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- PDB-4umw: CRYSTAL STRUCTURE OF A ZINC-TRANSPORTING PIB-TYPE ATPASE IN E2.PI... -

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Basic information

Entry
Database: PDB / ID: 4umw
TitleCRYSTAL STRUCTURE OF A ZINC-TRANSPORTING PIB-TYPE ATPASE IN E2.PI STATE
ComponentsZINC-TRANSPORTING ATPASE
KeywordsHYDROLASE / CPC / CXXC / ATP-BINDING / ION TRANSPORT / MAGNESIUM / ZN2+ / METAL-BINDING / NUCLEOTIDE-BINDING / TRANSMEMBRANE / TRANSPORT / HEAVY-METAL BINDING / P-TYPE ATPASE / PIB-ATPASE / ZN2+ EXPORTING / ZINC TRANSPORT / PI-ATPASE / MEMBRANE PROTEIN
Function / homology
Function and homology information


Cd2+-exporting ATPase / P-type Zn2+ transporter / P-type zinc transporter activity / P-type cadmium transporter activity / Translocases; Catalysing the translocation of inorganic cations; Linked to the hydrolysis of a nucleoside triphosphate / zinc ion transport / ATP hydrolysis activity / ATP binding / metal ion binding / plasma membrane
Similarity search - Function
P-type ATPase, subfamily IB / Calcium-transporting ATPase, cytoplasmic transduction domain A / Calcium-transporting ATPase, cytoplasmic transduction domain A / Calcium-transporting ATPase, cytoplasmic domain N / Calcium-transporting ATPase, cytoplasmic domain N / Heavy-metal-associated, conserved site / Heavy-metal-associated domain. / Heavy-metal-associated domain / Heavy metal-associated domain superfamily / Heavy-metal-associated domain profile. ...P-type ATPase, subfamily IB / Calcium-transporting ATPase, cytoplasmic transduction domain A / Calcium-transporting ATPase, cytoplasmic transduction domain A / Calcium-transporting ATPase, cytoplasmic domain N / Calcium-transporting ATPase, cytoplasmic domain N / Heavy-metal-associated, conserved site / Heavy-metal-associated domain. / Heavy-metal-associated domain / Heavy metal-associated domain superfamily / Heavy-metal-associated domain profile. / Heavy metal-associated domain, HMA / E1-E2 ATPase / P-type ATPase, haloacid dehalogenase domain / P-type ATPase, phosphorylation site / P-type ATPase, cytoplasmic domain N / E1-E2 ATPases phosphorylation site. / P-type ATPase, A domain superfamily / P-type ATPase / P-type ATPase, transmembrane domain superfamily / haloacid dehalogenase-like hydrolase / HAD superfamily/HAD-like / HAD superfamily / HAD-like superfamily / Distorted Sandwich / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
TETRAFLUOROALUMINATE ION / Zinc/cadmium/lead-transporting P-type ATPase
Similarity search - Component
Biological speciesSHIGELLA SONNEI (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.705 Å
AuthorsWang, K.T. / Sitsel, O. / Meloni, G. / Autzen, H.E. / Andersson, M. / Klymchuk, T. / Nielsen, A.M. / Rees, D.C. / Nissen, P. / Gourdon, P.
CitationJournal: Nature / Year: 2014
Title: Structure and Mechanism of Zn(2+)-Transporting P-Type Atpases.
Authors: Wang, K. / Sitsel, O. / Meloni, G. / Autzen, H.E. / Andersson, M. / Klymchuk, T. / Nielsen, A.M. / Rees, D.C. / Nissen, P. / Gourdon, P.
History
DepositionMay 21, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 13, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 27, 2014Group: Database references
Revision 1.2Oct 29, 2014Group: Database references
Revision 1.3Jan 10, 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: ZINC-TRANSPORTING ATPASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,9693
Polymers76,8421
Non-polymers1272
Water1,00956
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)77.641, 83.560, 319.818
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein ZINC-TRANSPORTING ATPASE / ZINC EFFLUX ATPASE


Mass: 76841.508 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SHIGELLA SONNEI (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): C43 / References: UniProt: Q3YW59, EC: 3.6.3.5
#2: Chemical ChemComp-ALF / TETRAFLUOROALUMINATE ION


Mass: 102.975 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: AlF4
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 56 / 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: 3.38 Å3/Da / Density % sol: 63.56 % / Description: NONE
Crystal growDetails: 300 MM LITHIUM ACETATE, 3% V/V T-BUOH, 14 % POLY ETHYLENE GLYCOL 2000 MONOMETHYL ETHER (PEG2000-MME), 7 % V/V SORBITOL,10 % V/V GLYCEROL AND 5 MM BME

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 24, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→30 Å / Num. obs: 28953 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Redundancy: 4.6 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 15.47
Reflection shellResolution: 2.7→2.87 Å / Redundancy: 4.5 % / Rmerge(I) obs: 1.12 / Mean I/σ(I) obs: 1.11 / % possible all: 99.1

