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- PDB-4av3: Crystal structure of Thermotoga Maritima sodium pumping membrane ... -

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Basic information

Entry
Database: PDB / ID: 4av3
TitleCrystal structure of Thermotoga Maritima sodium pumping membrane integral pyrophosphatase with metal ions in active site
ComponentsK(+)-STIMULATED PYROPHOSPHATE-ENERGIZED SODIUM PUMP
KeywordsHYDROLASE / MEMBRANE PYROPHOSPHOTASE / ION PUMP
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
K(+)-stimulated pyrophosphate-energized sodium pump
Similarity search - Component
Biological speciesTHERMOTOGA MARITIMA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsKajander, T. / Kogan, K. / Kellosalo, J. / 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 1.1Jan 17, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.2May 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.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

Downloads & links

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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)156,5636
Polymers156,4342
Non-polymers1294
Water34219
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6040 Å2
ΔGint-113.1 kcal/mol
Surface area43010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.520, 107.779, 102.521
Angle α, β, γ (deg.)90.00, 108.50, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.587, 0.021, -0.809), (0.016, -1, -0.014), (-0.809, -0.005, -0.587)
Vector: 22.25765, 153.78954, 47.42078)

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Components

#1: Protein K(+)-STIMULATED PYROPHOSPHATE-ENERGIZED SODIUM PUMP / MEMBRANE INTEGRAL PYROPHOSPHATASE MEMBRANE-BOUND SODIUM-TRANSLOCATING PYROPHOSPHATASE / ...MEMBRANE INTEGRAL PYROPHOSPHATASE 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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 19 / Source method: isolated from a natural source / Formula: H2O
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

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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: 2.96 Å3/Da / Density % sol: 58.43 %
Description: INITIALLY THE STRUCTURE WAS DETERMINED BY MIRAS USING TWO DIFFERENT DERIVATIVES. THEN UTILIZING 3.3 A NATIVE DATASET THE PHASES WERE EXTENDED AND BACKBONE HELICAL MODEL WAS BUILD. THIS ...Description: INITIALLY THE STRUCTURE WAS DETERMINED BY MIRAS USING TWO DIFFERENT DERIVATIVES. THEN UTILIZING 3.3 A NATIVE DATASET THE PHASES WERE EXTENDED AND BACKBONE HELICAL MODEL WAS BUILD. THIS MODEL WAS USED AS A STARTING MODEL WITH ROSETTA-MR IMPLEMENTED IN PHENIX.
Crystal growDetails: 19-22% PEG 350, 0.1 M MES-NAOH PH 6.5, 0.2 M CA2CL, 2 MM DTT

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 1
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 10, 2012
Details: RH-COATED SI MIRROR AND RH- COATED TOROIDAL SI MIRROR
RadiationMonochromator: SI (111) DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 49279 / % possible obs: 97.8 % / Observed criterion σ(I): 2 / Redundancy: 7.43 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 22.7
Reflection shellResolution: 2.6→2.76 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.84 / Mean I/σ(I) obs: 2.14 / % possible all: 95.1

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Processing

Software
NameClassification
REFMACmodel building
XDSdata reduction
XDSdata scaling
SHELXCDphasing
SHELXDphasing
SHARPphasing
REFMACphasing
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: OUR BACKBONE HELICAL LOW RESOLUTION MODEL

Resolution: 2.6→50 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.935 / SU B: 24.872 / SU ML: 0.239 / Cross valid method: THROUGHOUT / ESU R: 0.564 / ESU R Free: 0.294 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.24478 2622 5.1 %RANDOM
Rwork0.20458 ---
obs0.20658 49279 97.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 71.691 Å2
Baniso -1Baniso -2Baniso -3
1--6.51 Å20 Å21.57 Å2
2---0.08 Å20 Å2
3---7.58 Å2
Refinement stepCycle: LAST / Resolution: 2.6→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9965 0 4 19 9988
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0210170
X-RAY DIFFRACTIONr_bond_other_d0.0050.026296
X-RAY DIFFRACTIONr_angle_refined_deg1.7031.96513879
X-RAY DIFFRACTIONr_angle_other_deg1.281315492
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.35651393
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.91723.912294
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.878151431
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9941513
X-RAY DIFFRACTIONr_chiral_restr0.0960.21682
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02111541
X-RAY DIFFRACTIONr_gen_planes_other0.0040.022092
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.305 187 -
Rwork0.293 3276 -
obs--91.28 %
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)
13.91340.30240.24352.34030.06172.1679-0.14490.8911-0.5391-0.5907-0.0181-0.10720.0653-0.15130.16310.2633-0.02560.05240.2261-0.13970.095-2.484968.388910.1976
22.789-0.3182-0.07892.19010.56822.3642-0.1487-0.70470.52590.24470.1059-0.5852-0.31180.28440.04280.20520.0308-0.14490.2246-0.11780.26215.018785.322842.3976
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 726
2X-RAY DIFFRACTION2B2 - 726

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