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- PDB-5jzv: The structure of D77G hCINAP-ADP -

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Basic information

Entry
Database: PDB / ID: 5jzv
TitleThe structure of D77G hCINAP-ADP
ComponentsAdenylate kinase isoenzyme 6
KeywordsTRANSFERASE / ATPASE / ADENYLATE KINASE
Function / homology
Function and homology information


nucleoside monophosphate kinase activity / adenylate kinase / adenylate kinase activity / nucleobase-containing small molecule interconversion / Interconversion of nucleotide di- and triphosphates / Cajal body / nuclear speck / phosphorylation / centrosome / ATP hydrolysis activity ...nucleoside monophosphate kinase activity / adenylate kinase / adenylate kinase activity / nucleobase-containing small molecule interconversion / Interconversion of nucleotide di- and triphosphates / Cajal body / nuclear speck / phosphorylation / centrosome / ATP hydrolysis activity / nucleoplasm / ATP binding / membrane / nucleus / cytoplasm
Similarity search - Function
Adenylate kinase isoenzyme 6 / AAA domain / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Adenylate kinase isoenzyme 6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.07 Å
AuthorsLiu, Y. / Yang, Z. / Yang, Y. / Cai, X. / Zheng, X.
Funding support China, 3items
OrganizationGrant numberCountry
National Science Foundation of China31470754 China
Doctoral Fund of the Ministry of Education of China20130001130003 China
Beijing Natural Science Foundation Grant5152012 China
CitationJournal: Nat Commun / Year: 2016
Title: The ATPase hCINAP regulates 18S rRNA processing and is essential for embryogenesis and tumour growth.
Authors: Bai, D. / Zhang, J. / Li, T. / Hang, R. / Liu, Y. / Tian, Y. / Huang, D. / Qu, L. / Cao, X. / Ji, J. / Zheng, X.
History
DepositionMay 17, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 10, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 6, 2017Group: Database references / Derived calculations
Category: citation / citation_author / pdbx_struct_oper_list
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 8, 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: Adenylate kinase isoenzyme 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,0052
Polymers23,5771
Non-polymers4271
Water3,081171
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)101.757, 101.757, 58.854
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein Adenylate kinase isoenzyme 6 / AK6 / Adrenal gland protein AD-004 / Coilin-interacting nuclear ATPase protein / hCINAP / Dual ...AK6 / Adrenal gland protein AD-004 / Coilin-interacting nuclear ATPase protein / hCINAP / Dual activity adenylate kinase/ATPase / AK/ATPase


Mass: 23577.316 Da / Num. of mol.: 1 / Mutation: D77G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AK6, CINAP, AD-004, CGI-137 / Plasmid: pET28a / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9Y3D8, adenylate kinase
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 171 / 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: 3.73 Å3/Da / Density % sol: 67.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.01M MAGNESIUM CHLORIDE HEXAHYDRATE, 0.05M MES MONOHYDRATE PH 5.6, 1.8M LITHIUM SULFATE MONOHYDRATE, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BSRF / Beamline: 3W1A / Wavelength: 0.9792 Å
DetectorType: MAR CCD 130 mm / Detector: CCD / Date: Jun 15, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.07→50 Å / Num. obs: 21343 / % possible obs: 100 % / Observed criterion σ(I): 8.1 / Redundancy: 22.9 % / Net I/σ(I): 50.2
Reflection shellResolution: 2.07→2.14 Å / Redundancy: 21.7 % / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
REFMAC5.5.0110refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3IIL

3iil


Resolution: 2.07→44.06 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.933 / SU B: 3.48 / SU ML: 0.095 / Cross valid method: THROUGHOUT / ESU R: 0.138 / ESU R Free: 0.141 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.235 1095 5.1 %RANDOM
Rwork0.19 ---
obs0.192 20248 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å
Displacement parametersBiso mean: 34.76 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å2-0.01 Å20 Å2
2---0.02 Å20 Å2
3---0.03 Å2
Refinement stepCycle: LAST / Resolution: 2.07→44.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1430 0 27 171 1628
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0330.0221494
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0231.9852031
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6345176
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.89325.37580
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.51815260
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.99158
X-RAY DIFFRACTIONr_chiral_restr0.1570.2218
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0211144
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.4071.5873
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.46221414
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.8293621
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it6.1684.5617
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.07→2.12 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.295 76 -
Rwork0.238 1498 -
obs--99.62 %

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