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- PDB-3tau: Crystal Structure of a Putative Guanylate Monophosphaste Kinase f... -

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Basic information

Entry
Database: PDB / ID: 3tau
TitleCrystal Structure of a Putative Guanylate Monophosphaste Kinase from Listeria monocytogenes EGD-e
ComponentsGuanylate kinase
KeywordsTRANSFERASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / Putative guanylate kinase / reversible phosphoryl transfer
Function / homology
Function and homology information


guanylate kinase / guanylate kinase activity / ATP binding / cytosol
Similarity search - Function
Guanylate kinase / Guanylate Kinase phosphate binding domain / Guanylate Kinase phosphate binding domain / Guanylate kinase, conserved site / Guanylate kinase-like signature. / Guanylate kinase-like domain profile. / Guanylate kinase-like domain / Guanylate kinase/L-type calcium channel beta subunit / Guanylate kinase / Guanylate kinase homologues. ...Guanylate kinase / Guanylate Kinase phosphate binding domain / Guanylate Kinase phosphate binding domain / Guanylate kinase, conserved site / Guanylate kinase-like signature. / Guanylate kinase-like domain profile. / Guanylate kinase-like domain / Guanylate kinase/L-type calcium channel beta subunit / Guanylate kinase / Guanylate kinase homologues. / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesListeria monocytogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.05 Å
AuthorsBrunzelle, J.S. / Wawrzak, Z. / Onopriyenko, O. / Kwok, J. / Anderson, W.F. / Savchenko, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: Crystal Structure of a Putative Guanylate Monophosphaste Kinase from Listeria monocytogenes EGD-e
Authors: Brunzelle, J.S. / Wawrzak, Z. / Onopriyenko, O. / Kwok, J. / Anderson, W.F. / Savchenko, A.
History
DepositionAug 4, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 24, 2011Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Guanylate kinase
B: Guanylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,4136
Polymers48,1022
Non-polymers3114
Water5,837324
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3250 Å2
ΔGint-75 kcal/mol
Surface area20750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.733, 65.321, 107.320
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Guanylate kinase / GMP kinase


Mass: 24050.854 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria monocytogenes (bacteria) / Strain: EGD-e / Gene: gmk, lmo1827 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL / References: UniProt: Q8Y672, guanylate kinase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 324 / 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: 2.14 Å3/Da / Density % sol: 42.52 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 20%PEG 3350.0.2M Na Sulfate0.1M Bis-Tris, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 13, 2009 / Details: Be Lens
RadiationMonochromator: Diamond 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.05→30 Å / Num. all: 26526 / Num. obs: 26526 / % possible obs: 100 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 12.5 % / Biso Wilson estimate: 29.14 Å2 / Rmerge(I) obs: 0.102 / Net I/σ(I): 39.25
Reflection shellResolution: 2.05→2.09 Å / Redundancy: 12.1 % / Rmerge(I) obs: 0.658 / Mean I/σ(I) obs: 4.47 / Num. unique all: 1323 / % possible all: 100

