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- PDB-4x82: Crystal Structure of the Extracellular Domain of ZIP4 -

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Basic information

Entry
Database: PDB / ID: 4x82
TitleCrystal Structure of the Extracellular Domain of ZIP4
ComponentsZinc transporter ZIP4
KeywordsTRANSPORT PROTEIN / zinc transporter / extracellular domain
Function / homology
Function and homology information


zinc ion sensor activity / monoatomic cation:bicarbonate symporter activity / zinc ion import across plasma membrane / zinc ion transmembrane transporter activity / zinc ion transmembrane transport / intracellular zinc ion homeostasis / recycling endosome membrane / apical plasma membrane / metal ion binding / identical protein binding / plasma membrane
Similarity search - Function
Zinc transporter ZIP4, N-terminal / : / : / Zinc transporter ZIP4 domain / Zip protein EF-hand / Zinc/iron permease / ZIP Zinc transporter
Similarity search - Domain/homology
Zinc transporter ZIP4
Similarity search - Component
Biological speciesPteropus alecto (black flying fox)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.76 Å
AuthorsZhang, T. / Sui, D.X. / Hu, J.
CitationJournal: Nat Commun / Year: 2016
Title: Structural insights of ZIP4 extracellular domain critical for optimal zinc transport.
Authors: Zhang, T. / Sui, D. / Hu, J.
History
DepositionDec 9, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 15, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2017Group: Database references / Derived calculations
Category: citation / citation_author / pdbx_struct_oper_list
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Zinc transporter ZIP4
A: Zinc transporter ZIP4


Theoretical massNumber of molelcules
Total (without water)60,1312
Polymers60,1312
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3410 Å2
ΔGint-34 kcal/mol
Surface area21160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.182, 68.731, 93.971
Angle α, β, γ (deg.)90.000, 95.790, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21A

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: ASP / Beg label comp-ID: ASP / End auth comp-ID: CYS / End label comp-ID: CYS / Refine code: _ / Auth seq-ID: 42 - 305 / Label seq-ID: 7 - 270

Dom-IDAuth asym-IDLabel asym-ID
1BA
2AB

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Components

#1: Protein Zinc transporter ZIP4


Mass: 30065.699 Da / Num. of mol.: 2 / Fragment: Residues 36-322
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pteropus alecto (black flying fox) / Gene: PAL_GLEAN10010497 / Production host: Escherichia coli (E. coli) / Strain (production host): Origami (DE3) / References: UniProt: L5KLU7
Has protein modificationY

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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: 1.83 Å3/Da / Density % sol: 32.65 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 18% PEG 3350, 50 mM NH4Cl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.979 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 25, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.76→40 Å / Num. obs: 11028 / % possible obs: 99.4 % / Redundancy: 21.7 % / Rmerge(I) obs: 0.175 / Rpim(I) all: 0.038 / Rrim(I) all: 0.179 / Χ2: 0.986 / Net I/av σ(I): 20.885 / Net I/σ(I): 5.4 / Num. measured all: 239259
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.76-2.9180.92710430.9170.2140.9520.84294.9
2.9-3.02200.87910730.9390.1970.9020.8899.8
3.02-3.1521.50.73711460.9680.1610.7540.958100
3.15-3.3222.70.55510530.9750.1190.5681.017100
3.32-3.5322.90.3711290.9910.0790.3780.979100
3.53-3.822.90.25211010.9940.0540.2571.028100
3.8-4.1822.80.17911020.9960.0380.1831.037100
4.18-4.7922.60.12411170.9980.0270.1271.05999.9
4.79-6.0322.40.11611140.9980.0250.1191.041100
6.03-40210.06711500.9990.0150.0690.96799.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
SCALEPACKdata scaling
PDB_EXTRACT3.15data extraction
HKL-2000data scaling
PHASERphasing
RefinementResolution: 2.76→38.65 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.908 / SU B: 17.742 / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.423 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2639 1104 10 %RANDOM
Rwork0.2058 ---
obs0.2117 9913 98.17 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 139.63 Å2 / Biso mean: 58.555 Å2 / Biso min: 33.03 Å2
Baniso -1Baniso -2Baniso -3
1-7.49 Å2-0 Å20.55 Å2
2---3.61 Å2-0 Å2
3----3.91 Å2
Refinement stepCycle: final / Resolution: 2.76→38.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3078 0 0 0 3078
Num. residues----444
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0193140
X-RAY DIFFRACTIONr_bond_other_d0.0040.022951
X-RAY DIFFRACTIONr_angle_refined_deg1.441.9824302
X-RAY DIFFRACTIONr_angle_other_deg1.0836704
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4575434
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.06922.65398
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.25815403
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4171521
X-RAY DIFFRACTIONr_chiral_restr0.0710.2522
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213631
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02678
X-RAY DIFFRACTIONr_mcbond_it3.8266.0271766
X-RAY DIFFRACTIONr_mcbond_other3.8266.0261765
X-RAY DIFFRACTIONr_mcangle_it6.0779.0172190
Refine LS restraints NCS

Ens-ID: 1 / Number: 9067 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.16 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1B
2A
LS refinement shellResolution: 2.764→2.835 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.312 67 -
Rwork0.343 590 -
all-657 -
obs--78.49 %

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