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- PDB-2qw6: Crystal structure of the C-terminal domain of an AAA ATPase from ... -

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Basic information

Entry
Database: PDB / ID: 2qw6
TitleCrystal structure of the C-terminal domain of an AAA ATPase from Enterococcus faecium DO
ComponentsAAA ATPase, central region
KeywordsHYDROLASE / STRUCTURAL GENOMICS / ATPASE / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC / ATP-binding / Nucleotide-binding
Function / homologyZinc Finger, Delta Prime; domain 3 - #10 / Zinc Finger, Delta Prime; domain 3 / Up-down Bundle / Mainly Alpha / :
Function and homology information
Biological speciesEnterococcus faecium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.3 Å
AuthorsBonanno, J.B. / Rutter, M. / Bain, K.T. / Ozyurt, S. / Smith, D. / Wasserman, S. / Sauder, J.M. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal structure of the C-terminal domain of an AAA ATPase from Enterococcus faecium DO.
Authors: Bonanno, J.B. / Rutter, M. / Bain, K.T. / Ozyurt, S. / Smith, D. / Wasserman, S. / Sauder, J.M. / Burley, S.K. / Almo, S.C.
History
DepositionAug 9, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 28, 2007Provider: 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 1.3Nov 14, 2018Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.4Feb 3, 2021Group: Database references / Structure summary
Category: audit_author / citation_author / struct_ref_seq_dif
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_ref_seq_dif.details
Revision 1.5Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 300 BIOMOLECULE: 1 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND PROGRAM GENERATED ASSEMBLY INFORMATION ... BIOMOLECULE: 1 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND PROGRAM GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON BURIED SURFACE AREA. AUTHORS STATE THAT THE TETRAMERIC ASSEMBLY SHOWN IN REMARK 350 IS PROBABLE.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: AAA ATPase, central region
B: AAA ATPase, central region
C: AAA ATPase, central region
D: AAA ATPase, central region


Theoretical massNumber of molelcules
Total (without water)47,9954
Polymers47,9954
Non-polymers00
Water1,17165
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.868, 87.016, 87.703
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Detailsprobable tetramer

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Components

#1: Protein
AAA ATPase, central region


Mass: 11998.666 Da / Num. of mol.: 4 / Fragment: C-terminal domain: Residues 230-330
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus faecium (bacteria) / Strain: DO / Gene: EfaeDRAFT_0938 / Plasmid: Modified pET26 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q3XY27
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 65 / 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: 2.5 Å3/Da / Density % sol: 50.78 %
Crystal growTemperature: 294 K / Method: vapor diffusion / pH: 6.5
Details: 100mM Imidazole pH 6.5, 1M Sodium acetate hydrate, VAPOR DIFFUSION, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97958 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jul 29, 2007
RadiationMonochromator: diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97958 Å / Relative weight: 1
ReflectionResolution: 2.3→87.706 Å / Num. all: 22041 / Num. obs: 22041 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 14.3 % / Biso Wilson estimate: 30.9 Å2 / Rmerge(I) obs: 0.149 / Rsym value: 0.149 / Net I/σ(I): 16.1
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 14.5 % / Rmerge(I) obs: 0.662 / Mean I/σ(I) obs: 4.1 / Num. unique all: 3160 / Rsym value: 0.662 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
REFMACrefinement
PDB_EXTRACT3data extraction
MAR345CCDdata collection
MOSFLMdata reduction
SHELXCDphasing
SHELXEmodel building
RefinementResolution: 2.3→20 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.919 / SU B: 7.066 / SU ML: 0.172 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.261 / ESU R Free: 0.227 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.275 1128 5.1 %RANDOM
Rwork0.224 ---
obs0.227 21975 99.99 %-
all-21975 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 39.761 Å2
Baniso -1Baniso -2Baniso -3
1-3.52 Å20 Å20 Å2
2---2.07 Å20 Å2
3----1.45 Å2
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2528 0 0 65 2593
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0222555
X-RAY DIFFRACTIONr_angle_refined_deg1.5491.9963471
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2555331
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.77523.2100
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.22215419
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.2011524
X-RAY DIFFRACTIONr_chiral_restr0.0970.2431
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021876
X-RAY DIFFRACTIONr_nbd_refined0.2170.21275
X-RAY DIFFRACTIONr_nbtor_refined0.2990.21808
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1340.290
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1080.226
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1850.25
X-RAY DIFFRACTIONr_mcbond_it0.9671.51735
X-RAY DIFFRACTIONr_mcangle_it1.622689
X-RAY DIFFRACTIONr_scbond_it2.6423909
X-RAY DIFFRACTIONr_scangle_it4.4424.5782
LS refinement shellResolution: 2.3→2.359 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.311 73 -
Rwork0.259 1509 -
all-1582 -
obs-1509 100 %

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