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- PDB-3tr0: Structure of guanylate kinase (gmk) from Coxiella burnetii -

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Basic information

Entry
Database: PDB / ID: 3tr0
TitleStructure of guanylate kinase (gmk) from Coxiella burnetii
ComponentsGuanylate kinase
KeywordsTRANSFERASE / Purines / pyrimidines / nucleosides / nucleotides
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
GUANOSINE-5'-MONOPHOSPHATE / Guanylate kinase
Similarity search - Component
Biological speciesCoxiella burnetii (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.851 Å
AuthorsCheung, J. / Franklin, M. / Rudolph, M. / Cassidy, M. / Gary, E. / Burshteyn, F. / Love, J.
CitationJournal: Proteins / Year: 2015
Title: Structural genomics for drug design against the pathogen Coxiella burnetii.
Authors: Franklin, M.C. / Cheung, J. / Rudolph, M.J. / Burshteyn, F. / Cassidy, M. / Gary, E. / Hillerich, B. / Yao, Z.K. / Carlier, P.R. / Totrov, M. / Love, J.D.
History
DepositionSep 9, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 21, 2011Provider: repository / Type: Initial release
Revision 1.1Jun 24, 2015Group: Database references
Revision 1.2Jan 27, 2016Group: Database references
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software
Revision 1.4Sep 13, 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_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_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Guanylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,3284
Polymers23,7731
Non-polymers5553
Water3,189177
1
A: Guanylate kinase
hetero molecules

A: Guanylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,6568
Polymers47,5462
Non-polymers1,1116
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_554-x,y,-z-11
Buried area4780 Å2
ΔGint-79 kcal/mol
Surface area19740 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.834, 45.899, 70.042
Angle α, β, γ (deg.)90.00, 90.35, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Guanylate kinase / GMP kinase


Mass: 23772.820 Da / Num. of mol.: 1 / Fragment: UNP residues 1-202
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Coxiella burnetii (bacteria) / Strain: RSA493 / Gene: CBU_0301, gmk / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q83EL7, guanylate kinase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-5GP / GUANOSINE-5'-MONOPHOSPHATE


Mass: 363.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O8P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 177 / 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: 2.29 Å3/Da / Density % sol: 46.36 %
Crystal growTemperature: 295 K / Method: sitting drop / pH: 8.5
Details: 0.1 M Tris, pH 8.5, 2.4 M ammonium sulfate, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Jun 2, 2011
RadiationMonochromator: VARIMAX HF / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. all: 18517 / Num. obs: 17943 / % possible obs: 96.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Rmerge(I) obs: 0.033 / Net I/σ(I): 22.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.85-1.881.70.186179.3
1.88-1.9220.119187.8
1.92-1.952.30.105193.1
1.95-1.992.40.101193.6
1.99-2.042.60.094197.6
2.04-2.082.70.076195.8
2.08-2.142.90.066198.9
2.14-2.193.10.061197.1
2.19-2.263.50.059199.6
2.26-2.333.60.053198.1
2.33-2.413.60.043198.6
2.41-2.513.60.041199.8
2.51-2.633.60.036199.1
2.63-2.763.60.034199.2
2.76-2.943.60.027199.6
2.94-3.163.60.0241100
3.16-3.483.60.022199.6
3.48-3.994.40.028199.8
3.99-5.026.40.0331100
5.02-506.70.0311100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PHENIX1.7_650refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2AN9

