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- PDB-3iij: The structure of hCINAP-ADP complex at 1.76 angstroms resolution. -

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Basic information

Entry
Database: PDB / ID: 3iij
TitleThe structure of hCINAP-ADP complex at 1.76 angstroms resolution.
ComponentsCoilin-interacting nuclear ATPase protein
KeywordsPROTEIN BINDING / TRANSFERASE / Alpha and beta proteins (a/b) / phosphotransferase
Function / homology
Function and homology information


nucleoside monophosphate kinase activity / adenylate kinase / AMP kinase activity / nucleobase-containing small molecule interconversion / Interconversion of nucleotide di- and triphosphates / Cajal body / rRNA processing / ribosomal small subunit biogenesis / nuclear speck / centrosome ...nucleoside monophosphate kinase activity / adenylate kinase / AMP kinase activity / nucleobase-containing small molecule interconversion / Interconversion of nucleotide di- and triphosphates / Cajal body / rRNA processing / ribosomal small subunit biogenesis / nuclear speck / centrosome / ATP hydrolysis activity / nucleoplasm / ATP binding / nucleus / membrane / cytoplasm
Similarity search - Function
Adenylate kinase isoenzyme 6 / AAA domain / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Adenylate kinase isoenzyme 6 / Adenylate kinase isoenzyme 6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.76 Å
AuthorsZographos, S.E. / Drakou, C.E. / Leonidas, D.D.
CitationJournal: Proteins / Year: 2012
Title: hCINAP is an atypical mammalian nuclear adenylate kinase with an ATPase motif: Structural and functional studies.
Authors: Drakou, C.E. / Malekkou, A. / Hayes, J.M. / Lederer, C.W. / Leonidas, D.D. / Oikonomakos, N.G. / Lamond, A.I. / Santama, N. / Zographos, S.E.
History
DepositionAug 2, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 6, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 5, 2011Group: Advisory / Database references
Revision 1.3Nov 23, 2011Group: Database references
Revision 1.4Jan 18, 2012Group: Database references
Revision 1.5Sep 6, 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: Coilin-interacting nuclear ATPase protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,6796
Polymers20,8671
Non-polymers8115
Water3,423190
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)99.144, 99.144, 57.838
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 Coilin-interacting nuclear ATPase protein / Coilin-interacting nuclear ATPase protein / TAF9 RNA polymerase II / TATA box binding protein (TBP)- ...Coilin-interacting nuclear ATPase protein / TAF9 RNA polymerase II / TATA box binding protein (TBP)-associated factor / 32kDa / isoform CRA_b / human adenylate kinase 6


Mass: 20867.262 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CINAP, TAF9, hCG_37060 / Plasmid: pGEX-6P-3 / Production host: Escherichia coli (E. coli)
References: UniProt: Q5F2S9, UniProt: Q9Y3D8*PLUS, adenylate kinase
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 190 / 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: 3.93 Å3/Da / Density % sol: 68.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M HEPES pH 7.5, 1.5 M Li2SO4, 0.2 M NaCl, 0.5 mM DTT, 25 mM MgCl2, 2 mM ADP, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX10.1 / Wavelength: 1.11665 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jan 1, 2007 / Details: Rh Coated mirrors
RadiationMonochromator: double crystal monochromator with sagittal focussing
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11665 Å / Relative weight: 1
ReflectionResolution: 1.76→30 Å / Num. all: 32104 / Num. obs: 31610 / % possible obs: 98.1 % / Observed criterion σ(I): 2 / Redundancy: 4.9 % / Biso Wilson estimate: 32.8 Å2 / Rsym value: 0.044 / Net I/σ(I): 17.92
Reflection shellResolution: 1.76→1.79 Å / Redundancy: 4.3 % / Mean I/σ(I) obs: 3.41 / Rsym value: 0.499 / % possible all: 88.4

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Processing

Software
NameVersionClassification
MOLREPphasing
REFMAC5.5.0072refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1RKB

