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- PDB-2fna: Crystal structure of an archaeal aaa+ atpase (sso1545) from sulfo... -

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Basic information

Entry
Database: PDB / ID: 2fna
TitleCrystal structure of an archaeal aaa+ atpase (sso1545) from sulfolobus solfataricus p2 at 2.00 A resolution
ComponentsConserved hypothetical protein
KeywordsATP-BINDING PROTEIN / Structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


ATPase domain / ATPase domain predominantly from Archaea / Helicase, Ruva Protein; domain 3 - #60 / Helicase, Ruva Protein; domain 3 / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / P-loop containing nucleotide triphosphate hydrolases / Winged helix-like DNA-binding domain superfamily / P-loop containing nucleoside triphosphate hydrolase ...ATPase domain / ATPase domain predominantly from Archaea / Helicase, Ruva Protein; domain 3 - #60 / Helicase, Ruva Protein; domain 3 / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / P-loop containing nucleotide triphosphate hydrolases / Winged helix-like DNA-binding domain superfamily / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / : / ATPase_2 domain-containing protein
Similarity search - Component
Biological speciesSulfolobus solfataricus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: Proteins / Year: 2009
Title: Crystal structure of a novel archaeal AAA+ ATPase SSO1545 from Sulfolobus solfataricus.
Authors: Xu, Q. / Rife, C.L. / Carlton, D. / Miller, M.D. / Krishna, S.S. / Elsliger, M.A. / Abdubek, P. / Astakhova, T. / Chiu, H.J. / Clayton, T. / Duan, L. / Feuerhelm, J. / Grzechnik, S.K. / ...Authors: Xu, Q. / Rife, C.L. / Carlton, D. / Miller, M.D. / Krishna, S.S. / Elsliger, M.A. / Abdubek, P. / Astakhova, T. / Chiu, H.J. / Clayton, T. / Duan, L. / Feuerhelm, J. / Grzechnik, S.K. / Hale, J. / Han, G.W. / Jaroszewski, L. / Jin, K.K. / Klock, H.E. / Knuth, M.W. / Kumar, A. / McMullan, D. / Morse, A.T. / Nigoghossian, E. / Okach, L. / Oommachen, S. / Paulsen, J. / Reyes, R. / van den Bedem, H. / Hodgson, K.O. / Wooley, J. / Deacon, A.M. / Godzik, A. / Lesley, S.A. / Wilson, I.A.
History
DepositionJan 10, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 7, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.3Jan 25, 2023Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_conn_type / 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 / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ...SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Conserved hypothetical protein
B: Conserved hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,46113
Polymers84,1242
Non-polymers1,33711
Water6,251347
1
A: Conserved hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,8869
Polymers42,0621
Non-polymers8248
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Conserved hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,5754
Polymers42,0621
Non-polymers5143
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.360, 108.350, 70.570
Angle α, β, γ (deg.)90.00, 100.31, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Conserved hypothetical protein


Mass: 42061.824 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Strain: P2 / Gene: 13814777 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / References: GenBank: 13814777, UniProt: Q97Y08*PLUS
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 347 / 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: 2.41 Å3/Da / Density % sol: 48.53 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop, nanodrop / pH: 9.5
Details: 20.0% PEG-8000, 0.1M CHES, pH 9.5, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.95372, 0.979996
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 31, 2005 / Details: Adjustable focusing mirrors in K-B geometry
RadiationMonochromator: DOUBLE CRYSTAL, SI(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.953721
20.9799961
ReflectionResolution: 2→69.5 Å / Num. obs: 53921 / % possible obs: 91.6 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 9.53
Reflection shell

Diffraction-ID: 1

Resolution (Å)% possible obs (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2-2.0779.60.4242.0510419851779.6
2.07-2.15850.5992.73109958992
2.15-2.2587.70.5993.42120029794
2.25-2.3790.50.5994.37121709971
2.37-2.5291.40.5995.391234310138
2.52-2.7193.10.5996.81121149964
2.71-2.9994.20.5999.61271110484
2.99-3.4296.70.59914.042179110512
3.42-4.398.40.59917.823339910680
4.3-69.598.70.59925.043356310852

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0005refinement
XSCALEdata scaling
PDB_EXTRACT1.601data extraction
XDSdata reduction
SHELXphasing
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2→69.5 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.94 / SU B: 8.233 / SU ML: 0.124 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.172 / ESU R Free: 0.161
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. ADP AND MG WERE MODELED BASED ON ELECTRON DENSITY AND THE PROTEIN'S PROPOSED FUNCTION AS AN ATPASE. 4. RESIDUES 115-119 ARE DISORDERED IN EACH CHAIN AND WERE NOT MODELED.
RfactorNum. reflection% reflectionSelection details
Rfree0.226 2733 5.1 %RANDOM
Rwork0.174 ---
all0.177 ---
obs0.17656 51161 97.51 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.569 Å2
Baniso -1Baniso -2Baniso -3
1--2.3 Å20 Å2-0.71 Å2
2--1.17 Å20 Å2
3---0.88 Å2
Refinement stepCycle: LAST / Resolution: 2→69.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5688 0 84 347 6119
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0225942
X-RAY DIFFRACTIONr_bond_other_d0.0010.025552
X-RAY DIFFRACTIONr_angle_refined_deg1.42528020
X-RAY DIFFRACTIONr_angle_other_deg0.818312865
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7725720
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.82723.791277
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.787151092
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0741543
X-RAY DIFFRACTIONr_chiral_restr0.0820.2884
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.026483
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021256
X-RAY DIFFRACTIONr_nbd_refined0.2140.21193
X-RAY DIFFRACTIONr_nbd_other0.1760.25483
X-RAY DIFFRACTIONr_nbtor_refined0.1850.22880
X-RAY DIFFRACTIONr_nbtor_other0.0820.23445
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1630.2321
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0180.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1190.27
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2180.253
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.120.212
X-RAY DIFFRACTIONr_mcbond_it1.96133629
X-RAY DIFFRACTIONr_mcbond_other0.48531440
X-RAY DIFFRACTIONr_mcangle_it2.92355686
X-RAY DIFFRACTIONr_scbond_it4.93482634
X-RAY DIFFRACTIONr_scangle_it6.568112324
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.295 203 -
Rwork0.236 3667 -
obs--94.81 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.4925-0.49420.39271.1371-0.16820.9742-0.01740.0343-0.09240.0755-0.05620.1694-0.02460.05240.0736-0.0904-0.06130.0265-0.0747-0.0038-0.1257-0.505150.276149.4028
21.8422-0.26080.21921.4717-0.11280.70580.11290.23310.0451-0.1593-0.05450.1436-0.03140.0556-0.0584-0.09230.04340.0037-0.0962-0.0193-0.1318.413548.846384.7034
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: all / Auth seq-ID: 0 - 356 / Label seq-ID: 1 - 357

IDRefine TLS-IDAuth asym-IDLabel asym-ID
11AA
22BB

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