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- PDB-4np6: Crystal Structure of Adenylate Kinase from Vibrio cholerae O1 bio... -

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Basic information

Entry
Database: PDB / ID: 4np6
TitleCrystal Structure of Adenylate Kinase from Vibrio cholerae O1 biovar eltor
ComponentsAdenylate kinase
KeywordsTRANSFERASE / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Center for Structural Genomics of Infectious Diseases / CSGID / alpha-beta fold / alpha-beta-alpha sandwich
Function / homology
Function and homology information


nucleoside monophosphate metabolic process / purine nucleotide metabolic process / nucleoside diphosphate metabolic process / adenylate kinase / adenylate kinase activity / nucleobase-containing small molecule interconversion / AMP salvage / nucleoside diphosphate kinase activity / ATP binding / cytosol / cytoplasm
Similarity search - Function
Adenylate kinase, active site lid domain / Adenylate kinase, active site lid / Adenylate kinase subfamily / Adenylate kinase / Adenylate kinase, conserved site / Adenylate kinase signature. / Adenylate kinase/UMP-CMP kinase / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold ...Adenylate kinase, active site lid domain / Adenylate kinase, active site lid / Adenylate kinase subfamily / Adenylate kinase / Adenylate kinase, conserved site / Adenylate kinase signature. / Adenylate kinase/UMP-CMP kinase / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesVibrio cholerae O1 biovar El Tor (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD, Molecular replacement / Resolution: 2.004 Å
AuthorsKim, Y. / Zhou, M. / Grimshaw, S. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: Crystal Structure of Adenylate Kinase from Vibrio cholerae O1 biovar eltor
Authors: Kim, Y. / Zhou, M. / Grimshaw, S. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionNov 20, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 18, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)95,2534
Polymers95,2534
Non-polymers00
Water2,468137
1
A: Adenylate kinase
B: Adenylate kinase


Theoretical massNumber of molelcules
Total (without water)47,6272
Polymers47,6272
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2080 Å2
ΔGint-5 kcal/mol
Surface area21880 Å2
MethodPISA
2
C: Adenylate kinase
D: Adenylate kinase


Theoretical massNumber of molelcules
Total (without water)47,6272
Polymers47,6272
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1940 Å2
ΔGint-6 kcal/mol
Surface area22020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.617, 101.617, 89.637
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

#1: Protein
Adenylate kinase / / AK / ATP-AMP transphosphorylase / ATP:AMP phosphotransferase / Adenylate monophosphate kinase


Mass: 23813.354 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae O1 biovar El Tor (bacteria)
Strain: N16961 / Gene: adk, VC_0986 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 magic / References: UniProt: Q9KTB7, adenylate kinase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 137 / 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: 2.43 Å3/Da / Density % sol: 49.37 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M Hepes pH 7.5, 1.4 M sodium citrate tribasic, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 12, 2012 / Details: mirrors
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
Reflection twinOperator: h,-k,-l / Fraction: 0.5
ReflectionResolution: 2→50 Å / Num. all: 61011 / Num. obs: 61011 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 36.35 Å2 / Rsym value: 0.095 / Net I/σ(I): 8.7
Reflection shellResolution: 2→2.03 Å / Redundancy: 4.9 % / Mean I/σ(I) obs: 2.4 / Num. unique all: 3049 / Rsym value: 0.655 / % possible all: 100

