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- PDB-2r9g: Crystal structure of the C-terminal fragment of AAA ATPase from E... -

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Basic information

Entry
Database: PDB / ID: 2r9g
TitleCrystal structure of the C-terminal fragment of AAA ATPase from Enterococcus faecium
ComponentsAAA ATPase, central regionAAA proteins
KeywordsHYDROLASE / STRUCTURAL GENOMICS / ATPASE / PSI-2 / PROTEIN STRUCTURE INITIATIVE / New York SGX Research Center for Structural Genomics / NYSGXRC / ATP-BINDING / NUCLEOTIDE-BINDING
Function / homologypost-AAA+ oligomerization domain-like / DNA polymerase III clamp loader subunits, C-terminal domain / Zinc Finger, Delta Prime; domain 3 - #10 / Zinc Finger, Delta Prime; domain 3 / Up-down Bundle / Orthogonal Bundle / Mainly Alpha / ACETATE ION / :
Function and homology information
Biological speciesEnterococcus faecium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.09 Å
AuthorsRamagopal, U.A. / Patskovsky, Y. / Bonanno, J.B. / Shi, W. / Toro, R. / Meyer, A.J. / Rutter, M. / Wu, B. / Groshong, C. / Gheyi, T. ...Ramagopal, U.A. / Patskovsky, Y. / Bonanno, J.B. / Shi, W. / Toro, R. / Meyer, A.J. / Rutter, M. / Wu, B. / Groshong, C. / Gheyi, T. / 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 AAA ATPase from Enterococcus faecium.
Authors: Ramagopal, U.A. / Patskovsky, Y. / Bonanno, J.B. / Shi, W. / Toro, R. / Meyer, A.J. / Rutter, M. / Wu, B. / Groshong, C. / Gheyi, T. / Sauder, J.M. / Burley, S.K. / Almo, S.C.
History
DepositionSep 12, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 2, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Nov 14, 2018Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.3Feb 3, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / struct_ref_seq_dif / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 30, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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
E: AAA ATPase, central region
F: AAA ATPase, central region
G: AAA ATPase, central region
H: AAA ATPase, central region
I: AAA ATPase, central region
J: AAA ATPase, central region
K: AAA ATPase, central region
L: AAA ATPase, central region
M: AAA ATPase, central region
N: AAA ATPase, central region
O: AAA ATPase, central region
P: AAA ATPase, central region
hetero molecules


Theoretical massNumber of molelcules
Total (without water)364,59032
Polymers363,51316
Non-polymers1,07716
Water24,1041338
1
A: AAA ATPase, central region
B: AAA ATPase, central region
C: AAA ATPase, central region
D: AAA ATPase, central region
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,0557
Polymers90,8784
Non-polymers1773
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17750 Å2
MethodPISA
2
E: AAA ATPase, central region
F: AAA ATPase, central region
G: AAA ATPase, central region
H: AAA ATPase, central region
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,2409
Polymers90,8784
Non-polymers3615
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17550 Å2
MethodPISA
3
I: AAA ATPase, central region
J: AAA ATPase, central region
K: AAA ATPase, central region
L: AAA ATPase, central region
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,1478
Polymers90,8784
Non-polymers2694
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18130 Å2
MethodPISA
4
M: AAA ATPase, central region
N: AAA ATPase, central region
O: AAA ATPase, central region
P: AAA ATPase, central region
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,1478
Polymers90,8784
Non-polymers2694
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17960 Å2
MethodPISA
5
A: AAA ATPase, central region
B: AAA ATPase, central region
C: AAA ATPase, central region
D: AAA ATPase, central region
I: AAA ATPase, central region
J: AAA ATPase, central region
K: AAA ATPase, central region
L: AAA ATPase, central region
hetero molecules


