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- PDB-3zq6: ADP-ALF4 COMPLEX OF M. THERM. TRC40 -

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Basic information

Entry
Database: PDB / ID: 3zq6
TitleADP-ALF4 COMPLEX OF M. THERM. TRC40
ComponentsPUTATIVE ARSENICAL PUMP-DRIVING ATPASE
KeywordsHYDROLASE / TAIL-ANCHORED / MEMBRANE PROTEIN / TARGETING FACTOR ATP-BINDING / ARSA / NUCLEOTIDE-BINDING
Function / homology
Function and homology information


arsenite-transporting ATPase / ATPase-coupled arsenite transmembrane transporter activity / ATP hydrolysis activity / ATP binding
Similarity search - Function
Arsenical pump ATPase, ArsA/GET3 / Anion-transporting ATPase-like domain / Anion-transporting ATPase / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / TETRAFLUOROALUMINATE ION / : / Putative arsenical pump-driving ATPase
Similarity search - Component
Biological speciesMETHANOTHERMOBACTER THERMAUTOTROPHICUS (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.107 Å
AuthorsSherrill, J. / Mariappan, M. / Dominik, P. / Hegde, R.S. / Keenan, R.J.
CitationJournal: Traffic / Year: 2011
Title: A Conserved Archaeal Pathway for Tail-Anchored Membrane Protein Insertion.
Authors: Sherrill, J. / Mariappan, M. / Dominik, P. / Hegde, R.S. / Keenan, R.J.
History
DepositionJun 8, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 22, 2011Provider: repository / Type: Initial release
Revision 1.1Aug 3, 2011Group: Derived calculations / Non-polymer description
Revision 1.2Aug 24, 2011Group: Database references
Revision 1.3Dec 20, 2023Group: 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_asym_id / _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_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_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_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_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: PUTATIVE ARSENICAL PUMP-DRIVING ATPASE
B: PUTATIVE ARSENICAL PUMP-DRIVING ATPASE
C: PUTATIVE ARSENICAL PUMP-DRIVING ATPASE
D: PUTATIVE ARSENICAL PUMP-DRIVING ATPASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)148,86122
Polymers146,3564
Non-polymers2,50518
Water8,215456
1
A: PUTATIVE ARSENICAL PUMP-DRIVING ATPASE
B: PUTATIVE ARSENICAL PUMP-DRIVING ATPASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,43011
Polymers73,1782
Non-polymers1,2539
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8120 Å2
ΔGint-97 kcal/mol
Surface area25490 Å2
MethodPISA
2
C: PUTATIVE ARSENICAL PUMP-DRIVING ATPASE
D: PUTATIVE ARSENICAL PUMP-DRIVING ATPASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,43011
Polymers73,1782
Non-polymers1,2539
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7950 Å2
ΔGint-92.4 kcal/mol
Surface area26190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)206.948, 49.768, 147.363
Angle α, β, γ (deg.)90.00, 115.04, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-2055-

HOH

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
PUTATIVE ARSENICAL PUMP-DRIVING ATPASE / ATPASE TRC40 / TRC40 / ARSENICAL RESISTANCE ATPASE / ARSENITE-TRANSLOCATING ATPASE / ARSENITE- ...ATPASE TRC40 / TRC40 / ARSENICAL RESISTANCE ATPASE / ARSENITE-TRANSLOCATING ATPASE / ARSENITE-TRANSPORTING ATPASE / GET3 / ARR4 / ASNA-1 / ATPASE SUBUNIT OF THE GET COMPLEX /


Mass: 36588.883 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) METHANOTHERMOBACTER THERMAUTOTROPHICUS (archaea)
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PRIL / References: UniProt: O27555, EC: 3.6.3.16

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Non-polymers , 6 types, 474 molecules

#2: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical
ChemComp-ALF / TETRAFLUOROALUMINATE ION


Mass: 102.975 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: AlF4
#4: Chemical
ChemComp-MG / MAGNESIUM ION


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


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#6: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 456 / 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: 2.4 Å3/Da / Density % sol: 48 % / Description: NONE
Crystal growpH: 7
Details: 34% PENTAERYTHRITOL PROPOXYLATE, 50 MM HEPES PH 7.0 AND 25 MM KCL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97856
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 2, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 77439 / % possible obs: 96.3 % / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 30.69 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 19.5
Reflection shellResolution: 2.11→2.15 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 1.7 / % possible all: 51.9

