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- PDB-4av6: Crystal structure of Thermotoga maritima sodium pumping membrane ... -

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Basic information

Entry
Database: PDB / ID: 4av6
TitleCrystal structure of Thermotoga maritima sodium pumping membrane integral pyrophosphatase at 4 A in complex with phosphate and magnesium
ComponentsK(+)-STIMULATED PYROPHOSPHATE-ENERGIZED SODIUM PUMP
KeywordsHYDROLASE / SODIUM PUMP / MEMBRANE PROTEIN
Function / homology
Function and homology information


Na+-exporting diphosphatase / diphosphate hydrolysis-driven proton transmembrane transporter activity / sodium ion transmembrane transporter activity / inorganic diphosphate phosphatase activity / potassium ion binding / sodium ion transmembrane transport / calcium ion binding / magnesium ion binding / protein homodimerization activity / membrane / plasma membrane
Similarity search - Function
Pyrophosphate-energised proton pump / Inorganic H+ pyrophosphatase
Similarity search - Domain/homology
: / PHOSPHATE ION / K(+)-stimulated pyrophosphate-energized sodium pump
Similarity search - Component
Biological speciesTHERMOTOGA MARITIMA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4 Å
AuthorsKajander, T. / Kellosalo, J. / Kogan, K. / Pokharel, K. / Goldman, A.
CitationJournal: Science / Year: 2012
Title: The Structure and Catalytic Cycle of a Sodium-Pumping Pyrophosphatase.
Authors: Kellosalo, J. / Kajander, T. / Kogan, K. / Pokharel, K. / Goldman, A.
History
DepositionMay 23, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 8, 2012Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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_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
A: K(+)-STIMULATED PYROPHOSPHATE-ENERGIZED SODIUM PUMP
B: K(+)-STIMULATED PYROPHOSPHATE-ENERGIZED SODIUM PUMP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)157,08716
Polymers156,4342
Non-polymers65314
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8020 Å2
ΔGint-184.8 kcal/mol
Surface area40470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.800, 112.266, 109.714
Angle α, β, γ (deg.)90.00, 103.00, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN A AND (RESSEQ 5:28 OR RESSEQ 38:113 OR RESSEQ 119:148 OR RESSEQ 600:726 )
211CHAIN B AND (RESSEQ 5:28 OR RESSEQ 38:113 OR RESSEQ 119:148 OR RESSEQ 600:726 )

NCS oper: (Code: given
Matrix: (0.87653, -0.02531, 0.48068), (-0.0263, -0.99964, -0.00468), (0.48063, -0.00854, -0.87688)
Vector: -12.81174, 32.84422, 52.47643)

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Components

#1: Protein K(+)-STIMULATED PYROPHOSPHATE-ENERGIZED SODIUM PUMP / MEMBRANE-BOUND SODIUM-TRANSLOCATING PYROPHOSPHATASE / PYROPHOSPHATE-ENERGIZED INORGANIC ...MEMBRANE-BOUND SODIUM-TRANSLOCATING PYROPHOSPHATASE / PYROPHOSPHATE-ENERGIZED INORGANIC PYROPHOSPHATASE / NA(+)-PPASE / TM-PPASE


Mass: 78217.141 Da / Num. of mol.: 2 / Fragment: RESIDUES 2-726 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) THERMOTOGA MARITIMA (bacteria) / Production host: SACCHAROMYCES CEREVISIAE (brewer's yeast) / Strain (production host): BJ1991 / References: UniProt: Q9S5X0, inorganic diphosphatase
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
Compound detailsENGINEERED RESIDUE IN CHAIN A, VAL 353 TO LEU ENGINEERED RESIDUE IN CHAIN A, SER 395 TO GLY ...ENGINEERED RESIDUE IN CHAIN A, VAL 353 TO LEU ENGINEERED RESIDUE IN CHAIN A, SER 395 TO GLY ENGINEERED RESIDUE IN CHAIN B, VAL 353 TO LEU ENGINEERED RESIDUE IN CHAIN B, SER 395 TO GLY
Nonpolymer detailsPOTASSIUM ION (K): MODELLED INTO THE FO-FC PEAK AT 4 A. MAGNESIUM ION (MG): MODELLED INTO THE FO-FC ...POTASSIUM ION (K): MODELLED INTO THE FO-FC PEAK AT 4 A. MAGNESIUM ION (MG): MODELLED INTO THE FO-FC PEAK AROUND THE PO4 MOLECULES AT 4 A ACCORDING TO OTHER PPASE COMPLEXES.

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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: 3.24 Å3/Da / Density % sol: 62 % / Description: NONE
Crystal growDetails: 35% PEG 400, 50 MM TRIS PH 8.0, 50 MM LISO4, 50 MM NASO4
PH range: PH 8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.873
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD
RadiationMonochromator: SI (111) MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 4→30 Å / Num. obs: 17075 / % possible obs: 98.2 % / Observed criterion σ(I): -3 / Redundancy: 4.3 % / Biso Wilson estimate: 178.27 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 8.85
Reflection shellResolution: 4→4.22 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.97 / Mean I/σ(I) obs: 1.82 / % possible all: 96.8

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: HIGH RESOLUTION RESTING STATE TMPPASE STRUCTURE

Resolution: 4→29.832 Å / SU ML: 1.7 / σ(F): 2.01 / Phase error: 43.81 / Stereochemistry target values: ML
Details: SOME DISORDERED REGIONS AND SOME SIDE CHAINS WERE MODELLED BASED ON HIGH RESOLUTION RESTING TMPPASE STRUCTURE USED AS THE SEARCH MODEL.
RfactorNum. reflection% reflection
Rfree0.365 863 5.1 %
Rwork0.2952 --
obs0.2988 17061 98.88 %
Solvent computationShrinkage radii: 0.49 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 154.483 Å2 / ksol: 0.235 e/Å3
Displacement parametersBiso mean: 239 Å2
Baniso -1Baniso -2Baniso -3
1-35.461 Å20 Å2-23.7725 Å2
2---24.6168 Å20 Å2
3----10.8441 Å2
Refinement stepCycle: LAST / Resolution: 4→29.832 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9376 0 30 0 9406
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.019606
X-RAY DIFFRACTIONf_angle_d2.16913080
X-RAY DIFFRACTIONf_dihedral_angle_d16.0513190
X-RAY DIFFRACTIONf_chiral_restr0.1111599
X-RAY DIFFRACTIONf_plane_restr0.0111611
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A1833X-RAY DIFFRACTIONPOSITIONAL
12B1833X-RAY DIFFRACTIONPOSITIONAL0.046
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4-4.24990.39491470.3652659X-RAY DIFFRACTION98
4.2499-4.5770.37951360.3142680X-RAY DIFFRACTION99
4.577-5.03560.42481330.30062717X-RAY DIFFRACTION99
5.0356-5.75980.43441570.33712682X-RAY DIFFRACTION99
5.7598-7.23950.37611390.28332729X-RAY DIFFRACTION99
7.2395-29.83230.32371510.27272731X-RAY DIFFRACTION99
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)
10.3930.0610.10360.1886-0.13190.2690.23080.1653-0.4616-0.27230.211-0.01140.36130.04110.6326-0.7858-0.34980.16150.4580.18130.87819.3004-0.241819.6878
20.5384-0.35940.21170.7396-0.11530.1414-0.1429-0.13050.2406-0.07520.3207-0.5918-1.1280.10230.03881.7622-0.0936-0.03710.6691-0.04830.67814.176932.571639.5443
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B

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