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- PDB-3iik: The structure of hCINAP-SO4 complex at 1.95 angstroms resolution -

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Basic information

Entry
Database: PDB / ID: 3iik
TitleThe structure of hCINAP-SO4 complex at 1.95 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 / 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
Adenylate kinase isoenzyme 6 / Adenylate kinase isoenzyme 6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 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

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Assembly

Deposited unit
A: Coilin-interacting nuclear ATPase protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,3486
Polymers20,8671
Non-polymers4805
Water3,585199
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)98.670, 98.670, 57.650
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-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 199 / 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: 3.88 Å3/Da / Density % sol: 68.32 %
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, 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: 1.95→85.4 Å / Num. all: 23468 / Num. obs: 23444 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 8 % / Biso Wilson estimate: 34.2 Å2 / Rsym value: 0.05 / Net I/σ(I): 25.8
Reflection shellResolution: 1.95→2.06 Å / Redundancy: 8 % / Mean I/σ(I) obs: 4.5 / Rsym value: 0.449 / % possible all: 100

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Processing

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

1rkb


Resolution: 1.95→24.89 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.955 / SU B: 5.601 / SU ML: 0.076 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.118 / ESU R Free: 0.112 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20559 1202 5.1 %RANDOM
Rwork0.17977 ---
all0.18107 23444 --
obs0.18107 22238 99.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.198 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20.01 Å20 Å2
2--0.01 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.95→24.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1441 0 25 199 1665
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0221521
X-RAY DIFFRACTIONr_angle_refined_deg1.1131.9782074
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8965184
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.81625.76585
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.52315267
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.399157
X-RAY DIFFRACTIONr_chiral_restr0.0840.2221
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0211171
X-RAY DIFFRACTIONr_mcbond_it0.4991.5886
X-RAY DIFFRACTIONr_mcangle_it0.94621445
X-RAY DIFFRACTIONr_scbond_it1.5833635
X-RAY DIFFRACTIONr_scangle_it2.6594.5624
LS refinement shellResolution: 1.95→2 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.288 89 -
Rwork0.231 1648 -
obs--100 %
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)
19.5266-3.5611-2.499112.74226.50311.586-0.1414-1.24511.27510.9325-0.01880.554-1.2248-1.12710.16020.46110.15080.03250.5637-0.26420.5495-43.758217.3413-9.2689
20.90850.0784-0.04391.6862-0.47991.3016-0.0949-0.09330.1610.2210.0337-0.1052-0.18360.03520.06120.16130.0039-0.00390.1208-0.0190.1507-35.69672.57721.3983
36.15213.0586-1.55971.5511-0.71084.1460.3153-0.5202-0.12730.2381-0.2304-0.01870.032-0.0299-0.08490.28960.06160.06790.14580.02450.139-49.2947-2.639210.0971
47.1903-3.6869-3.24395.03383.16814.4321-0.0477-0.0051-0.77420.91170.308-0.70081.07731.3556-0.26030.53250.4356-0.17010.6907-0.09220.8616-48.0823-17.393413.0969
54.48860.4636-2.02966.8818-3.73875.7393-0.17180.07850.10360.10310.21620.5280.005-0.464-0.04440.12940.02080.02440.1868-0.00320.1556-52.2417-0.4587-0.6358
61.486-0.2287-0.14821.175-0.23110.9442-0.071-0.0032-0.0857-0.02310.06130.06280.0703-0.12990.00970.1588-0.0020.01350.1278-0.00140.1279-40.7648-3.8983-3.6791
75.405-1.5545-1.60953.6229-1.92925.2906-0.1776-0.56140.23940.59730.1758-0.237-0.26610.01040.00180.19760.0395-0.02290.1564-0.01490.1528-26.7629-12.15911.8406
86.1357-1.00490.0032.46483.598710.36620.0048-0.8365-0.06220.69460.04510.16130.1548-0.2849-0.04990.40760.01080.05590.19050.02540.2356-34.7473-18.229213.1566
94.8597-2.72944.5542.9716-1.934.74670.07870.0653-0.1301-0.235-0.0483-0.070.16680.055-0.03050.23860.00540.08490.135-0.00160.2003-34.7983-16.4164-2.5392
1013.08493.6343-4.87488.18292.309613.8332-0.16280.5752-0.3786-0.5690.0999-0.25050.41270.30210.06290.18150.008-0.00990.1498-0.00030.1556-37.878-7.0126-13.7291
113.0928-0.46590.84883.7236-0.7344.2815-0.0674-0.03460.03990.1779-0.0629-0.6375-0.09220.50730.13030.11620.00350.00820.14160.02640.2141-24.4841-2.3032-1.0353
124.8124-0.73561.74893.5871-0.19073.559-0.01990.27670.0852-0.2292-0.0504-0.1783-0.01550.13020.07030.1655-0.02520.02470.13020.00450.151-32.79048.9312-11.904
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-2 - 2
2X-RAY DIFFRACTION2A3 - 32
3X-RAY DIFFRACTION3A33 - 45
4X-RAY DIFFRACTION4A46 - 55
5X-RAY DIFFRACTION5A56 - 71
6X-RAY DIFFRACTION6A72 - 97
7X-RAY DIFFRACTION7A98 - 110
8X-RAY DIFFRACTION8A111 - 120
9X-RAY DIFFRACTION9A121 - 135
10X-RAY DIFFRACTION10A136 - 140
11X-RAY DIFFRACTION11A141 - 156
12X-RAY DIFFRACTION12A157 - 172

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