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- PDB-2zfh: Crystal structure of putative CutA1 from Homo sapiens at 2.05A re... -

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Basic information

Entry
Database: PDB / ID: 2zfh
TitleCrystal structure of putative CutA1 from Homo sapiens at 2.05A resolution
ComponentsCutA
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Human brain / Trimeric structure / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


response to metal ion / intracellular protein localization / copper ion binding / enzyme binding / mitochondrion / 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 / Resolution: 2.05 Å
AuthorsBagautdinov, B. / Yutani, K. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2008
Title: Structure of putative CutA1 from Homo sapiens determined at 2.05 A resolution.
Authors: Bagautdinov, B. / Matsuura, Y. / Bagautdinova, S. / Kunishima, N. / Yutani, K.
History
DepositionJan 7, 2008Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 22, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 18, 2012Group: Database references / Derived calculations
Revision 1.3Nov 1, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CutA
B: CutA
C: CutA
D: CutA
E: CutA
F: CutA


Theoretical massNumber of molelcules
Total (without water)114,7816
Polymers114,7816
Non-polymers00
Water4,540252
1
A: CutA
B: CutA
C: CutA


Theoretical massNumber of molelcules
Total (without water)57,3913
Polymers57,3913
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6840 Å2
ΔGint-45.4 kcal/mol
Surface area13210 Å2
MethodPISA
2
D: CutA
E: CutA
F: CutA


Theoretical massNumber of molelcules
Total (without water)57,3913
Polymers57,3913
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6810 Å2
ΔGint-42 kcal/mol
Surface area13370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.693, 88.844, 125.334
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
CutA / Brain acetylcholinesterase putative membrane anchor / Acetylcholinesterase-associated protein


Mass: 19130.230 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CUTA, ACHAP, C6orf82 / Plasmid: pET 11a / Production host: Escherichia coli (E. coli) / Strain (production host): (DE3)RIL / References: UniProt: O60888
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 252 / 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: 2.2 Å3/Da / Density % sol: 43 %
Crystal growTemperature: 295 K / Method: microbatch / pH: 4.6
Details: 25% PEG4000, 0.17M Ammonium Acetate, 0.085M Sodium acetate, 15% glycerol, pH4.6, microbatch, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 22, 2007 / Details: mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.05→40 Å / Num. all: 48457 / Num. obs: 45947 / % possible obs: 94.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.6 % / Biso Wilson estimate: 33.8 Å2 / Rmerge(I) obs: 0.069 / Rsym value: 0.057 / Net I/σ(I): 12.5
Reflection shellResolution: 2.05→2.12 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.374 / Mean I/σ(I) obs: 2.3 / Num. unique all: 3214 / Rsym value: 0.335 / % possible all: 79.2

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1XK8

1xk8


Resolution: 2.05→37.81 Å / Isotropic thermal model: Overall / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.265 2291 -RANDOM
Rwork0.221 ---
obs0.221 45947 94.7 %-
all-45947 --
Displacement parametersBiso mean: 51.1 Å2
Baniso -1Baniso -2Baniso -3
1-30.57 Å20 Å20 Å2
2---12.26 Å20 Å2
3----18.3 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.62 Å0.63 Å
Refinement stepCycle: LAST / Resolution: 2.05→37.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5027 0 0 252 5279
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d24.4
X-RAY DIFFRACTIONc_improper_angle_d0.84

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