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2WOJ

2woj


Resolution: 2.107→41.206 Å / SU ML: 0.57 / σ(F): 1.34 / Phase error: 22.01 / Stereochemistry target values: ML
Details: DISORDERED SIDECHAINS WERE MODELED STEREOCHEMICALLY
RfactorNum. reflection% reflection
Rfree0.2214 3881 5 %
Rwork0.173 --
obs0.1755 77439 97.48 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 37.328 Å2 / ksol: 0.315 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.1841 Å20 Å2-1.4782 Å2
2---8.1905 Å20 Å2
3---8.0064 Å2
Refinement stepCycle: LAST / Resolution: 2.107→41.206 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9323 0 138 456 9917
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0099639
X-RAY DIFFRACTIONf_angle_d1.23412957
X-RAY DIFFRACTIONf_dihedral_angle_d14.183759
X-RAY DIFFRACTIONf_chiral_restr0.0761421
X-RAY DIFFRACTIONf_plane_restr0.0051645
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.107-2.13270.3234720.23641919X-RAY DIFFRACTION70
2.1327-2.15960.26991230.2142336X-RAY DIFFRACTION87
2.1596-2.18810.26921540.20472371X-RAY DIFFRACTION91
2.1881-2.2180.23151250.19512497X-RAY DIFFRACTION94
2.218-2.24970.22861250.19012606X-RAY DIFFRACTION96
2.2497-2.28330.27021400.2012571X-RAY DIFFRACTION97
2.2833-2.3190.24871340.19562620X-RAY DIFFRACTION98
2.319-2.3570.23191440.19172672X-RAY DIFFRACTION99
2.357-2.39760.24251230.18412670X-RAY DIFFRACTION100
2.3976-2.44120.24721390.18232644X-RAY DIFFRACTION100
2.4412-2.48820.22051540.16422724X-RAY DIFFRACTION100
2.4882-2.5390.25691330.17622653X-RAY DIFFRACTION100
2.539-2.59420.24731520.16782704X-RAY DIFFRACTION100
2.5942-2.65450.23271270.16752666X-RAY DIFFRACTION100
2.6545-2.72090.22671570.1762659X-RAY DIFFRACTION100
2.7209-2.79440.23741580.18172678X-RAY DIFFRACTION100
2.7944-2.87660.23361360.19242681X-RAY DIFFRACTION100
2.8766-2.96940.26551250.19012705X-RAY DIFFRACTION100
2.9694-3.07550.23611430.18582681X-RAY DIFFRACTION100
3.0755-3.19860.241620.17992655X-RAY DIFFRACTION100
3.1986-3.34410.21971470.16822720X-RAY DIFFRACTION100
3.3441-3.52040.24021320.17342710X-RAY DIFFRACTION100
3.5204-3.74080.1791310.15882710X-RAY DIFFRACTION100
3.7408-4.02940.21151280.15092711X-RAY DIFFRACTION100
4.0294-4.43450.20281610.15092720X-RAY DIFFRACTION100
4.4345-5.07510.1821540.14172737X-RAY DIFFRACTION100
5.0751-6.39030.22581460.18932741X-RAY DIFFRACTION100
6.3903-41.2140.18981560.17612797X-RAY DIFFRACTION98
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)
10.52850.0216-0.18080.11630.11020.72480.00290.07650.07190.04010.03380.0393-0.0271-0.09020.0090.0598-0.00470.01430.09960.03920.135534.8253-16.405365.5275
20.9321-0.102-0.16110.70950.25180.7955-0.0022-0.0316-0.04550.21340.0888-0.12220.21380.03710.04640.15760.0106-0.05050.08860.01810.13152.5896-31.552176.2591
30.92170.0624-0.36950.7291-0.21170.7808-0.16660.1094-0.00480.16350.2371-0.10870.1101-0.20780.02420.34190.0093-0.00480.2948-0.02890.10662.7349-15.124411.3075
40.7013-0.2494-0.11530.21780.63540.5370.1194-0.03490.29480.14840.3531-0.7377-0.25350.04760.06610.3034-0.01960.0370.2396-0.19830.504384.0484-0.61748.4208
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B
3X-RAY DIFFRACTION3CHAIN C
4X-RAY DIFFRACTION4CHAIN D

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