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- PDB-1vhf: Crystal structure of periplasmic divalent cation tolerance protein -

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Basic information

Entry
Database: PDB / ID: 1vhf
TitleCrystal structure of periplasmic divalent cation tolerance protein
Componentsperiplasmic divalent cation tolerance protein
KeywordsStructural genomics / unknown function
Function / homology
Function and homology information


response to metal ion / copper ion binding / cytoplasm
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
Divalent-cation tolerance protein CutA
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Se-Met SAD phasing / Resolution: 1.54 Å
AuthorsStructural GenomiX
CitationJournal: Proteins / Year: 2005
Title: Structural analysis of a set of proteins resulting from a bacterial genomics project
Authors: Badger, J. / Sauder, J.M. / Adams, J.M. / Antonysamy, S. / Bain, K. / Bergseid, M.G. / Buchanan, S.G. / Buchanan, M.D. / Batiyenko, Y. / Christopher, J.A. / Emtage, S. / Eroshkina, A. / ...Authors: Badger, J. / Sauder, J.M. / Adams, J.M. / Antonysamy, S. / Bain, K. / Bergseid, M.G. / Buchanan, S.G. / Buchanan, M.D. / Batiyenko, Y. / Christopher, J.A. / Emtage, S. / Eroshkina, A. / Feil, I. / Furlong, E.B. / Gajiwala, K.S. / Gao, X. / He, D. / Hendle, J. / Huber, A. / Hoda, K. / Kearins, P. / Kissinger, C. / Laubert, B. / Lewis, H.A. / Lin, J. / Loomis, K. / Lorimer, D. / Louie, G. / Maletic, M. / Marsh, C.D. / Miller, I. / Molinari, J. / Muller-Dieckmann, H.J. / Newman, J.M. / Noland, B.W. / Pagarigan, B. / Park, F. / Peat, T.S. / Post, K.W. / Radojicic, S. / Ramos, A. / Romero, R. / Rutter, M.E. / Sanderson, W.E. / Schwinn, K.D. / Tresser, J. / Winhoven, J. / Wright, T.A. / Wu, L. / Xu, J. / Harris, T.J.
History
DepositionDec 1, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 30, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 1.5Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: periplasmic divalent cation tolerance protein


Theoretical massNumber of molelcules
Total (without water)13,6461
Polymers13,6461
Non-polymers00
Water2,018112
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: periplasmic divalent cation tolerance protein

A: periplasmic divalent cation tolerance protein

A: periplasmic divalent cation tolerance protein


Theoretical massNumber of molelcules
Total (without water)40,9393
Polymers40,9393
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area6740 Å2
ΔGint-37 kcal/mol
Surface area13160 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)52.499, 52.499, 66.635
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63
Components on special symmetry positions
IDModelComponents
11A-219-

HOH

21A-220-

HOH

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Components

#1: Protein periplasmic divalent cation tolerance protein


Mass: 13646.282 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: cutA / Production host: Escherichia coli (E. coli) / References: UniProt: Q9X0E6
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 112 / Source method: isolated from a natural source / Formula: H2O
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: 1.94 Å3/Da / Density % sol: 36.68 %
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110 mMHEPES1droppH7.5
2150 mM1dropNaCl
310 mMmethionine1drop
410 %glycerol1drop
55 mMdithiothreitol1drop
610 mg/mlprotein1drop

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 32-ID / Wavelength: 0.9795 Å
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.54→37.53 Å / Num. all: 15362 / Num. obs: 15362 / % possible obs: 99.7 % / Redundancy: 21.6 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 30
Reflection shellResolution: 1.54→1.62 Å / Redundancy: 15.8 % / Rmerge(I) obs: 0.291 / Mean I/σ(I) obs: 11.2 / % possible all: 99.7
Reflection shell
*PLUS
% possible obs: 99.7 %

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
TRUNCATEdata reduction
REFMAC4refinement
CCP4(SCALAdata scaling
TRUNCATEdata scaling
RefinementMethod to determine structure: Se-Met SAD phasing / Resolution: 1.54→37.53 Å / σ(F): 0
RfactorNum. reflection
Rfree0.215 767
Rwork0.185 -
obs-15359
Solvent computationSolvent model: Babinet bulk solvent correction / Bsol: 338.279 Å2 / ksol: 0.999 e/Å3
Displacement parametersBiso mean: 17.011 Å2
Baniso -1Baniso -2Baniso -3
1--0.105 Å2-0.052 Å20 Å2
2---0.105 Å20 Å2
3---0.157 Å2
Refine Biso Class: all / Treatment: isotropic
Refinement stepCycle: LAST / Resolution: 1.54→37.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms850 0 0 112 962
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.013
X-RAY DIFFRACTIONp_angle_d2.319
X-RAY DIFFRACTIONp_planar_tor3.333
X-RAY DIFFRACTIONp_chiral_restr0.148
X-RAY DIFFRACTIONp_plane_restr0.014
X-RAY DIFFRACTIONp_mcbond_it1.568
X-RAY DIFFRACTIONp_mcangle_it2.854
X-RAY DIFFRACTIONp_scbond_it3.086
X-RAY DIFFRACTIONp_scangle_it4.911
Software
*PLUS
Version: 4 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg2.3

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