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- PDB-1rkb: The structure of adrenal gland protein AD-004 -

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Basic information

Entry
Database: PDB / ID: 1rkb
TitleThe structure of adrenal gland protein AD-004
ComponentsProtein AD-004
KeywordsTRANSFERASE / five-stranded parallel beta-sheet flanked by 7 alpha-helices
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
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SAD / Resolution: 2 Å
AuthorsRen, H. / Liang, Y. / Bennett, M. / Su, X.D.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2005
Title: The crystal structure of human adenylate kinase 6: An adenylate kinase localized to the cell nucleus
Authors: Ren, H. / Wang, L. / Bennett, M. / Liang, Y. / Zheng, X. / Lu, F. / Li, L. / Nan, J. / Luo, M. / Eriksson, S. / Zhang, C. / Su, X.D.
History
DepositionNov 21, 2003Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 11, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_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

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Assembly

Deposited unit
A: Protein AD-004
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,6979
Polymers20,1961
Non-polymers5018
Water2,900161
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)99.555, 99.555, 57.191
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 Protein AD-004 / Protein CGI-137


Mass: 20195.561 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Tissue: adrenal gland / Plasmid: pET21G-DEST / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21-(DE3) / References: UniProt: Q9Y3D8
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-LI / LITHIUM ION / Lithium


Mass: 6.941 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Li
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 161 / 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: 68.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: HEPES-Na, Lithium Sulfate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5418 Å
DetectorType: BRUKER SMART 6000 / Detector: CCD / Date: Mar 3, 2003 / Details: MONTEL
RadiationMonochromator: MONTEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→57 Å / Num. all: 22042 / Num. obs: 21969 / % possible obs: 99.67 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.15 % / Biso Wilson estimate: 18.4 Å2 / Rsym value: 0.0337 / Net I/σ(I): 15.15
Reflection shellResolution: 2→2.04 Å / Redundancy: 2.37 % / Mean I/σ(I) obs: 1.73 / Num. unique all: 1125 / Rsym value: 0.2065 / % possible all: 99.38

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Processing

Software
NameVersionClassification
CNS1.1refinement
PROTEUM PLUSdata reduction
PROTEUM PLUSdata scaling
SOLVEphasing
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2→49.78 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1294034.22 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.218 1071 4.9 %RANDOM
Rwork0.203 ---
obs0.203 21924 99.6 %-
all-22005 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 47.724 Å2 / ksol: 0.369811 e/Å3
Displacement parametersBiso mean: 30 Å2
Baniso -1Baniso -2Baniso -3
1--1.03 Å21.9 Å20 Å2
2---1.03 Å20 Å2
3---2.06 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.19 Å0.14 Å
Refinement stepCycle: LAST / Resolution: 2→49.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1426 0 28 161 1615
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
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_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.77
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.561.5
X-RAY DIFFRACTIONc_mcangle_it2.412
X-RAY DIFFRACTIONc_scbond_it2.312
X-RAY DIFFRACTIONc_scangle_it3.562.5
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.256 174 4.8 %
Rwork0.233 3416 -
obs-3590 98.4 %
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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