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3RFU

3rfu


Resolution: 2.705→46.347 Å / SU ML: 0.39 / σ(F): 1.06 / Phase error: 30.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2406 2725 5 %
Rwork0.2243 --
obs0.2251 28861 98.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.705→46.347 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4421 0 6 56 4483
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054519
X-RAY DIFFRACTIONf_angle_d0.9326157
X-RAY DIFFRACTIONf_dihedral_angle_d15.531626
X-RAY DIFFRACTIONf_chiral_restr0.059767
X-RAY DIFFRACTIONf_plane_restr0.004786
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7047-2.75390.45561410.41092588X-RAY DIFFRACTION95
2.7539-2.80680.43041420.4022709X-RAY DIFFRACTION99
2.8068-2.86410.40751450.38652756X-RAY DIFFRACTION99
2.8641-2.92640.43051410.3622649X-RAY DIFFRACTION99
2.9264-2.99450.35091500.35262814X-RAY DIFFRACTION99
2.9945-3.06930.38891360.33522612X-RAY DIFFRACTION99
3.0693-3.15230.34311500.30952766X-RAY DIFFRACTION99
3.1523-3.2450.31251360.3012641X-RAY DIFFRACTION98
3.245-3.34970.30821490.29012803X-RAY DIFFRACTION99
3.3497-3.46940.34361380.27352623X-RAY DIFFRACTION99
3.4694-3.60830.33691470.22732753X-RAY DIFFRACTION99
3.6083-3.77240.22781430.22312748X-RAY DIFFRACTION99
3.7724-3.97120.22381390.2082699X-RAY DIFFRACTION99
3.9712-4.21990.18071460.19872707X-RAY DIFFRACTION99
4.2199-4.54540.1941400.18042715X-RAY DIFFRACTION99
4.5454-5.00240.20271440.16762737X-RAY DIFFRACTION99
5.0024-5.72510.22831470.20482747X-RAY DIFFRACTION99
5.7251-7.20870.20131430.20682696X-RAY DIFFRACTION99
7.2087-46.35390.15651480.17012716X-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)
11.2331-0.1686-1.62940.7776-0.38692.21830.05680.1625-0.2475-0.58460.22210.14850.31650.0951-0.53761.68280.1081-0.14141.06780.07930.709581.0461113.84113.7455
21.6788-0.4024-2.39711.01721.02015.26020.07940.18830.1921-0.45380.32790.0219-0.98640.1024-0.30241.5593-0.0861-0.1060.59060.06320.622884.9999105.4387.6516
33.93682.20011.7218.20251.6854.14570.3144-0.41070.5341.0077-0.49030.7547-0.2369-0.09830.19860.7446-0.22640.15480.4697-0.07760.410282.6714106.067364.8443
42.042-0.60810.04823.21390.39052.9688-0.09410.5420.3117-1.32020.1484-0.356-1.73561.9191-0.31351.0262-0.35420.12730.9404-0.04630.577991.1581101.099743.7345
54.595-0.0371-4.43611.7480.49886.3336-0.23330.30220.3262-0.94530.1890.0562-0.3513-0.01110.02771.4641-0.11510.05480.7187-0.01710.364491.148397.28922.9013
62.45121.45050.02144.3926-0.62737.3687-0.16190.36960.2446-0.89540.3184-0.149-0.48070.4087-0.09150.7179-0.12910.00930.4277-0.02230.348779.373287.867837.4
77.3524-0.89111.13734.6825-0.7253.50970.13-0.67370.36770.2236-0.08420.21110.4115-0.3131-0.08840.7502-0.23210.09230.4056-0.0940.362165.06182.041272.14
83.04820.96041.09153.9905-0.0586.48780.03330.1962-0.2904-0.1447-0.0863-0.08740.72180.34760.00350.6721-0.05130.10360.4051-0.07390.25581.394985.815144.5393
90.97190.2096-2.26440.5852-0.2943.0145-0.43660.2082-0.4668-0.4046-0.17050.02950.83230.03520.55941.1379-0.07670.01140.8033-0.04590.462881.259586.315513.1492
104.67-0.4102-2.74762.48461.12782.4267-0.48840.71630.4879-0.69810.15180.15450.4885-0.99380.4090.9743-0.1077-0.14010.8129-0.06710.405275.635492.00784.9464
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND ((RESSEQ 124:179))
2X-RAY DIFFRACTION2CHAIN A AND ((RESSEQ 180:223))
3X-RAY DIFFRACTION3CHAIN A AND ((RESSEQ 228:321))
4X-RAY DIFFRACTION4CHAIN A AND ((RESSEQ 322:343))
5X-RAY DIFFRACTION5CHAIN A AND ((RESSEQ 344:415))
6X-RAY DIFFRACTION6CHAIN A AND ((RESSEQ 416:444))
7X-RAY DIFFRACTION7CHAIN A AND ((RESSEQ 445:560))
8X-RAY DIFFRACTION8CHAIN A AND ((RESSEQ 561:663))
9X-RAY DIFFRACTION9CHAIN A AND ((RESSEQ 664:705))
10X-RAY DIFFRACTION10CHAIN A AND ((RESSEQ 706:730))

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