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- PDB-3iil: The structure of hCINAP-MgADP-Pi complex at 2.0 angstroms resolution -

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Basic information

Entry
Database: PDB / ID: 3iil
TitleThe structure of hCINAP-MgADP-Pi complex at 2.0 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 / : / PHOSPHATE ION / Adenylate kinase isoenzyme 6 / Adenylate kinase isoenzyme 6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_seq_id / _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)21,85411
Polymers20,8671
Non-polymers98610
Water3,621201
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)99.173, 99.173, 58.048
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Coilin-interacting nuclear ATPase protein / Coilin-interacting nulcear ATPase protein / TAF9 RNA polymerase II / TATA box binding protein (TBP)- ...Coilin-interacting nulcear 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) / Strain (production host): B834(DE3)pLysS
References: UniProt: Q5F2S9, UniProt: Q9Y3D8*PLUS, adenylate kinase

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Non-polymers , 6 types, 211 molecules

#2: Chemical ChemComp-LI / LITHIUM ION


Mass: 6.941 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Li
#3: 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
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#6: Chemical
ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 201 / 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: 3.95 Å3/Da / Density % sol: 68.85 %
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, 25 mM P1,P5-Di(Adenosine-5')Pentaphosphate, 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: 1.04498 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 17, 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: 1.04498 Å / Relative weight: 1
ReflectionResolution: 2→34.52 Å / Num. all: 22145 / Num. obs: 22102 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 6.5 % / Biso Wilson estimate: 32.9 Å2 / Rsym value: 0.057 / Net I/σ(I): 20.13
Reflection shellResolution: 2→2.03 Å / Redundancy: 6.5 % / Mean I/σ(I) obs: 4.25 / Rsym value: 0.461 / % possible all: 100

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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: 2→34.52 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.957 / SU B: 5.391 / SU ML: 0.074 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.121 / ESU R Free: 0.112 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19269 1131 5.1 %RANDOM
Rwork0.17099 ---
all0.17211 22102 --
obs0.17211 20968 99.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.776 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2→34.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1441 0 56 201 1698
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0221532
X-RAY DIFFRACTIONr_angle_refined_deg1.2581.9992086
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9415174
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.78625.71484
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.25815265
X-RAY DIFFRACTIONr_dihedral_angle_4_deg7.893157
X-RAY DIFFRACTIONr_chiral_restr0.0950.2221
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211158
X-RAY DIFFRACTIONr_mcbond_it0.5431.5872
X-RAY DIFFRACTIONr_mcangle_it1.03321421
X-RAY DIFFRACTIONr_scbond_it1.6743660
X-RAY DIFFRACTIONr_scangle_it2.7944.5665
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.25 81 -
Rwork0.208 1530 -
obs--98.47 %
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)
15.03551.81060.2038.279-1.42111.927-0.11590.66720.692-0.27450.1073-0.5041-0.66110.54830.00860.4039-0.15470.02420.33990.09570.381144.175317.44999.4335
20.7160.54480.22781.43180.94661.6328-0.13820.05260.1523-0.19560.04210.1241-0.1604-0.10320.09610.1537-0.0007-0.01250.10730.01170.137235.2492-0.6883-1.2394
34.2586-2.3022-0.39191.680.94031.5488-0.20140.15080.3989-0.08070.0274-0.0571-0.2779-0.01040.1740.2249-0.0383-0.0580.13310.08380.165138.64065.7306-3.1438
42.6932-1.3345-1.01168.3703-0.66219.37110.1710.3258-0.0438-0.5392-0.12350.1565-0.1339-0.0391-0.04750.1805-0.03440.06390.12330.01580.118250.8384-2.0841-11.226
57.13363.70361.56539.5868-3.04952.34640.3517-0.4022-0.1561-0.95870.05930.94370.7525-0.3355-0.4110.44-0.15960.12320.4264-0.16980.485148.6586-17.1267-13.2243
65.1868-0.3873-2.0388.55784.63866.3791-0.19650.0378-0.0078-0.16270.0219-0.53180.09580.39180.17460.1305-0.02260.0640.13210.01460.119152.9147-2.8649-1.5906
74.32810.4380.78947.07182.57894.4438-0.0948-0.04360.0894-0.00760.1238-0.2281-0.15160.271-0.02910.1453-0.01870.01960.14670.00690.127143.92410.22421.8224
80.94790.59220.18621.53830.85511.3104-0.0553-0.0233-0.003-0.00620.01160.05580.05160.00510.04380.15970.0020.00360.09640.00990.111336.7177-7.2042.077
93.4423-1.2482-1.34478.83632.82436.8544-0.24560.6731-0.257-0.54720.0623-0.03380.24430.16290.18330.223-0.073-0.00660.1668-0.0380.070431.8778-14.3174-15.2822
101.59410.5218-1.51022.56361.34088.29910.04140.1487-0.1423-0.2089-0.0399-0.01410.15220.2178-0.00160.1275-0.0201-0.00460.0988-0.03040.174432.7953-19.5978-5.5498
112.29990.01390.31322.63640.59912.0314-0.0721-0.1556-0.01710.1372-0.07180.27710.0699-0.24030.14390.1482-0.02880.03160.1174-0.01980.129830.5895-6.4934.8233
125.36880.87031.99774.1965-0.31543.77830.1016-0.33450.00070.2589-0.10950.2396-0.0709-0.23730.00790.17240.03530.00720.1004-0.03260.131233.35459.162512.5515
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-2 - 2
2X-RAY DIFFRACTION2A3 - 22
3X-RAY DIFFRACTION3A23 - 36
4X-RAY DIFFRACTION4A37 - 44
5X-RAY DIFFRACTION5A45 - 54
6X-RAY DIFFRACTION6A55 - 68
7X-RAY DIFFRACTION7A69 - 81
8X-RAY DIFFRACTION8A82 - 103
9X-RAY DIFFRACTION9A104 - 116
10X-RAY DIFFRACTION10A117 - 125
11X-RAY DIFFRACTION11A126 - 157
12X-RAY DIFFRACTION12A158 - 172

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