHIBITOR


Theoretical massNumber of molelcules
Total (without water)38,3824
Polymers38,3824
Non-polymers00
Water00
1
A: ATPASE INHIBITOR
B: ATPASE INHIBITOR


Theoretical massNumber of molelcules
Total (without water)19,1912
Polymers19,1912
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
C: ATPASE INHIBITOR
D: ATPASE INHIBITOR


Theoretical massNumber of molelcules
Total (without water)19,1912
Polymers19,1912
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)32.010, 53.290, 156.940
Angle α, β, γ (deg.)90.00, 95.89, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given / Matrix: (1), (1), (1))
DetailsTHE ACTIVE FORM OF THE PROTEIN IS DIMERIC . IN THE CRYSTALTWO DIMERS INSTERACT TO FORM A DIMER OF DIMERS.

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Components

#1: Protein
ATPASE INHIBITOR / F1-ATPASE INHIBITOR PROTEIN


Mass: 9595.572 Da / Num. of mol.: 4 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: THE ACTIVE FORM OF THE PROTEIN IS DIMERIC (DIMERS AB OR CD)
Source: (gene. exp.) BOS TAURUS (cattle) / Description: MITOCHONDRIAL PROTEIN / Organ: HEART / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: P01096
Compound detailsCHAIN A, B, C, D ENGINEERED MUTATION HIS74LYS
Sequence detailsSEQUENCE DATABASE CORRESPONDS TO THE UNPROCESSED PRECURSOR, WITH 25 RESIDUES LEADER SEQUENCE.

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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: 3.6 Å3/Da / Density % sol: 65 %
Description: ANISOTROPIC DATA. WITHIN THE ANISOTROPIC RESOLUTION LIMITS USED FOR THE INTEGRATION, THE DATA SET IS 96% COMPLETE.
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / pH: 8
Details: CRYSTALS WERE GROWN BY EQUILIBRATING A IF1-H49K SOLUTION, AT 6 MG/ML IN BUFFER 10 MM TRIS-HCL PH 8.0, RESERVOIR CONTAINING 0.8 M MONO-SODIUM DIHYDROGEN PHOSPHAT AGAINST A 0.8 M MONO- ...Details: CRYSTALS WERE GROWN BY EQUILIBRATING A IF1-H49K SOLUTION, AT 6 MG/ML IN BUFFER 10 MM TRIS-HCL PH 8.0, RESERVOIR CONTAINING 0.8 M MONO-SODIUM DIHYDROGEN PHOSPHAT AGAINST A 0.8 M MONO-POTASSIUM DIHYDROGEN PHOSPHATE AND 0.1 M HEPES-NA BUFFER PH 8, AT 23C, IN SITTING-DROP VAPOR-DIFFUSION TRAYS.
Crystal grow
*PLUS
Temperature: 23 ℃ / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
16 mg/mlprotein1drop
210 mMTris-HCl1droppH8.0
30.8 Mmono-sodium dihydrogen phosphate1reservoir
40.8 Mmono-potassium dihydrogen phosphate1reservoir
50.1 MHEPES-Na1reservoirpH8.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 15, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.2→14.2 Å / Num. obs: 18750 / % possible obs: 72.3 % / Redundancy: 2.4 % / Biso Wilson estimate: 33.1 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 10.5
Reflection shellResolution: 2.2→2.35 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.227 / Mean I/σ(I) obs: 3.7 / % possible all: 10.8
Reflection
*PLUS
Highest resolution: 2.2 Å
Reflection shell
*PLUS
% possible obs: 10.8 % / Redundancy: 2 %

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
CCP4data scaling
MLPHAREphasing
SHARPphasing
CNS1.1refinement
RefinementMethod to determine structure: SIRAS / Resolution: 2.2→26 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 10000 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Stereochemistry target values: MAXIMUM LIKELIHOOD USING AMPLITUDES
Details: 14 DIFFERENT GROUPS WERE USED IN THE NCS RESTRAINTS (TYPICAL WEIGHT 25, RMS 0.2,SIGB 10, RMSB 8) AN IN-HOUSE DATASET WAS USED TO PROVIDE LOW RESOLUTION STRUCTURE FACTORS (26-14A). . THERE ...Details: 14 DIFFERENT GROUPS WERE USED IN THE NCS RESTRAINTS (TYPICAL WEIGHT 25, RMS 0.2,SIGB 10, RMSB 8) AN IN-HOUSE DATASET WAS USED TO PROVIDE LOW RESOLUTION STRUCTURE FACTORS (26-14A). . THERE WAS NOT INTERPRETABLE ELECTRON DENSITY AT THE N-TERMINUS FOR RESIDUES 1-18; 1-19; 1-19 AND 1- 22 IN CHAINS A, B, C AND D, RESPECTIVELY AND FOR RESIDUES 84; 80-84; 79-84 AND 79-84 AT THE C-TERMINUS IN CHAINS A, B, C AND D, RESPECTIVELY.
RfactorNum. reflection% reflectionSelection details
Rfree0.28 1860 10 %RANDOM
Rwork0.258 ---
obs0.258 18832 69.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 53.1 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 72.8 Å2
Baniso -1Baniso -2Baniso -3
1-15.13 Å20 Å27.1 Å2
2---45.2 Å20 Å2
3---30.07 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.36 Å0.35 Å
Luzzati d res low-5 Å
Luzzati sigma a0.4 Å0.43 Å
Refinement stepCycle: LAST / Resolution: 2.2→26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2037 0 0 0 2037
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.16
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d15.05
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.73
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it4.12
X-RAY DIFFRACTIONc_mcangle_it63
X-RAY DIFFRACTIONc_scbond_it10.54
X-RAY DIFFRACTIONc_scangle_it14.66
LS refinement shellResolution: 2.2→2.28 Å / Rfactor Rfree error: 0.068 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.235 12 0.4 %
Rwork0.33 101 -
obs--4 %
Xplor fileSerial no: 1 / Param file: PROTEIN_REP.PARAM / Topol file: PROTEIN.TOP
Software
*PLUS
Name: CNS / Version: 1.1 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 26 Å / Rfactor Rfree: 0.28
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg15.05
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.73
LS refinement shell
*PLUS
Rfactor Rwork: 0.33

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