Theoretical massNumber of molelcules
Total (without water)182,20315
Polymers181,7568
Non-polymers4467
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area39510 Å2
MethodPISA
6
E: AAA ATPase, central region
F: AAA ATPase, central region
G: AAA ATPase, central region
H: AAA ATPase, central region
M: AAA ATPase, central region
N: AAA ATPase, central region
O: AAA ATPase, central region
P: AAA ATPase, central region
hetero molecules


Theoretical massNumber of molelcules
Total (without water)182,38717
Polymers181,7568
Non-polymers6319
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area39070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.778, 103.390, 103.374
Angle α, β, γ (deg.)90.01, 88.69, 86.05
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
71G
81H
91I
101J
111K
121L
131M
141N
151O
161P

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ASP / Beg label comp-ID: ASP / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: 1 / Auth seq-ID: 238 - 422 / Label seq-ID: 12 - 196

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD
5EE
6FF
7GG
8HH
9II
10JJ
11KK
12LL
13MM
14NN
15OO
16PP

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Components

#1: Protein
AAA ATPase, central region / AAA proteins


Mass: 22719.553 Da / Num. of mol.: 16 / Fragment: C-terminal domain: Residues 230-422
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: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1338 / 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: 2.43 Å3/Da / Density % sol: 49.33 %
Crystal growTemperature: 294 K / pH: 7.5
Details: 100mM HEPES pH 7.5, 25% PEG 3350, 200mM Ammonium acetate, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.979
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 31, 2007 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.09→50 Å / Num. obs: 202788 / % possible obs: 87.3 % / Observed criterion σ(I): -0.5 / Redundancy: 3.6 % / Biso Wilson estimate: 33.04 Å2 / Rmerge(I) obs: 0.126 / Rsym value: 0.091 / Net I/σ(I): 2.8
Reflection shellResolution: 2.09→2.18 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.76 / Mean I/σ(I) obs: 2.1 / Rsym value: 0.54 / % possible all: 44.4

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Processing

Software
NameVersionClassification
MOLREPphasing
REFMAC5.3.0034refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2QW6

2qw6


Resolution: 2.09→20 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.934 / SU B: 5.794 / SU ML: 0.154 / Cross valid method: THROUGHOUT / ESU R: 0.255 / ESU R Free: 0.208 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.248 5299 3 %RANDOM
Rwork0.197 ---
obs0.199 171031 87.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.79 Å2
Baniso -1Baniso -2Baniso -3
1-1.82 Å2-0.55 Å2-0.52 Å2
2---0.86 Å2-0.19 Å2
3----0.86 Å2
Refinement stepCycle: LAST / Resolution: 2.09→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22720 0 72 1338 24130
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.02223878
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1511.95832429
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.20253007
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.48123.8151203
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.434153912
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.30215184
X-RAY DIFFRACTIONr_chiral_restr0.080.23430
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0218682
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1510.312083
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2930.516063
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.160.52610
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.130.3160
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0930.534
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.841215042
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.017323371
X-RAY DIFFRACTIONr_scbond_it4.754310065
X-RAY DIFFRACTIONr_scangle_it6.86758997
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Number: 1271 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDTypeRms dev position (Å)Weight position
Atight positional0.250.05
Btight positional0.210
Ctight positional0.250
Dtight positional0.220
Etight positional0.20
Ftight positional0.220
Gtight positional0.240
Htight positional0.310
Itight positional0.190
Jtight positional0.190
Ktight positional0.280
Ltight positional0.210
Mtight positional0.210
Ntight positional0.20
Otight positional0.250
Ptight positional0.210
Atight thermal4.282.5
Btight thermal4.070
Ctight thermal4.960
Dtight thermal4.50
Etight thermal4.370
Ftight thermal4.680
Gtight thermal4.430
Htight thermal4.760
Itight thermal4.390
Jtight thermal3.940
Ktight thermal4.10
Ltight thermal4.870
Mtight thermal4.740
Ntight thermal4.160
Otight thermal3.960
Ptight thermal4.710
LS refinement shellResolution: 2.09→2.14 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.401 181 -
Rwork0.308 5730 -
obs--39.67 %

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