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- PDB-1xk8: Divalent cation tolerant protein CUTA from Homo sapiens O60888 -

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Basic information

Entry
Database: PDB / ID: 1xk8
TitleDivalent cation tolerant protein CUTA from Homo sapiens O60888
ComponentsDivalent cation tolerant protein CUTA
Keywordsstructural genomics / unknown function / human / Homo sapiens / divalent cation tolerant protein CUTA / PSI / Protein Structure Initiative / Southeast Collaboratory for Structural Genomics / SECSG
Function / homology
Function and homology information


response to metal ion / protein localization / copper ion binding / enzyme binding / extracellular exosome / membrane
Similarity search - Function
Divalent ion tolerance protein, CutA / CutA1 divalent ion tolerance protein / Alpha-Beta Plaits - #120 / Nitrogen regulatory PII-like, alpha/beta / Nitrogen regulatory protein PII/ATP phosphoribosyltransferase, C-terminal / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.7 Å
AuthorsTempel, W. / Chen, L. / Liu, Z.-J. / Lee, D. / Shah, A. / Dailey, T.A. / Mayer, M.R. / Arendall III, W.B. / Rose, J.P. / Dailey, H.A. ...Tempel, W. / Chen, L. / Liu, Z.-J. / Lee, D. / Shah, A. / Dailey, T.A. / Mayer, M.R. / Arendall III, W.B. / Rose, J.P. / Dailey, H.A. / Richardson, J.S. / Richardson, D.C. / Wang, B.-C. / Southeast Collaboratory for Structural Genomics (SECSG)
CitationJournal: To be published
Title: Divalent cation tolerant protein CUTA from Homo sapiens O60888
Authors: Tempel, W. / Chen, L. / Liu, Z.-J. / Lee, D. / Shah, A. / Dailey, T.A. / Mayer, M.R. / Arendall III, W.B. / Rose, J.P. / Dailey, H.A. / Richardson, J.S. / Richardson, D.C. / Wang, B.-C.
History
DepositionSep 27, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 19, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.ptnr1_symmetry / _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.ptnr3_symmetry / _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.ptnr1_symmetry / _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_conn.ptnr2_symmetry / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 300BIOMOLECULE: THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 6 CHAIN(S). ...BIOMOLECULE: THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 6 CHAIN(S). THE BIOLOGICAL UNIT IS UNKNOWN.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Divalent cation tolerant protein CUTA
B: Divalent cation tolerant protein CUTA
C: Divalent cation tolerant protein CUTA
D: Divalent cation tolerant protein CUTA
E: Divalent cation tolerant protein CUTA
F: Divalent cation tolerant protein CUTA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,4279
Polymers95,3586
Non-polymers693
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16040 Å2
ΔGint-136 kcal/mol
Surface area23490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.157, 89.517, 125.847
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
71A
81B
91C
101D
111E
121F
131A
141B
151C
161D
171E
181F

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11TYRTYRTYRTYRAA40 - 8431 - 75
21TYRTYRTYRTYRBB40 - 8431 - 75
31TYRTYRTYRTYRCC40 - 8431 - 75
41TYRTYRTYRTYRDD40 - 8431 - 75
51TYRTYRTYRTYREE40 - 8431 - 75
61TYRTYRTYRTYRFF40 - 8431 - 75
72ILEILEVALVALAA90 - 11481 - 105
82ILEILEVALVALBB90 - 11481 - 105
92ILEILEVALVALCC90 - 11481 - 105
102ILEILEVALVALDD90 - 11481 - 105
112ILEILEVALVALEE90 - 11481 - 105
122ILEILEVALVALFF90 - 11481 - 105
133GLUGLUGLUGLUAA121 - 146112 - 137
143GLUGLUGLUGLUBB121 - 146112 - 137
153GLUGLUGLUGLUCC121 - 146112 - 137
163GLUGLUGLUGLUDD121 - 146112 - 137
173GLUGLUGLUGLUEE121 - 146112 - 137
183GLUGLUGLUGLUFF121 - 146112 - 137

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Components

#1: Protein
Divalent cation tolerant protein CUTA


Mass: 15892.998 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: O60888
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na

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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: 2.07 Å3/Da / Density % sol: 40.59 %
Crystal growTemperature: 291 K / Method: modified microbatch / pH: 8.6
Details: 1.5M potassium hydrogen phosphate, 0.1M TRIS, pH 8.6, modified microbatch, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.9793 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 19, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 24132 / Rmerge(I) obs: 0.073
Reflection shell
Resolution (Å)Rmerge(I) obs% possible all
2.4-2.490.3226.7
2.49-2.590.37335.5
2.59-2.70.27754.2
2.7-2.850.22772.9
2.85-3.020.19590.3
3.02-3.260.15499.1
3.26-3.580.10599.8
3.58-4.10.08483.3
4.1-5.170.055100
5.17-500.04699.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefmac_5.2.0005refinement
PDB_EXTRACT1data extraction
MAR345data collection
EPMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1OSC

1osc


Resolution: 2.7→32.67 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.894 / Cross valid method: THROUGHOUT / ESU R: 3.511 / ESU R Free: 0.387 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28316 1053 5.1 %RANDOM
Rwork0.24459 ---
obs0.24664 19505 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 52.063 Å2
Baniso -1Baniso -2Baniso -3
1-4.61 Å20 Å20 Å2
2---0.48 Å20 Å2
3----4.13 Å2
Refinement stepCycle: LAST / Resolution: 2.7→32.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4828 0 3 0 4831
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0224934
X-RAY DIFFRACTIONr_bond_other_d00.024577
X-RAY DIFFRACTIONr_angle_refined_deg1.0481.9626764
X-RAY DIFFRACTIONr_angle_other_deg3.69310574
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0055637
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.81725.137183
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.45515747
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.8811515
X-RAY DIFFRACTIONr_chiral_restr0.060.2816
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.025476
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02908
X-RAY DIFFRACTIONr_nbd_refined0.2030.2949
X-RAY DIFFRACTIONr_nbd_other0.2130.23898
X-RAY DIFFRACTIONr_nbtor_refined0.1730.22401
X-RAY DIFFRACTIONr_nbtor_other0.1090.22338
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1390.2135
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.1650.21
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2240.212
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1380.238
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2070.21
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.2561.53215
X-RAY DIFFRACTIONr_mcbond_other01.51274
X-RAY DIFFRACTIONr_mcangle_it0.50525230
X-RAY DIFFRACTIONr_scbond_it0.78131719
X-RAY DIFFRACTIONr_scangle_it1.4674.51534
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDNumberTypeRms dev position (Å)Weight position
A567tight positional0.020.05
B567tight positional0.020.05
C567tight positional0.030.05
D567tight positional0.020.05
E567tight positional0.020.05
F567tight positional0.030.05
A744medium positional0.290.5
B744medium positional0.330.5
C744medium positional0.30.5
D744medium positional0.340.5
E744medium positional0.290.5
F744medium positional0.310.5
A567tight thermal0.050.5
B567tight thermal0.050.5
C567tight thermal0.050.5
D567tight thermal0.040.5
E567tight thermal0.050.5
F567tight thermal0.050.5
A744medium thermal0.282
B744medium thermal0.252
C744medium thermal0.252
D744medium thermal0.222
E744medium thermal0.232
F744medium thermal0.242
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.471 81 -
Rwork0.378 1022 -
obs--100 %

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