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- PDB-2oaq: Crystal structure of the archaeal secretion ATPase GspE in comple... -

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Basic information

Entry
Database: PDB / ID: 2oaq
TitleCrystal structure of the archaeal secretion ATPase GspE in complex with phosphate
ComponentsType II secretion system protein
KeywordsHYDROLASE / Hexameric ATPase
Function / homology
Function and homology information


Beta-Lactamase - #380 / Type II/IV secretion system protein / Type II/IV secretion system protein / Beta-Lactamase / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Type II secretion system protein (GspE-2)
Similarity search - Component
Biological speciesArchaeoglobus fulgidus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 3.15 Å
AuthorsYamagata, A. / Tainer, J.A.
CitationJournal: Embo J. / Year: 2007
Title: Hexameric structures of the archaeal secretion ATPase GspE and implications for a universal secretion mechanism.
Authors: Yamagata, A. / Tainer, J.A.
History
DepositionDec 17, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 13, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
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 1.4Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / 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_conn.pdbx_leaving_atom_flag / _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

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Assembly

Deposited unit
1: Type II secretion system protein
2: Type II secretion system protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,1716
Polymers119,7912
Non-polymers3804
Water00
1
1: Type II secretion system protein
2: Type II secretion system protein
hetero molecules

1: Type II secretion system protein
2: Type II secretion system protein
hetero molecules

1: Type II secretion system protein
2: Type II secretion system protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)360,51318
Polymers359,3736
Non-polymers1,14012
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Unit cell
Length a, b, c (Å)132.608, 132.608, 445.283
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
DetailsThe biological assembly is a hexamer generated from the dimer in the asymmetric unit by the operations: y-x,-x,z and -y,x-y,z

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Components

#1: Protein Type II secretion system protein / GspE-2


Mass: 59895.570 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Strain: DSM 4304 / Plasmid: pET11 / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: O29598
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4

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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: 3.14 Å3/Da / Density % sol: 60.88 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.9
Details: 10% PEG 8000, 5% PEG 400, 1.5 M NaCl, 0.1 M Na/K phosphate, pH 8.9, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.97802
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 3, 2004
RadiationMonochromator: Double-crystal, Si(111) liquid N2 cooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97802 Å / Relative weight: 1
ReflectionResolution: 3.15→50.09 Å / Num. all: 25970 / Num. obs: 25970 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Redundancy: 6 % / Limit h max: 36 / Limit h min: 0 / Limit k max: 36 / Limit k min: 0 / Limit l max: 141 / Limit l min: 0 / Observed criterion F max: 99384.3 / Observed criterion F min: 0.32 / Rmerge(I) obs: 0.12 / Χ2: 0.975 / Net I/σ(I): 6
Reflection shellResolution: 3.15→3.26 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.478 / Mean I/σ(I) obs: 2.2 / Num. unique all: 2400 / Χ2: 0.528 / % possible all: 92.9

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNS1.1refinement
PDB_EXTRACT2data extraction
HKL-2000data collection
HKL-2000data reduction
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 3.15→20 Å / Rfactor Rfree error: 0.007 / Occupancy max: 1 / Occupancy min: 0.6 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.236 1200 4.5 %RANDOM
Rwork0.221 ---
all-26318 --
obs-24657 93.2 %-
Solvent computationSolvent model: CNS bulk solvent model used / Bsol: 21.179 Å2 / ksol: 0.270783 e/Å3
Displacement parametersBiso max: 127.81 Å2 / Biso mean: 60.691 Å2 / Biso min: 19.78 Å2
Baniso -1Baniso -2Baniso -3
1-18.741 Å2-6.005 Å20 Å2
2--18.741 Å20 Å2
3----37.482 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.38 Å0.36 Å
Luzzati d res low-5 Å
Luzzati sigma a0.57 Å0.61 Å
Luzzati d res high-3.16
Refinement stepCycle: LAST / Resolution: 3.15→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7977 0 20 0 7997
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_angle_deg1.5
X-RAY DIFFRACTIONx_torsion_deg23.2
X-RAY DIFFRACTIONx_torsion_impr_deg0.92
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRfactor Rfree errorNum. reflection allNum. reflection obs% reflection obs (%)
3.15-3.30.3251405.40.3324320.0273231257279.6
3.3-3.470.2781324.60.29527480.0243242288088.8
3.47-3.690.241394.60.25129150.023273305493.3
3.69-3.970.251504.80.20929600.023255311095.5
3.97-4.370.2191645.20.18929990.0173261316397
4.37-4.990.1981584.90.17330800.0163298323898.2
4.99-6.260.2291544.70.2131120.0183326326698.2
6.26-19.980.231634.80.22532110.0183440337498.1
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2po4_xplor.parpo4_xplor.top

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