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- PDB-2zd2: D202K mutant of P. denitrificans Atp12p -

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Basic information

Entry
Database: PDB / ID: 2zd2
TitleD202K mutant of P. denitrificans Atp12p
ComponentsATP12 ATPase
KeywordsCHAPERONE / ATPase chaperone F1 assembly
Function / homology
Function and homology information


proton-transporting ATP synthase complex assembly
Similarity search - Function
ATP12-like fold / ATP12 ATPase / ATP12-like / ATP12-like / ATP12, ATP synthase F1-assembly protein / ATP12 orthogonal Bundle domain superfamily / ATP12, ATP synthase F1-assembly protein, N-terminal / ATP12 chaperone protein / 2-Layer Sandwich / Orthogonal Bundle ...ATP12-like fold / ATP12 ATPase / ATP12-like / ATP12-like / ATP12, ATP synthase F1-assembly protein / ATP12 orthogonal Bundle domain superfamily / ATP12, ATP synthase F1-assembly protein, N-terminal / ATP12 chaperone protein / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesParacoccus denitrificans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsGatti, D.L. / Ludlam, A. / Brunzelle, J. / Ackerman, S.H.
CitationJournal: J.Biol.Chem. / Year: 2009
Title: Chaperones of F1-ATPase
Authors: Ludlam, A. / Brunzelle, J. / Pribyl, T. / Xu, X. / Gatti, D.L. / Ackerman, S.H.
History
DepositionNov 19, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 25, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Nov 10, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3Nov 1, 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

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Assembly

Deposited unit
A: ATP12 ATPase
B: ATP12 ATPase


Theoretical massNumber of molelcules
Total (without water)51,5972
Polymers51,5972
Non-polymers00
Water9,620534
1
A: ATP12 ATPase


Theoretical massNumber of molelcules
Total (without water)25,7981
Polymers25,7981
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: ATP12 ATPase


Theoretical massNumber of molelcules
Total (without water)25,7981
Polymers25,7981
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)43.160, 51.047, 67.117
Angle α, β, γ (deg.)102.91, 105.45, 90.07
Int Tables number1
Space group name H-MP1

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Components

#1: Protein ATP12 ATPase


Mass: 25798.365 Da / Num. of mol.: 2 / Mutation: D1202K, D2202K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paracoccus denitrificans (bacteria) / Strain: PD1222 / Gene: PDEN_0792 / Plasmid: PET28A-atp12D202K / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: A1B060
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 534 / 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: 2.69 Å3/Da / Density % sol: 54.22 %
Crystal growTemperature: 278 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 12% PEG 4000, 100mM Hepes-Na, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 278K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97924 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 20, 2007
RadiationMonochromator: refractive beryllium lenses / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97924 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. all: 48230 / Num. obs: 48230 / % possible obs: 97.5 % / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 20.7 Å2 / Rmerge(I) obs: 0.082 / Net I/σ(I): 15.3
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.555 / Mean I/σ(I) obs: 2.269 / Num. unique all: 2304 / % possible all: 95.6

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Processing

Software
NameVersionClassification
CNS1.2refinement
AccelDB2data collection
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2P4X

2p4x


Resolution: 1.8→35.21 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 113038.34 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.279 4716 10.1 %RANDOM
Rwork0.225 ---
obs0.225 46717 93.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 63.948 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 28.8 Å2
Baniso -1Baniso -2Baniso -3
1--0.87 Å2-0.59 Å2-0.27 Å2
2---2.62 Å20.75 Å2
3---3.49 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.25 Å0.18 Å
Refinement stepCycle: LAST / Resolution: 1.8→35.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3642 0 0 534 4176
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_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d20.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.01
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it2.531.5
X-RAY DIFFRACTIONc_mcangle_it3.32
X-RAY DIFFRACTIONc_scbond_it3.782
X-RAY DIFFRACTIONc_scangle_it5.062.5
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.343 701 10.2 %
Rwork0.29 6151 -
obs--82.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top

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