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- PDB-3aon: Crystal structure of the central axis (NtpD-NtpG) in the catalyti... -

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Basic information

Entry
Database: PDB / ID: 3aon
TitleCrystal structure of the central axis (NtpD-NtpG) in the catalytic portion of Enterococcus hirae V-type sodium ATPase
Components
  • V-type sodium ATPase subunit D
  • V-type sodium ATPase subunit G
KeywordsHYDROLASE / V-ATPase / Enterococcus / Coiled-coil / Alpha/beta fold / Na(+)-ATPase / NtpA3-NtpB3 / NtpC / central axis
Function / homology
Function and homology information


proton motive force-driven plasma membrane ATP synthesis / sodium ion transport / proton-transporting ATPase activity, rotational mechanism / proton-transporting ATP synthase activity, rotational mechanism / ATP binding
Similarity search - Function
Helix Hairpins - #3240 / ATPase, V1 complex, subunit F / ATPase, V1 complex, subunit F, bacterial/archaeal / ATPase, V1 complex, subunit D / ATPase, V1 complex, subunit F / ATPase, V1 complex, subunit F superfamily / ATP synthase subunit D / ATP synthase (F/14-kDa) subunit / Helix Hairpins / Rossmann fold ...Helix Hairpins - #3240 / ATPase, V1 complex, subunit F / ATPase, V1 complex, subunit F, bacterial/archaeal / ATPase, V1 complex, subunit D / ATPase, V1 complex, subunit F / ATPase, V1 complex, subunit F superfamily / ATP synthase subunit D / ATP synthase (F/14-kDa) subunit / Helix Hairpins / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
NITRATE ION / V-type sodium ATPase subunit D / V-type sodium ATPase subunit G
Similarity search - Component
Biological speciesEnterococcus hirae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsSaijo, S. / Arai, S. / Hossain, K.M.M. / Yamato, I. / Kakinuma, Y. / Ishizuka-Katsura, Y. / Terada, T. / Shirouzu, M. / Yokoyama, S. / Iwata, S. / Murata, T.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2011
Title: Crystal structure of the central axis DF complex of the prokaryotic V-ATPase
Authors: Saijo, S. / Arai, S. / Hossain, K.M.M. / Yamato, I. / Suzuki, K. / Kakinuma, Y. / Ishizuka-Katsura, Y. / Ohsawa, N. / Terada, T. / Shirouzu, M. / Yokoyama, S. / Iwata, S. / Murata, T.
History
DepositionOct 4, 2010Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 5, 2011Provider: repository / Type: Initial release
Revision 1.1Dec 28, 2011Group: Database references
Revision 1.2Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq / 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_entry_details.has_protein_modification / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _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: V-type sodium ATPase subunit D
B: V-type sodium ATPase subunit G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,4333
Polymers38,3712
Non-polymers621
Water2,738152
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4230 Å2
ΔGint-32 kcal/mol
Surface area15610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.787, 68.433, 51.153
Angle α, β, γ (deg.)90.00, 114.99, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-239-

HOH

21A-295-

HOH

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Components

#1: Protein V-type sodium ATPase subunit D / Na(+)-translocating ATPase subunit D / V-type sodium pump subunit D


Mass: 25587.996 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus hirae (bacteria) / Gene: ntpD / Production host: Cell free synthesis
References: UniProt: P43435*PLUS, H+-transporting two-sector ATPase
#2: Protein V-type sodium ATPase subunit G / Na(+)-translocating ATPase subunit G / V-type sodium pump subunit G


Mass: 12783.129 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus hirae (bacteria) / Gene: ntpG, ntpQ / Production host: Cell free synthesis
References: UniProt: P43455, H+-transporting two-sector ATPase
#3: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 152 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsA SEQUENCE DATABASE REFERENCE FOR THIS PROTEIN DOES NOT CURRENTLY EXIST AND WILL BE DEPOSITED TO ...A SEQUENCE DATABASE REFERENCE FOR THIS PROTEIN DOES NOT CURRENTLY EXIST AND WILL BE DEPOSITED TO DATABASE. THE N-TERMINAL GSSGSSG ARE EXPRESSION TAGS.

