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- PDB-1umj: Crystal structure of Pyrococcus horikoshii CutA in the presence o... -

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Basic information

Entry
Database: PDB / ID: 1umj
TitleCrystal structure of Pyrococcus horikoshii CutA in the presence of 3M guanidine hydrochloride
Componentsperiplasmic divalent cation tolerance protein CutA
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / CUTA / COPPER TOLERANCE
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
GUANIDINE / Divalent-cation tolerance protein CutA
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsTanaka, Y. / Tsumoto, K. / Yasutake, Y. / Sakai, N. / Yao, M. / Tanaka, I. / Kumagai, I.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2004
Title: Structural evidence for guanidine-protein side chain interactions: crystal structure of CutA from Pyrococcus horikoshii in 3M guanidine hydrochloride
Authors: Tanaka, Y. / Tsumoto, K. / Umetsu, M. / Nakanishi, T. / Yasutake, Y. / Sakai, N. / Yao, M. / Tanaka, I. / Arakawa, T. / Kumagai, I.
History
DepositionOct 2, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 5, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Oct 25, 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: periplasmic divalent cation tolerance protein CutA
B: periplasmic divalent cation tolerance protein CutA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9716
Polymers24,7342
Non-polymers2364
Water2,252125
1
A: periplasmic divalent cation tolerance protein CutA
hetero molecules

A: periplasmic divalent cation tolerance protein CutA
hetero molecules

A: periplasmic divalent cation tolerance protein CutA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,4569
Polymers37,1023
Non-polymers3546
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area6870 Å2
ΔGint-37 kcal/mol
Surface area12990 Å2
MethodPISA, PQS
2
B: periplasmic divalent cation tolerance protein CutA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,4853
Polymers12,3671
Non-polymers1182
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: periplasmic divalent cation tolerance protein CutA
hetero molecules

B: periplasmic divalent cation tolerance protein CutA
hetero molecules

B: periplasmic divalent cation tolerance protein CutA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,4569
Polymers37,1023
Non-polymers3546
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_755-y+2,x-y,z1
crystal symmetry operation3_775-x+y+2,-x+2,z1
MethodPQS
Unit cell
Length a, b, c (Å)53.210, 53.210, 59.665
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number143
Space group name H-MP3
Components on special symmetry positions
IDModelComponents
11A-1001-

GAI

21A-1002-

GAI

31B-1003-

GAI

41B-1004-

GAI

DetailsThe biological assembly of this protein is a trimer. One can be generated from the chain A with operators of (-y+1, x-y, z) and (1+y-x, 1-x, z), and the other from the chain B with operators of (-y+2, x-y, z) and (2+y-x, 2-x, z).

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Components

#1: Protein periplasmic divalent cation tolerance protein CutA


Mass: 12367.188 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Strain: OT3 / Gene: PH0992 / Plasmid: PET20B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O58720
#2: Chemical
ChemComp-GAI / GUANIDINE


Mass: 59.070 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CH5N3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 125 / 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: 1.87 Å3/Da / Density % sol: 33.56 %
Crystal growTemperature: 293 K / Method: oil batch method / pH: 4
Details: Acetate buffer (pH 4.0), PEG4000, Ammonium sulfate, 3M guanidine hydrochloride, Oil batch method, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 13, 2003
RadiationMonochromator: DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.6→40 Å / Num. all: 24828 / Num. obs: 24828 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 3.9 % / Biso Wilson estimate: 18.3 Å2 / Rsym value: 0.039 / Net I/σ(I): 19.9
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 3.8 % / Num. unique all: 2499 / Rsym value: 0.221 / % possible all: 100

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1J2V

1j2v


Resolution: 1.6→20 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.253 2502 10 %RANDOM
Rwork0.214 ---
obs-24828 99.6 %-
Displacement parametersBiso mean: 21.06 Å2
Baniso -1Baniso -2Baniso -3
1-0.123 Å2-0.731 Å20 Å2
2--0.123 Å20 Å2
3----0.246 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.14 Å0.1 Å
Refinement stepCycle: LAST / Resolution: 1.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1726 0 16 125 1867
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.017
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_dihedral_angle_d22.7
X-RAY DIFFRACTIONc_improper_angle_d1.12
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 1.6→1.66 Å
RfactorNum. reflection% reflection
Rfree0.2949 239 9.58 %
Rwork0.2374 2257 -
obs-2153 100 %

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