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- PDB-2an1: Structural Genomics, The crystal structure of a putative kinase f... -

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Basic information

Entry
Database: PDB / ID: 2an1
TitleStructural Genomics, The crystal structure of a putative kinase from Salmonella typhimurim LT2
Componentsputative kinase
KeywordsTRANSFERASE / Structural Genomics / putative kinase / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


NAD+ kinase / NADP biosynthetic process / NAD+ kinase activity / NAD metabolic process / NAD binding / ATP binding / metal ion binding / cytoplasm
Similarity search - Function
Probable inorganic polyphosphate/atp-NAD kinase; domain 1 / Probable inorganic polyphosphate/atp-NAD kinase; domain 2 / ATP-NAD kinase C-terminal domain / NAD kinase / ATP-NAD kinase, PpnK-type, C-terminal / ATP-NAD kinase N-terminal domain / Inorganic polyphosphate/ATP-NAD kinase, N-terminal / NAD kinase/diacylglycerol kinase-like domain superfamily / Tumour Suppressor Smad4 / Sandwich ...Probable inorganic polyphosphate/atp-NAD kinase; domain 1 / Probable inorganic polyphosphate/atp-NAD kinase; domain 2 / ATP-NAD kinase C-terminal domain / NAD kinase / ATP-NAD kinase, PpnK-type, C-terminal / ATP-NAD kinase N-terminal domain / Inorganic polyphosphate/ATP-NAD kinase, N-terminal / NAD kinase/diacylglycerol kinase-like domain superfamily / Tumour Suppressor Smad4 / Sandwich / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsZhang, R. / Zhou, M. / Holzle, D. / Collart, F. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of a putative kinase from Salmonella typhimurim LT2
Authors: Zhang, R. / Zhou, M. / Holzle, D. / Collart, F. / Joachimiak, A.
History
DepositionAug 10, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 27, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: putative kinase
B: putative kinase
C: putative kinase
D: putative kinase


Theoretical massNumber of molelcules
Total (without water)130,4854
Polymers130,4854
Non-polymers00
Water9,764542
1
A: putative kinase
D: putative kinase


Theoretical massNumber of molelcules
Total (without water)65,2422
Polymers65,2422
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3490 Å2
ΔGint-25 kcal/mol
Surface area23980 Å2
MethodPISA
2
B: putative kinase
C: putative kinase


Theoretical massNumber of molelcules
Total (without water)65,2422
Polymers65,2422
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3150 Å2
ΔGint-21 kcal/mol
Surface area24070 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10010 Å2
ΔGint-70 kcal/mol
Surface area44690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.535, 99.323, 144.842
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThis protein existed as dimer, MolA/MolD, MolB/MolC are two dimers in the asymmetric unit

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Components

#1: Protein
putative kinase /


Mass: 32621.158 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Strain: LT2 / Gene: yfjB / Plasmid: PDM68 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P65774, NAD+ kinase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 542 / 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: 2.72 Å3/Da / Density % sol: 54 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: 1.5M Ammonium Sulfate, 0.1 M Sodium Acetate, pH 4.2, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9798 Å
DetectorType: SBC-2 / Detector: CCD / Date: Feb 14, 2002 / Details: mirrors
RadiationMonochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 97358 / Num. obs: 94632 / % possible obs: 97.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 8.1 % / Biso Wilson estimate: 36 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 26
Reflection shellResolution: 2→2.07 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.523 / Mean I/σ(I) obs: 1.87 / Num. unique all: 9612 / % possible all: 81

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
SBC-Collectdata collection
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: SAD / Resolution: 2→50 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.937 / SU B: 7.656 / SU ML: 0.108 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.169 / ESU R Free: 0.152
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23262 4738 5 %RANDOM
Rwork0.19999 ---
obs0.20163 89824 97.25 %-
all-92365 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.088 Å2
Baniso -1Baniso -2Baniso -3
1--0.63 Å20 Å20 Å2
2---0.96 Å20 Å2
3---1.59 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.34 Å0.32 Å
Refinement stepCycle: LAST / Resolution: 2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8566 0 0 542 9108
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0228721
X-RAY DIFFRACTIONr_angle_refined_deg1.2261.96411822
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.75151078
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.38824.081397
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.008151490
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.91558
X-RAY DIFFRACTIONr_chiral_restr0.0840.21372
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.026531
X-RAY DIFFRACTIONr_nbd_refined0.1990.23981
X-RAY DIFFRACTIONr_nbtor_refined0.30.25934
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1660.2597
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1980.286
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1580.223
X-RAY DIFFRACTIONr_mcbond_it0.8031.55607
X-RAY DIFFRACTIONr_mcangle_it1.41128772
X-RAY DIFFRACTIONr_scbond_it1.84633506
X-RAY DIFFRACTIONr_scangle_it2.9784.53050
LS refinement shellResolution: 2→2.047 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.279 282 -
Rwork0.24 5243 -
obs--78.16 %
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)
10.2336-0.16510.06591.98660.22850.22430.0277-0.0422-0.11480.01390.0159-0.09980.00920.0328-0.0436-0.08620.0051-0.0196-0.0548-0.00470.068786.71136.34434.452
21.84170.5658-0.18151.0115-0.06770.24170.03920.03320.0249-0.0043-0.03270.1960.00150.0099-0.0065-0.0580.00890.0034-0.0865-0.00370.03945.68659.20240.966
30.99180.63940.27351.25620.47422.07060.1849-0.2122-0.00960.1644-0.1278-0.0124-0.13510.2653-0.0571-0.0233-0.07270.00580.03820.0015-0.092572.34361.15964.269
41.04960.29420.47430.98940.1141.8384-0.1240.18790.0296-0.17820.0819-0.0446-0.38780.17990.04210.0346-0.04460.0066-0.0320.0061-0.059480.03265.71518.629
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA4 - 1004 - 100
2X-RAY DIFFRACTION1AA101 - 200101 - 200
3X-RAY DIFFRACTION1AA201 - 292201 - 292
4X-RAY DIFFRACTION2BB4 - 1004 - 100
5X-RAY DIFFRACTION2BB101 - 200101 - 200
6X-RAY DIFFRACTION2BB201 - 292201 - 292
7X-RAY DIFFRACTION3CC5 - 1005 - 100
8X-RAY DIFFRACTION3CC101 - 200101 - 200
9X-RAY DIFFRACTION3CC201 - 290201 - 290
10X-RAY DIFFRACTION4DD4 - 1004 - 100
11X-RAY DIFFRACTION4DD101 - 200101 - 200
12X-RAY DIFFRACTION4DD201 - 292201 - 292

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