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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: 2.19 Å3/Da / Density % sol: 43.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 18% PEG 3350, 0.2 M Sodium Nitrate, 0.1M MES-Tris, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.9791, 0.9794, 1.0000
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Jul 17, 2009
RadiationMonochromator: Rotated-inclined double-crystal monochromator
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97911
20.97941
311
ReflectionResolution: 2→34.16 Å / Num. all: 21698 / Num. obs: 21698 / % possible obs: 97.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.1 % / Biso Wilson estimate: 29 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 10.7
Reflection shellResolution: 2→2.11 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.561 / Mean I/σ(I) obs: 2.8 / Num. unique all: 3128 / % possible all: 96.3

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Processing

Software
NameVersionClassification
BSSdata collection
SOLVEphasing
REFMAC5.5.0110refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2→31.98 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.922 / SU B: 10.876 / SU ML: 0.135 / Cross valid method: THROUGHOUT / ESU R Free: 0.179 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.25161 1085 5 %RANDOM
Rwork0.19445 ---
all0.1974 22398 --
obs0.1974 21696 96.87 %-
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: 41.498 Å2
Baniso -1Baniso -2Baniso -3
1--0.45 Å20 Å2-3.3 Å2
2---1.54 Å20 Å2
3----0.8 Å2
Refinement stepCycle: LAST / Resolution: 2→31.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2284 0 4 152 2440
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0222332
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2761.9873149
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0195289
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.26725.619105
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.46815452
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.4111512
X-RAY DIFFRACTIONr_chiral_restr0.0910.2373
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211698
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6781.51447
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.30622351
X-RAY DIFFRACTIONr_scbond_it2.0093885
X-RAY DIFFRACTIONr_scangle_it3.3994.5797
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.002→2.054 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.29 67 -
Rwork0.263 1503 -
obs-1570 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)
12.14-1.7672-3.1311.96182.84554.8242-0.0966-0.0307-0.07230.1435-0.1048-0.01940.07930.11190.20140.3152-0.0326-0.07410.32780.12250.29260.8338-32.601423.1548
20.60190.03171.19081.9910.91612.8555-0.1423-0.12050.08130.2453-0.0930.2903-0.0466-0.34840.23520.1773-0.010.08920.339-0.08530.2887-9.6583-1.041659.2585
30.0540.01590.04627.97738.03218.36140.1452-0.00190.00170.05590.0964-0.23180.09840.1075-0.24160.31720.0305-0.03870.2439-0.03590.27225.1259-16.74447.1255
44.99130.0720.70353.92152.33931.50910.4351-0.0198-0.44590.4802-0.4335-0.110.3707-0.3596-0.00160.5116-0.0914-0.01290.2212-0.07310.19745.8031-7.858467.5634
50.1459-0.05880.24042.05793.35876.45560.0599-0.03420.0279-0.0415-0.04260.07410.0359-0.067-0.01730.2519-0.030.02890.2889-0.00670.2635-4.669-14.50242.3793
66.2624-5.9525-9.318710.54148.795813.86810.37570.3683-0.3921-0.5849-0.98230.2095-0.5263-0.53880.60660.30410.39190.02020.57560.00730.06025.2918-38.4763-0.3754
70.6580.30991.062.10281.0071.9217-0.1426-0.00080.2285-0.0111-0.0981-0.1288-0.18870.08860.24070.2246-0.00770.01070.2411-0.00030.29330.25812.888149.2394
80.3737-0.25260.20611.63860.85231.5397-0.05040.02950.0866-0.0993-0.13240.0695-0.0709-0.03030.18280.19080.00890.02470.3001-0.02060.2845-5.3536-2.361642.9431
93.1591.65211.61128.51739.845111.4201-0.0578-0.12460.5062-0.0898-0.36080.3945-0.0477-0.44370.41860.3032-0.0521-0.02130.28330.00540.2534-14.3935-13.786834.5758
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 43
2X-RAY DIFFRACTION2A44 - 85
3X-RAY DIFFRACTION3A86 - 106
4X-RAY DIFFRACTION4A107 - 122
5X-RAY DIFFRACTION5A123 - 178
6X-RAY DIFFRACTION6A179 - 194
7X-RAY DIFFRACTION7B1 - 42
8X-RAY DIFFRACTION8B43 - 86
9X-RAY DIFFRACTION9B87 - 101

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