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000data collection
HKL-3000phasing
SHELXSphasing
MLPHAREphasing
DMmodel building
ARP/wARPmodel building
PHENIX(phenix.refine: 1.8.1_1161)refinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing
RefinementMethod to determine structure: SAD, Molecular replacement / Resolution: 2.004→45.445 Å / σ(F): 1.34 / Phase error: 26.46 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.222 3078 5.05 %
Rwork0.186 --
obs0.188 60974 99.58 %
all-60974 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 44.32 Å2
Refinement stepCycle: LAST / Resolution: 2.004→45.445 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6550 0 0 137 6687
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0116660
X-RAY DIFFRACTIONf_angle_d1.3488983
X-RAY DIFFRACTIONf_dihedral_angle_d15.5292523
X-RAY DIFFRACTIONf_chiral_restr0.0761019
X-RAY DIFFRACTIONf_plane_restr0.0061183
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
2.0053-2.03990.28121440.2672816296091
2.0399-2.0770.28481610.27432848300995
2.077-2.1170.28761760.2622901307794
2.117-2.16020.31021720.27352829300194
2.1602-2.20710.31811420.26652900304295
2.2071-2.25850.25271400.25212943308395
2.2585-2.3150.26891490.25682889303895
2.315-2.37750.26281470.24882855300295
2.3775-2.44750.27761620.25332871303395
2.4475-2.52650.30551440.26632929304495
2.5265-2.61680.28591440.24772900307395
2.6168-2.72150.33781180.25212929304796
2.7215-2.84540.29111540.25232867302195
2.8454-2.99540.28471980.22432895309394
2.9954-3.1830.25131710.20772861303294
3.183-3.42870.21211470.19282912305995
3.4287-3.77350.18281470.15192932307995
3.7735-4.31920.17331410.12092919306095
4.3192-5.44010.16681560.1082943309995
5.4401-44.21220.15891640.14132943310794
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)
13.35372.3562-0.55847.3618-0.71464.11010.0886-0.2799-0.1265-0.14210.09950.49110.3153-0.5301-0.16620.27140.0197-0.03590.47060.0620.341420.7789.2119-0.7123
21.64560.33160.59582.28341.63173.12420.0555-0.04340.199-0.1717-0.1091-0.0643-0.2039-0.2760.05510.29260.05850.03810.33470.01110.317718.777717.122719.3811
30.98730.7480.70380.9090.37042.57950.36740.1714-0.264-0.01590.00230.07510.52110.0275-0.34440.35740.0569-0.05390.33170.03020.298526.6089.09348.1747
43.2748-0.9571-0.81411.660.52921.4126-0.22670.0843-0.2110.0705-0.05930.21350.4027-0.12910.31410.3924-0.09230.00970.3451-0.04450.231615.305831.5651-7.0197
59.53051.39830.66343.47241.28292.3656-0.4943-0.2610.4358-0.19980.00760.43730.1479-0.65550.4770.3105-0.0134-0.02320.4052-0.08210.24649.270338.0862-6.5469
64.3488-2.80691.73483.4145-3.31653.68740.0044-0.31140.1274-0.012-0.0378-0.418-0.09830.38990.09370.2602-0.01720.00730.4391-0.01660.25534.216121.83192.4683
78.8927-2.05612.6514.4583-0.14842.1470.14530.8881-0.6099-0.0704-0.0159-0.06760.00850.6855-0.17810.47520.17330.07440.392-0.0330.32431.28159.7718-5.6767
86.5043-3.7844-1.10122.68541.28031.02850.74471.023-0.5702-0.4184-0.80620.22850.63360.64330.02330.58370.0813-0.07560.6368-0.14170.315124.0686.1778-10.7911
95.99160.60971.11965.2761-0.96295.29790.53290.0496-0.54191.33730.0775-0.4556-0.18840.619-0.33130.4411-0.0765-0.09310.4856-0.03180.243-2.301726.769120.8538
101.181-1.8852-2.35313.1924.13675.24440.0089-0.3319-0.0170.05980.1256-0.05410.03170.2152-0.18370.2451-0.0043-0.01140.49960.03340.26055.753221.246618.5132
112.8259-3.86613.74695.3372-5.17645.04360.49030.6331-0.3086-0.8911-0.73920.93180.29910.55950.28350.39910.0207-0.05560.6776-0.17450.4075.061812.4943-0.9123
123.16221.23950.38133.6682-1.20632.3764-0.01670.39430.1691-0.0703-0.15030.2540.18470.42970.18150.22-0.0193-0.04740.31470.00760.2416-1.557615.61865.8617
134.0183-2.00564.01745.330.64495.88260.0187-0.25850.30150.5935-0.2616-0.38330.2277-0.21950.4030.2744-0.00930.05330.31150.05480.3467-1.11618.111917.7896
142.59280.1494-0.39190.69380.11235.6743-0.1565-0.3753-0.5272-0.1114-0.15780.1230.1604-0.04580.31780.24480.00530.02260.2810.01090.296-8.730723.990216.7844
153.06910.7874-4.02230.9567-0.20176.17970.4394-0.48790.06750.1103-0.45370.0007-0.58650.44470.13510.4118-0.0245-0.04910.2865-0.01540.34749.966743.78615.6691
162.332-0.4116-1.6622.0392-0.05013.97840.4783-0.28270.0440.1914-0.081-0.22350.97911.2265-0.39160.41740.1054-0.06540.6124-0.10060.347523.124540.072113.3662
175.87343.5054-1.37894.3012-0.58670.5862-0.1722-0.09460.097-0.10090.02920.0660.0019-0.02410.11560.25220.0235-0.04730.29340.00370.2123-6.412235.153516.279
