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- PDB-2r31: Crystal structure of atp12p from paracoccus denitrificans -

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Basic information

Entry
Database: PDB / ID: 2r31
TitleCrystal structure of atp12p from paracoccus denitrificans
ComponentsATP12 ATPase
KeywordsCHAPERONE / CHAPERONE F1 ATPASE ASSEMBLY ATP12P
Function / homology
Function and homology information


proton-transporting ATP synthase complex assembly
Similarity search - Function
ATP12, ATP synthase F1-assembly protein, N-terminal / ATP12-like fold / ATP12 ATPase / ATP12-like / ATP12-like / ATP12, ATP synthase F1-assembly protein / ATP12 orthogonal Bundle domain superfamily / ATP12 chaperone protein / 2-Layer Sandwich / Orthogonal Bundle ...ATP12, ATP synthase F1-assembly protein, N-terminal / ATP12-like fold / ATP12 ATPase / ATP12-like / ATP12-like / ATP12, ATP synthase F1-assembly protein / ATP12 orthogonal Bundle domain superfamily / 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 Å
AuthorsLudlam, A.V. / Brunzelle, J.S. / Gatti, D.L. / 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
DepositionAug 28, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 25, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ATP12 ATPase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,3772
Polymers26,2551
Non-polymers1221
Water9,224512
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)43.553, 55.749, 96.616
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein ATP12 ATPase


Mass: 26254.795 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paracoccus denitrificans (bacteria) / Strain: PD1222 / Gene: PDEN_0792 / Plasmid: PET28A / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: A1B060
#2: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 512 / 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: 2.23 Å3/Da / Density % sol: 44.94 %
Crystal growTemperature: 278 K / Method: vapor diffusion / pH: 8.5
Details: 30% PEG4000, 50 MM MGCL2, 100 MM TRIS VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 278K, pH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 7, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1→50 Å / Num. all: 127208 / Num. obs: 127208 / % possible obs: 99.8 % / Redundancy: 14.49 % / Rmerge(I) obs: 0.062 / Net I/σ(I): 25.41
Reflection shellResolution: 1→1.06 Å / Redundancy: 14.34 % / Rmerge(I) obs: 0.745 / Mean I/σ(I) obs: 3.97 / % possible all: 99.9

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Processing

Software
NameClassification
MOLREPphasing
SHELXL-97refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2P4X

2p4x


Resolution: 1→50 Å / Num. parameters: 24397 / Num. restraintsaints: 32900 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
Details: ESD(A)=(0.00961+0.002600*B+0.0001299*B^2)/Z# Z# IS FOR C=2.494, FOR N=3.219, FOR O=4.089
RfactorNum. reflection% reflectionSelection details
Rfree0.1425 6370 5 %RANDOM
Rwork0.118 ---
obs0.1187 127208 99.8 %-
Displacement parametersBiso mean: 16.3 Å2
Refine analyzeNum. disordered residues: 58 / Occupancy sum hydrogen: 1806 / Occupancy sum non hydrogen: 2340.1
Refinement stepCycle: LAST / Resolution: 1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1833 0 8 512 2353
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.014
X-RAY DIFFRACTIONs_angle_d0.032
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0262
X-RAY DIFFRACTIONs_zero_chiral_vol0.089
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.154
X-RAY DIFFRACTIONs_anti_bump_dis_restr0
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.005
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.033
X-RAY DIFFRACTIONs_approx_iso_adps0.108

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