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- PDB-2p4f: Crystal Structure of Atp11 functional domain from Candida Glabrata -

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Basic information

Entry
Database: PDB / ID: 2p4f
TitleCrystal Structure of Atp11 functional domain from Candida Glabrata
ComponentsSimilar to sp|P32453 Saccharomyces cerevisiae YNL315c ATP11
KeywordsCHAPERONE / half barrel
Function / homologyATP11 / ATP11 protein / protein-containing complex assembly / mitochondrion / Uncharacterized protein
Function and homology information
Biological speciesCandida glabrata CBS 138 (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.4 Å
AuthorsLudlam, A.V. / Brunzelle, J.S. / Gatti, D.L. / Ackerman, S.H.
CitationJournal: To be Published
Title: Crystal Structure of Atp11 functional domain from Candida Glabrata
Authors: Ludlam, A.V. / Brunzelle, J.S. / Pribyl, T. / Gatti, D.L. / Ackerman, S.H.
History
DepositionMar 12, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 11, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 17, 2011Group: Other
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Jul 24, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.location / _software.name / _software.type
Revision 1.5Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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: Similar to sp|P32453 Saccharomyces cerevisiae YNL315c ATP11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,6892
Polymers34,4071
Non-polymers2821
Water3,063170
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.187, 63.187, 153.577
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number80
Space group name H-MI41

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Components

#1: Protein Similar to sp|P32453 Saccharomyces cerevisiae YNL315c ATP11


Mass: 34406.977 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candida glabrata CBS 138 (fungus) / Species: Candida glabrata / Strain: CBS138 / Gene: CAGL0M04037g / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3), Rosetta(DE3) / References: UniProt: Q6FJS2
#2: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400 / Polyethylene glycol


Mass: 282.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 170 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.23 Å3/Da / Density % sol: 44.77 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: PEG 400, MES, Acetate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 22-ID10.97625
SYNCHROTRONAPS 22-ID20.97931
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Jan 1, 2006
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si220SINGLE WAVELENGTHMx-ray1
2Si220SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.976251
20.979311
ReflectionRedundancy: 12.8 % / Av σ(I) over netI: 14.1 / Number: 305962 / Rmerge(I) obs: 0.072 / Χ2: 2.05 / D res high: 1.89 Å / D res low: 50 Å / Num. obs: 23868 / % possible obs: 100
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
5.135099.110.0545.77412.3
4.075.1310010.0524.25812.7
3.564.0710010.0624.64912.6
3.233.5610010.0623.70812.9
33.2310010.0642.71313.1
2.82310010.072.35813.1
2.682.8210010.0731.98613.1
2.572.6810010.081.70513.1
2.472.5710010.0861.56413.2
2.382.4710010.091.44113.1
2.312.3810010.0971.34513.1
2.242.3110010.1171.31113.1
2.182.2410010.1241.17513.1
2.132.1810010.1321.07413.1
2.082.1310010.1481.10513
2.042.0810010.1821.04213
22.0410010.20.9813
1.96210010.2420.93913.2
1.921.9610010.2810.94112.2
1.891.9210010.3250.92410.4
ReflectionResolution: 1.4→50 Å / Num. obs: 47858 / % possible obs: 81.2 % / Redundancy: 10.3 % / Rmerge(I) obs: 0.058 / Χ2: 1.044 / Net I/σ(I): 16.1
Reflection shellResolution: 1.4→1.42 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.476 / Mean I/σ(I) obs: 1.59 / Num. unique all: 442 / Rsym value: 0.405 / Χ2: 0.955 / % possible all: 15.3

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Phasing

PhasingMethod: SAD
Phasing MADD res high: 2.49 Å / D res low: 19.93 Å / FOM : 0.38 / FOM acentric: 0.385 / FOM centric: 0 / Reflection: 20408
Phasing MAD setWavelength: 0.97932 Å / Atom type: SE / F double prime refined: 2.78 / F prime refined: -6
Phasing MAD set site
IDCartn x (Å)Cartn y (Å)Cartn z (Å)Atom type symbolB isoOccupancy
11.914330.015825070.06598831SE5.118280.111111
22.35719-0.402951-1.69498SE3.699070.111111
31.69396-6.50986-0.645805SE3.025980.111111
Phasing MAD exptMean fom: 0.379
Phasing dmDelta phi final: 7.02 / Delta phi initial: 63.44 / FOM : 0.9605 / Mask type: RMS / Method: FLIP
Phasing dm shell
Resolution (Å)FOM Reflection
5.35-200.97042040
4.26-5.350.98292040
3.73-4.260.98252052
3.39-3.730.97782037
3.15-3.390.9662032
2.96-3.150.95382039
2.81-2.960.95992079
2.69-2.810.94992051
2.59-2.690.94542034
2.5-2.590.91712072

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Processing

Software
NameVersionClassificationNB
SHELXL-97refinement
SCALEPACKdata scaling
CNSphasing
REFMACrefinement
PDB_EXTRACT2data extraction
HKL-2000data collection
HKL-2000data reduction
SHELXphasing
DENZOdata reduction
RefinementMethod to determine structure: SAD / Resolution: 1.4→50 Å / Num. parameters: 15880 / Num. restraintsaints: 19517 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.1862 2394 5.3 %RANDOM
Rwork0.1449 ---
obs0.1449 45438 --
all-45438 --
Refine analyzeNum. disordered residues: 2 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 1752
Refinement stepCycle: LAST / Resolution: 1.4→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1563 0 19 170 1752
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.013
X-RAY DIFFRACTIONs_angle_d0.031
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0279
X-RAY DIFFRACTIONs_zero_chiral_vol0.056
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.076
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.009
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.004
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.077
X-RAY DIFFRACTIONs_approx_iso_adps0.107

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