188.97190.6829-2.87743.4006-0.23077.0821-0.286-1.2460.27670.1796-0.2020.0488-0.5085-0.31760.49110.47650.1009-0.06630.4748-0.03890.21010.401431.400432.9324
192.1321.92941.62614.8846-0.48644.4127-0.2661-0.6661-0.29560.2550.0645-0.37620.22530.77910.09320.33320.073-0.03790.2941-0.01170.233240.810925.689859.4047
205.75821.0924-0.88154.7193-1.46137.48840.2712-0.0058-0.1440.37850.349-0.2034-0.68080.5877-0.52970.40670.0569-0.07020.4659-0.09520.367842.361633.599863.8165
215.5887-3.53986.07674.0961-4.31788.3172-0.7541-0.28610.01040.19950.4658-0.2125-0.7075-0.52820.20960.38150.02270.06760.2732-0.06210.280534.151235.18347.63
221.0654-0.24161.60192.4775-0.80852.4348-0.10190.0915-0.049-0.2250.15120.0703-0.0610.0981-0.06130.33450.0010.06020.2922-0.02010.226134.004530.576338.6117
230.01910.1038-0.27697.43941.29175.21760.5896-0.48380.72960.9035-0.13260.303-0.0970.5202-0.39470.2905-0.00140.05980.335-0.09850.29442.656229.674451.8261
243.07770.5576-0.2681.3713-0.72824.3884-0.2674-0.4013-0.12770.11170.1903-0.2608-0.09460.37730.17260.27790.0999-0.00380.25280.00770.2640.98819.917653.9472
254.518-5.5532-0.5276.66820.64780.6316-0.1735-0.2333-0.13920.0188-0.18690.32580.08230.04440.34640.3571-0.0288-0.00790.3654-0.01370.28619.54930.136368.5379
263.1005-0.6921.32013.524-0.85985.2006-0.26750.60530.20920.18970.04260.0898-0.38760.5060.1860.3051-0.07560.00860.42060.00210.279614.774641.519767.5915
272.6348-0.3345-0.47061.43681.3973.3014-0.0816-0.0773-0.22790.18610.04630.02510.25740.24250.00940.44490.03980.03420.27960.05350.260432.917417.589661.2339
283.9484-3.3054-3.77553.38812.82993.81170.1334-0.8259-0.58320.714-0.1681-0.1340.8224-0.2820.0170.5674-0.0308-0.10640.60210.00140.261644.661326.894271.9237
296.67770.2729-2.86113.65411.68166.2652-0.29240.1367-0.2394-0.36520.11630.20120.47490.37210.1780.37650.0792-0.01490.2567-0.01230.252725.699748.43736.9305
301.2586-1.30651.58985.6182-0.20712.60820.0617-0.0074-0.1170.72530.1734-0.22440.38720.0153-0.27760.4036-0.03480.0340.3334-0.02390.301535.253944.825856.7113
314.21340.43372.35834.14870.4573.1445-0.10910.1304-0.1578-0.18660.0126-0.11290.01910.13630.10310.25740.00040.0270.1875-0.03840.225231.000755.285247.1033
323.0494-0.85610.05884.7523-4.08677.36490.40.1458-0.0577-0.8104-0.51990.30730.7851.15730.11340.40650.0162-0.03230.4986-0.03850.26019.852335.015545.3249
331.52740.5645-0.71710.698-0.7192.4331-0.14520.0095-0.0664-0.35640.10910.04810.4803-0.13770.0030.33930.0204-0.04180.2151-0.00990.216914.28248.847143.3295
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid -1 through 26 )
2X-RAY DIFFRACTION2chain 'A' and (resid 27 through 71 )
3X-RAY DIFFRACTION3chain 'A' and (resid 72 through 112 )
4X-RAY DIFFRACTION4chain 'A' and (resid 113 through 139 )
5X-RAY DIFFRACTION5chain 'A' and (resid 140 through 160 )
6X-RAY DIFFRACTION6chain 'A' and (resid 161 through 187 )
7X-RAY DIFFRACTION7chain 'A' and (resid 188 through 201 )
8X-RAY DIFFRACTION8chain 'A' and (resid 202 through 214 )
9X-RAY DIFFRACTION9chain 'B' and (resid 0 through 12 )
10X-RAY DIFFRACTION10chain 'B' and (resid 13 through 41 )
11X-RAY DIFFRACTION11chain 'B' and (resid 42 through 54 )
12X-RAY DIFFRACTION12chain 'B' and (resid 55 through 73 )
13X-RAY DIFFRACTION13chain 'B' and (resid 74 through 89 )
14X-RAY DIFFRACTION14chain 'B' and (resid 90 through 112 )
15X-RAY DIFFRACTION15chain 'B' and (resid 113 through 125 )
16X-RAY DIFFRACTION16chain 'B' and (resid 126 through 160 )
17X-RAY DIFFRACTION17chain 'B' and (resid 161 through 201 )
18X-RAY DIFFRACTION18chain 'B' and (resid 202 through 214 )
19X-RAY DIFFRACTION19chain 'C' and (resid -1 through 12 )
20X-RAY DIFFRACTION20chain 'C' and (resid 13 through 26 )
21X-RAY DIFFRACTION21chain 'C' and (resid 27 through 41 )
22X-RAY DIFFRACTION22chain 'C' and (resid 42 through 72 )
23X-RAY DIFFRACTION23chain 'C' and (resid 73 through 89 )
24X-RAY DIFFRACTION24chain 'C' and (resid 90 through 112 )
25X-RAY DIFFRACTION25chain 'C' and (resid 113 through 126 )
26X-RAY DIFFRACTION26chain 'C' and (resid 127 through 160 )
27X-RAY DIFFRACTION27chain 'C' and (resid 161 through 201 )
28X-RAY DIFFRACTION28chain 'C' and (resid 202 through 214 )
29X-RAY DIFFRACTION29chain 'D' and (resid 0 through 27 )
30X-RAY DIFFRACTION30chain 'D' and (resid 28 through 55 )
31X-RAY DIFFRACTION31chain 'D' and (resid 56 through 112 )
32X-RAY DIFFRACTION32chain 'D' and (resid 113 through 139 )
33X-RAY DIFFRACTION33chain 'D' and (resid 140 through 214 )

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