2an9


Resolution: 1.851→38.014 Å / Occupancy max: 1 / Occupancy min: 0.31 / SU ML: 0.24 / σ(F): 0 / Phase error: 22.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2326 918 5.12 %
Rwork0.1913 --
obs0.1936 17936 96.75 %
all-19487 -
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.434 Å2 / ksol: 0.355 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--3.5579 Å20 Å21.3509 Å2
2--10.5467 Å2-0 Å2
3----6.9889 Å2
Refinement stepCycle: LAST / Resolution: 1.851→38.014 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1639 0 34 177 1850
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031721
X-RAY DIFFRACTIONf_angle_d0.8332331
X-RAY DIFFRACTIONf_dihedral_angle_d15.067660
X-RAY DIFFRACTIONf_chiral_restr0.054258
X-RAY DIFFRACTIONf_plane_restr0.003299
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.851-1.94880.23781150.2062135X-RAY DIFFRACTION86
1.9488-2.07090.30151220.18292389X-RAY DIFFRACTION95
2.0709-2.23080.22481310.18862428X-RAY DIFFRACTION98
2.2308-2.45520.22341270.18442488X-RAY DIFFRACTION99
2.4552-2.81040.27921370.21242497X-RAY DIFFRACTION99
2.8104-3.54040.23681340.19652509X-RAY DIFFRACTION100
3.5404-38.02220.2091520.18262572X-RAY DIFFRACTION100
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)
10.0520.0932-0.05760.3939-0.1380.45450.032-0.1227-0.0143-0.0278-0.0993-0.0147-0.02020.14820.02350.1339-0.04120.01270.16140.00260.1337-4.424621.7766-22.6311
20.20380.00060.18570.01550.05370.35160.1868-0.15860.02170.2075-0.07930.0310.1423-0.1068-0.05920.2358-0.0326-0.01320.13910.03580.219-6.137211.3774-20.3608
31.03-0.2696-0.63950.22510.05850.4683-0.0727-0.3646-0.07290.14610.10020.1177-0.0249-0.1439-0.0260.182-0.03750.02610.38980.0320.177-6.320717.6526-11.1242
41.0557-0.41220.28950.7834-0.19560.1275-0.0087-0.79180.01590.60270.06320.1173-0.2853-0.0581-0.0130.4035-0.05510.04690.4048-0.05760.1878-9.813224.7743-4.8255
50.29190.0557-0.29150.2969-0.25790.4439-0.0027-0.21850.1310.2056-0.04550.0058-0.3868-0.01430.05180.2104-0.0627-0.00870.3682-0.03280.142-0.543825.0407-10.4481
60.0754-0.0644-0.0430.14220.04090.12760.0141-0.0512-0.02670.0254-0.02220.0816-0.02610.03960.0050.1153-0.0291-0.00280.1038-0.00670.1455-6.175825.9239-21.88
70.12570.0662-0.03190.0841-0.0260.05320.0075-0.0685-0.09840.2296-0.06310.13650.0327-0.0438-0.01850.1667-0.38310.18620.2158-0.08650.3681-25.944313.3977-16.6052
80.7515-0.0329-0.11640.4977-0.07770.24140.06970.13170.08620.4104-0.20880.4134-0.0911-0.23590.01340.2155-0.00830.03650.1672-0.05060.2424-17.592923.4021-25.9986
90.6103-0.32220.13090.20730.08220.81840.02050.074-0.0682-0.0175-0.06720.06580.2427-0.02450.01710.1522-0.0208-0.01030.1377-0.02070.1596-2.198614.1645-30.4444
100.56450.49050.41020.91950.39781.18350.1691-0.2103-0.01250.09640.0521-0.30730.02590.4672-0.13620.18-0.042-0.00980.3877-0.03770.220317.31823.1086-32.763
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 2:16)
2X-RAY DIFFRACTION2chain 'A' and (resseq 17:27)
3X-RAY DIFFRACTION3chain 'A' and (resseq 28:43)
4X-RAY DIFFRACTION4chain 'A' and (resseq 44:77)
5X-RAY DIFFRACTION5chain 'A' and (resseq 78:92)
6X-RAY DIFFRACTION6chain 'A' and (resseq 93:125)
7X-RAY DIFFRACTION7chain 'A' and (resseq 126:145)
8X-RAY DIFFRACTION8chain 'A' and (resseq 146:169)
9X-RAY DIFFRACTION9chain 'A' and (resseq 170:186)
10X-RAY DIFFRACTION10chain 'A' and (resseq 187:202)

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