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- PDB-4bga: Nucleotide-bound open form of a putative sugar kinase MK0840 from... -

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Basic information

Entry
Database: PDB / ID: 4bga
TitleNucleotide-bound open form of a putative sugar kinase MK0840 from Methanopyrus kandleri
ComponentsPREDICTED MOLECULAR CHAPERONE DISTANTLY RELATED TO HSP70-F OLD METALLOPROTEASES
KeywordsTRANSFERASE / ASKHA SUPERFAMILY / PHOSPHOTRANSFER / PSEUDOMUREIN
Function / homology
Function and homology information


amino sugar metabolic process / phosphotransferase activity, alcohol group as acceptor / peptidoglycan turnover / metallopeptidase activity / ATP binding / metal ion binding
Similarity search - Function
Nucleotidyltransferase; domain 5 - #430 / Anhydro-N-acetylmuramic acid kinase / Anhydro-N-acetylmuramic acid kinase / ATPase, nucleotide binding domain / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
sucrose / ADENOSINE-5'-DIPHOSPHATE / beta-D-glucopyranose / : / Predicted molecular chaperone distantly related to HSP70-fold metalloproteases
Similarity search - Component
Biological speciesMETHANOPYRUS KANDLERI (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsSchacherl, M. / Baumann, U.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2013
Title: Structural Characterization of the Ribonuclease H-Like Type Askha Superfamily Kinase Mk0840 from Methanopyrus Kandleri
Authors: Schacherl, M. / Waltersperger, S.M. / Baumann, U.
History
DepositionMar 24, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 27, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2013Group: Database references
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_database_status.status_code_sf / _pdbx_struct_assembly_gen.asym_id_list / _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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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_asym.entity_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _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: PREDICTED MOLECULAR CHAPERONE DISTANTLY RELATED TO HSP70-F OLD METALLOPROTEASES
B: PREDICTED MOLECULAR CHAPERONE DISTANTLY RELATED TO HSP70-F OLD METALLOPROTEASES
C: PREDICTED MOLECULAR CHAPERONE DISTANTLY RELATED TO HSP70-F OLD METALLOPROTEASES
D: PREDICTED MOLECULAR CHAPERONE DISTANTLY RELATED TO HSP70-F OLD METALLOPROTEASES
hetero molecules


Theoretical massNumber of molelcules
Total (without water)143,73825
Polymers140,2394
Non-polymers3,50021
Water3,999222
1
A: PREDICTED MOLECULAR CHAPERONE DISTANTLY RELATED TO HSP70-F OLD METALLOPROTEASES
C: PREDICTED MOLECULAR CHAPERONE DISTANTLY RELATED TO HSP70-F OLD METALLOPROTEASES
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,85712
Polymers70,1192
Non-polymers1,73810
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1410 Å2
ΔGint-7.1 kcal/mol
Surface area31970 Å2
MethodPISA
2
B: PREDICTED MOLECULAR CHAPERONE DISTANTLY RELATED TO HSP70-F OLD METALLOPROTEASES
D: PREDICTED MOLECULAR CHAPERONE DISTANTLY RELATED TO HSP70-F OLD METALLOPROTEASES
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,88113
Polymers70,1192
Non-polymers1,76211
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6740 Å2
ΔGint-45.9 kcal/mol
Surface area24220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.570, 111.670, 87.880
Angle α, β, γ (deg.)90.00, 89.55, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
PREDICTED MOLECULAR CHAPERONE DISTANTLY RELATED TO HSP70-F OLD METALLOPROTEASES / PUTATIVE SUGAR KINASE MK0840


Mass: 35059.656 Da / Num. of mol.: 4 / Fragment: RESIDUES 37-358
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) METHANOPYRUS KANDLERI (archaea) / Strain: AV19 / Description: DSM6324 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8TX37

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Sugars , 2 types, 6 molecules

#2: Polysaccharide beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose / sucrose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with reducing-end-to-reducing-end glycosidic bond
References: sucrose
DescriptorTypeProgram
DFrufb2-1DGlcpaGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[ha122h-2b_2-5][a2122h-1a_1-5]/1-2/a2-b1WURCSPDB2Glycan 1.1.0
[][b-D-Fruf]{[(2+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#4: Sugar
ChemComp-BGC / beta-D-glucopyranose / beta-D-glucose / D-glucose / glucose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranoseCOMMON NAMEGMML 1.0
b-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 4 types, 237 molecules

#3: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: K
#5: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 222 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer detailsSUCROSE (SUC): CRYOPROTECTANT
Sequence detailsTRUNCATED CONSTRUCT LACKING THE FIRST 36 AMINO ACIDS

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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: 2.37 Å3/Da / Density % sol: 48.24 % / Description: NONE
Crystal growpH: 7.5
Details: MIXED WITH 5 MM ADP, 10 MM MACL2, CRYSTALLIZED IN 0.2 M POTASSIUM SODIUM TARTRATE AND 20% PEG 3350, pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 6, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→73.6 Å / Num. obs: 54893 / % possible obs: 100 % / Observed criterion σ(I): 4 / Redundancy: 7.6 % / Biso Wilson estimate: 33.99 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 21.95
Reflection shellResolution: 2.6→2.76 Å / Redundancy: 7.69 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 5.98 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4BG8 CHAIN A

4bg8


Resolution: 2.6→73.568 Å / SU ML: 0.29 / σ(F): 2 / Phase error: 20.53 / Stereochemistry target values: ML
Details: FIRST 36 AMINO ACIDS OF THE PROTEIN ARE MISSING.GSH OVERHANG FROM THROMBIN-DIGESTED 6X-HIS TAG.
RfactorNum. reflection% reflection
Rfree0.208 2188 5 %
Rwork0.1542 --
obs0.1569 43757 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 40.44 Å2
Refinement stepCycle: LAST / Resolution: 2.6→73.568 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9611 0 213 222 10046
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00610011
X-RAY DIFFRACTIONf_angle_d1.18113642
X-RAY DIFFRACTIONf_dihedral_angle_d20.3793816
X-RAY DIFFRACTIONf_chiral_restr0.0651561
X-RAY DIFFRACTIONf_plane_restr0.0051799
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.65650.24961360.17732582X-RAY DIFFRACTION100
2.6565-2.71830.24661370.1782605X-RAY DIFFRACTION100
2.7183-2.78630.28871350.17722567X-RAY DIFFRACTION100
2.7863-2.86170.23351360.18422589X-RAY DIFFRACTION100
2.8617-2.94590.27741360.17842590X-RAY DIFFRACTION100
2.9459-3.0410.25111360.19032569X-RAY DIFFRACTION100
3.041-3.14960.28891360.18222592X-RAY DIFFRACTION100
3.1496-3.27570.24061360.17622592X-RAY DIFFRACTION100
3.2757-3.42480.19631360.16062585X-RAY DIFFRACTION100
3.4248-3.60540.22351370.15172602X-RAY DIFFRACTION100
3.6054-3.83130.20561370.14232602X-RAY DIFFRACTION100
3.8313-4.12710.16531370.13262600X-RAY DIFFRACTION100
4.1271-4.54230.15511370.11532595X-RAY DIFFRACTION100
4.5423-5.19950.15131380.12022617X-RAY DIFFRACTION100
5.1995-6.55010.20651380.15672622X-RAY DIFFRACTION100
6.5501-73.59720.19461400.16542660X-RAY DIFFRACTION100

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