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- PDB-1z94: X-Ray Crystal Structure of Protein CV1439 from Chromobacterium vi... -

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Basic information

Entry
Database: PDB / ID: 1z94
TitleX-Ray Crystal Structure of Protein CV1439 from Chromobacterium violaceum. Northeast Structural Genomics Consortium Target CvR12.
Componentsconserved hypothetical protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / hypothetical protein / NESG / CV1439 / PSI / Protein Structure Initiative / Northeast Structural Genomics Consortium
Function / homologyActivator of Hsp90 ATPase homologue 1-like / Activator of Hsp90 ATPase homolog 1-like protein / START domain / Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 / START-like domain superfamily / 2-Layer Sandwich / Alpha Beta / Activator of Hsp90 ATPase homologue 1/2-like C-terminal domain-containing protein
Function and homology information
Biological speciesChromobacterium violaceum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å
AuthorsKuzin, A. / Vorobiev, S.M. / Yong, W. / Forouhar, F. / Xio, R. / Ma, L.-C. / Acton, T. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Crystal Structure of the Hypothetical Protein CV1439 from Chromobacterium violaceum. Northeast Structural Genomics Consortium Target CVR12.
Authors: Kuzin, A. / Vorobiev, S.M. / Yong, W. / Forouhar, F. / Xio, R. / Ma, L.-C. / Acton, T. / Montelione, G.T. / Tong, L. / Hunt, J.F.
History
DepositionMar 31, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 10, 2005Provider: repository / Type: Initial release
Revision 1.1May 5, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: conserved hypothetical protein
B: conserved hypothetical protein
C: conserved hypothetical protein
D: conserved hypothetical protein
E: conserved hypothetical protein
F: conserved hypothetical protein


Theoretical massNumber of molelcules
Total (without water)98,0186
Polymers98,0186
Non-polymers00
Water7,350408
1
A: conserved hypothetical protein
B: conserved hypothetical protein
C: conserved hypothetical protein
D: conserved hypothetical protein


Theoretical massNumber of molelcules
Total (without water)65,3454
Polymers65,3454
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6290 Å2
ΔGint-41 kcal/mol
Surface area24580 Å2
MethodPISA
2
E: conserved hypothetical protein
F: conserved hypothetical protein

E: conserved hypothetical protein
F: conserved hypothetical protein


Theoretical massNumber of molelcules
Total (without water)65,3454
Polymers65,3454
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_656-x+1,y,-z+3/21
Unit cell
Length a, b, c (Å)105.095, 170.247, 128.126
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein
conserved hypothetical protein


Mass: 16336.344 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chromobacterium violaceum (bacteria) / Strain: ATCC 12472 / Gene: CV1439 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+Magic / References: UniProt: Q7NY36
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 408 / 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: 2.92 Å3/Da / Density % sol: 57.93 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 2 M Sodium chloride, 0.1 M sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97916 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 19, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97916 Å / Relative weight: 1
ReflectionResolution: 2.1→30 Å / Num. obs: 129114 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.5 % / Biso Wilson estimate: 20.6 Å2 / Rmerge(I) obs: 0.051
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.301 / Num. unique all: 12978 / % possible all: 100

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Processing

SoftwareName: CNS / Version: 1.1 / Classification: refinement
RefinementMethod to determine structure: SAD / Resolution: 2.1→26.75 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 322286.6 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.282 11979 9.8 %RANDOM
Rwork0.245 ---
obs0.245 121816 94 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 55.467 Å2 / ksol: 0.35906 e/Å3
Displacement parametersBiso mean: 37.8 Å2
Baniso -1Baniso -2Baniso -3
1--6.6 Å20 Å20 Å2
2--1.32 Å20 Å2
3---5.28 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.22 Å0.12 Å
Refinement stepCycle: LAST / Resolution: 2.1→26.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6623 0 0 408 7031
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.92
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.007 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.304 1776 9.6 %
Rwork0.246 16699 -
obs--85.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP

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