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- PDB-2j41: Crystal structure of Staphylococcus aureus guanylate monophosphat... -

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Basic information

Entry
Database: PDB / ID: 2j41
TitleCrystal structure of Staphylococcus aureus guanylate monophosphate kinase
ComponentsGUANYLATE KINASE
KeywordsTRANSFERASE / GMP / GMK / KINASE / ATP-BINDING / NUCLEOTIDE-BINDING / STAPHYLOCOCCUS AUREUS
Function / homology
Function and homology information


guanylate kinase / guanylate kinase activity / ATP binding / cytoplasm
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 speciesSTAPHYLOCOCCUS AUREUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsEl Omari, K. / Dhaliwal, B. / Lockyer, M. / Charles, I. / Hawkins, A.R. / Stammers, D.K.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2006
Title: Structure of Staphylococcus Aureus Guanylate Monophosphate Kinase
Authors: El Omari, K. / Dhaliwal, B. / Lockyer, M. / Charles, I. / Hawkins, A.R. / Stammers, D.K.
History
DepositionAug 24, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 11, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GUANYLATE KINASE
B: GUANYLATE KINASE
C: GUANYLATE KINASE
D: GUANYLATE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,98115
Polymers96,2944
Non-polymers1,68711
Water8,485471
1
A: GUANYLATE KINASE
B: GUANYLATE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,7416
Polymers48,1472
Non-polymers5944
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1930 Å2
ΔGint-31.6 kcal/mol
Surface area21520 Å2
MethodPQS
2
C: GUANYLATE KINASE
D: GUANYLATE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,2409
Polymers48,1472
Non-polymers1,0937
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2070 Å2
ΔGint-29.9 kcal/mol
Surface area22510 Å2
MethodPQS
Unit cell
Length a, b, c (Å)70.012, 93.986, 83.936
Angle α, β, γ (deg.)90.00, 110.59, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
GUANYLATE KINASE / / GMP KINASE / STAPHYLOCOCCUS AUREUS GUANYLATE MONOPHOSPHATE KINASE


Mass: 24073.416 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STAPHYLOCOCCUS AUREUS (bacteria) / Plasmid: PET15B / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q5HGM3, guanylate kinase
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


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


Mass: 39.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-5GP / GUANOSINE-5'-MONOPHOSPHATE / Guanosine monophosphate


Mass: 363.221 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H14N5O8P
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 471 / 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: 2.69 Å3/Da / Density % sol: 54.35 % / Description: NONE
Crystal growpH: 8.8 / Details: 20% PEG 3350, 0.2 M LISO4, 0.1 M TRIS/HCL PH 8.8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.93
DetectorType: ADSC CCD / Detector: CCD / Date: Sep 6, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. obs: 75428 / % possible obs: 99.3 % / Observed criterion σ(I): 2.9 / Redundancy: 3.6 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 31.6
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 2.96 / % possible all: 95.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
MrBUMPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2ANB

2anb


Resolution: 1.9→29.4 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.918 / SU B: 5.355 / SU ML: 0.089 / Cross valid method: THROUGHOUT / ESU R: 0.14 / ESU R Free: 0.133 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.239 3991 5 %RANDOM
Rwork0.207 ---
obs0.209 75423 99.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.46 Å2
Baniso -1Baniso -2Baniso -3
1--0.54 Å20 Å2-1.43 Å2
2---0.44 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.9→29.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5621 0 100 471 6192
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0225834
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3221.9927865
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7525686
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.46224.192291
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.711151064
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9231541
X-RAY DIFFRACTIONr_chiral_restr0.0960.2842
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024373
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2050.22783
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3030.23999
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1570.2481
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2590.260
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1650.222
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6151.53435
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.16825557
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.88732448
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.0354.52307
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.95 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.297 276
Rwork0.221 5243

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