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Processing

Software
NameVersionClassification
BLU-MAXdata collection
PHENIXmodel building
BUSTER2.8.0refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.05→24.38 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.936 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2197 1341 5.07 %RANDOM
Rwork0.1841 ---
obs0.1841 26458 100 %-
all-26526 --
Displacement parametersBiso mean: 42.43 Å2
Baniso -1Baniso -2Baniso -3
1-3.5843 Å20 Å20 Å2
2---6.7556 Å20 Å2
3---3.1713 Å2
Refine analyzeLuzzati coordinate error obs: 0.267 Å
Refinement stepCycle: LAST / Resolution: 2.05→24.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2997 0 16 324 3337
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013093HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.964172HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d01469SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes082HARMONIC2
X-RAY DIFFRACTIONt_gen_planes0442HARMONIC5
X-RAY DIFFRACTIONt_it03093HARMONIC20
X-RAY DIFFRACTIONt_nbd03SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.01
X-RAY DIFFRACTIONt_other_torsion2.92
X-RAY DIFFRACTIONt_chiral_improper_torsion0396SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact03799SEMIHARMONIC4
LS refinement shellResolution: 2.05→2.13 Å / Total num. of bins used: 13
RfactorNum. reflection% reflection
Rfree0.2592 139 4.88 %
Rwork0.1963 2708 -
all0.1993 2847 -
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)
11.3008-0.9314-0.94460.61870.40684.2169-0.0463-0.2019-0.07130.02170.04840.02040.14410.2222-0.0022-0.1862-0.00410.0258-0.1180.0122-0.12710.596116.966259.6497
213.5436-2.3216-0.80334.1467-2.812210.6320.0405-1.0879-1.0856-0.19090.00050.03830.7839-0.1785-0.041-0.1444-0.0447-0.0031-0.06280.034-0.1555-4.086512.016375.3513
39.0165-0.13881.93120-3.20586.58250.3396-0.2198-0.299-0.23330.00420.13750.3669-0.4376-0.3438-0.1061-0.06090.002-0.0949-0.0227-0.1603-6.173116.441769.7856
45.21230.89421.98510.89950.72274.47210.1836-0.2442-0.15730.2442-0.01070.0089-0.0702-0.0487-0.1729-0.0629-0.03840.0173-0.08020.0113-0.12034.501621.245465.0792
54.4812-0.5468-3.46194.21131.27644.82780.32260.11410.1348-0.06010.01080.111-0.4147-0.6937-0.3334-0.05750.05350.01630.01520.0372-0.03520.528524.385356.2716
60.7413-1.7585-1.29680.50522.49784.1394-0.01620.204-0.028-0.24460.0327-0.23970.293-0.0814-0.01650.1917-0.1003-0.12620.44230.03230.0819-1.244715.15232.3799
75.68391.62774.80845.58993.37882.8995-0.03330.69520.1526-0.483-0.07170.0746-0.2601-0.12140.105-0.1219-0.0538-0.00820.21210.0753-0.1157-6.202619.492838.9821
82.49070.48680.20070.693-1.05161.3630.05180.1040.0597-0.0809-0.01690.0316-0.0847-0.0557-0.0349-0.14730.00820.0145-0.1005-0.0061-0.11989.466621.719250.3385
91.72370.6478-0.92129.62860.32010.26140.0415-0.17730.02530.42540.0110.0202-0.0529-0.0191-0.0525-0.0304-0.04040.0661-0.1043-0.0299-0.086615.540635.263161.7274
100.32881.5316-0.72320.0158-0.49480-0.0054-0.284-0.06620.1777-0.1086-0.10590.19540.26570.1140.16860.00380.05550.2569-0.1812-0.052220.963140.474171.0663
113.3381-2.6735-0.32961.5195-3.28446.2147-0.08110.2516-0.1091-1.0102-0.0318-0.50420.86850.14880.11290.0834-0.12160.1708-0.1823-0.02540.024527.548936.729546.8222
126.28910.0518-0.63089.5421.12377.3186-0.19950.1709-0.32950.28340.2577-0.5420.3958-0.2568-0.0583-0.1013-0.07630.0138-0.2368-0.0593-0.190232.959251.042835.2744
132.6161.385-2.03650.91-3.13974.9565-0.0364-0.1899-0.0841-0.08240.2315-0.07130.6185-0.7391-0.19520.0583-0.13980.0206-0.0267-0.0328-0.051527.264754.102539.6371
142.246-3.77520.46045.50812.43520.3933-0.13780.4334-0.1656-0.87960.06560.06970.3816-0.48650.07220.2327-0.30380.12780.01360.0273-0.185221.142941.068439.1492
155.4042-0.59480.28487.0077-3.45684.5463-0.1117-0.20830.30140.0390.1849-0.3173-0.3333-0.1318-0.0732-0.0849-0.0580.0885-0.1517-0.0549-0.121522.000245.390353.7748
169.5582.9696-1.12443.94750.32462.90890.4717-1.04680.4910.3278-0.1816-0.0268-0.37260.6572-0.2901-0.0079-0.14220.08710.0312-0.118-0.131424.893845.798863.3613
179.21460.88131.97572.4488-0.35531.1117-0.10170.2283-0.2004-0.17570.136-0.29550.00170.1904-0.03420.0034-0.03680.1025-0.1008-0.0287-0.050119.868330.354150.6828
181.7313-0.7682-4.61385.0232-3.71730-0.00390.43530.1982-0.45040.0919-0.0792-0.0811-0.0731-0.0880.0653-0.0301-0.01170.07810.1386-0.07822.998828.549737.6584
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B

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