1rkb


Resolution: 1.76→28.3 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.955 / SU B: 3.051 / SU ML: 0.049 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.089 / ESU R Free: 0.084 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19509 1595 5 %RANDOM
Rwork0.18121 ---
all0.18193 31610 --
obs0.18193 30007 98.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.63 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20.01 Å20 Å2
2--0.03 Å20 Å2
3----0.04 Å2
Refinement stepCycle: LAST / Resolution: 1.76→28.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1441 0 47 190 1678
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0221547
X-RAY DIFFRACTIONr_angle_refined_deg1.1281.9952110
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6855180
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.31525.81486
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.86215269
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.765157
X-RAY DIFFRACTIONr_chiral_restr0.0770.2223
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0211182
X-RAY DIFFRACTIONr_mcbond_it0.4541.5883
X-RAY DIFFRACTIONr_mcangle_it0.87621441
X-RAY DIFFRACTIONr_scbond_it1.4483664
X-RAY DIFFRACTIONr_scangle_it2.3934.5667
LS refinement shellResolution: 1.76→1.809 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.308 108 -
Rwork0.271 2220 -
obs--98.85 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
113.813-1.381110.01457.57433.0159.4309-0.0246-0.3691-0.1618-0.9832-0.72161.6303-0.5592-0.6840.74620.17530.0673-0.16760.4348-0.0380.478712.161-56.55928.9306
22.08820.4062-0.91951.0309-0.39481.2113-0.00220.1463-0.12860.0023-0.04490.06770.0144-0.0170.04710.0981-0.0135-0.01020.1392-0.00370.127933.1153-54.1185-1.0799
31.84651.8132-0.78366.1885-1.61981.65470.030.3066-0.1988-0.0204-0.04880.14150.1185-0.17090.01880.067-0.0348-0.03310.1545-0.02580.131125.713-55.9728-4.0961
42.7023.1579-0.84729.91891.13118.5388-0.04290.2577-0.1053-0.4883-0.013-0.34020.027-0.0430.05590.08470.0131-0.03710.19250.07940.107126.5114-39.6215-11.2955
54.8596-1.88138.02023.7805-3.44813.28170.37541.488-0.4913-0.34680.1399-1.40370.53212.4197-0.51540.0660.09870.15740.83-0.18881.256240.022-35.726-13.1507
66.98942.7045-2.98987.2455-4.94367.1413-0.01820.24370.35670.18950.02840.5149-0.4373-0.2661-0.01020.10120.053-0.01690.11080.02540.133323.2585-40.28740.5805
71.9766-0.1372-0.11290.8787-0.33850.88480.01970.06460.06930.1204-0.01620.0386-0.1504-0.0186-0.00350.1213-0.0155-0.00340.11990.00640.104832.0963-48.14443.4831
88.9923-0.8466-0.11031.8333-1.47133.8236-0.05320.8481-0.2959-0.2304-0.0603-0.14810.0847-0.04990.11350.0827-0.00190.01590.1871-0.04550.104346.899-56.5523-11.643
95.82960.40074.22533.35284.15539.7578-0.09550.9230.3432-0.47270.1264-0.0047-0.50350.0442-0.03080.0872-0.05980.02260.37430.13860.156247.9449-46.464-14.05
107.0244-1.8726-4.47682.55373.24115.8630.1117-0.22340.20220.0483-0.0123-0.3177-0.03030.1291-0.09940.0795-0.0159-0.02050.1450.03720.153647.8213-47.96670.6375
112.8105-0.0313-0.68354.61031.71263.3257-0.1415-0.2008-0.34870.21240.0412-0.1280.150.27360.10030.08460.0065-0.01330.12440.03750.129339.0907-57.864.6243
125.0648-1.1311-2.26113.59972.26273.88210.0242-0.2814-0.19040.28710.0049-0.14620.12870.0841-0.02910.142-0.0464-0.00690.10430.02520.13525.8998-62.105310.8767
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-2 - 2
2X-RAY DIFFRACTION2A3 - 20
3X-RAY DIFFRACTION3A21 - 36
4X-RAY DIFFRACTION4A37 - 45
5X-RAY DIFFRACTION5A46 - 56
6X-RAY DIFFRACTION6A57 - 71
7X-RAY DIFFRACTION7A72 - 96
8X-RAY DIFFRACTION8A97 - 109
9X-RAY DIFFRACTION9A110 - 120
10X-RAY DIFFRACTION10A121 - 131
11X-RAY DIFFRACTION11A132 - 155
12X-RAY DIFFRACTION12A156 - 172

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