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- PDB-4bg9: Apo form of a putative sugar kinase MK0840 from Methanopyrus kand... -

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Basic information

Entry
Database: PDB / ID: 4bg9
TitleApo form of a putative sugar kinase MK0840 from Methanopyrus kandleri (orthorhombic space group)
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
ACETATE ION / : / Predicted molecular chaperone distantly related to HSP70-fold metalloproteases
Similarity search - Component
Biological speciesMETHANOPYRUS KANDLERI (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.902 Å
AuthorsSchacherl, M. / Waltersperger, S.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 1.2Mar 6, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_conn
Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3Dec 20, 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 / struct_site
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.ptnr1_symmetry / _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.ptnr3_symmetry / _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.ptnr1_symmetry / _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 / _struct_conn.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PREDICTED MOLECULAR CHAPERONE DISTANTLY RELATED TO HSP70-F OLD METALLOPROTEASES
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,1886
Polymers38,9761
Non-polymers2125
Water2,738152
1
A: PREDICTED MOLECULAR CHAPERONE DISTANTLY RELATED TO HSP70-F OLD METALLOPROTEASES
hetero molecules

A: PREDICTED MOLECULAR CHAPERONE DISTANTLY RELATED TO HSP70-F OLD METALLOPROTEASES
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,37612
Polymers77,9532
Non-polymers42410
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Buried area5090 Å2
ΔGint-47.6 kcal/mol
Surface area25330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.043, 115.967, 48.363
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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


Mass: 38976.352 Da / Num. of mol.: 1
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
#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: K
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 152 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsGSH OVERHANG FROM THROMBIN DIGEST OF THE N-TERMINAL 6XHIS- TAG

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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: 2.7 Å3/Da / Density % sol: 54.4 % / Description: NONE
Crystal growTemperature: 293 K / pH: 4.6
Details: 0.5 M POTASSIUM THIOCYANATE, 0.1 M SODIUM ACETATE PH 4.6 AT 293 K

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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: Feb 15, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→61.8 Å / Num. obs: 33085 / % possible obs: 99.5 % / Observed criterion σ(I): 2 / Redundancy: 4.6 % / Biso Wilson estimate: 21.31 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 14.6
Reflection shellResolution: 1.9→2.02 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.71 / Mean I/σ(I) obs: 2.17 / % possible all: 97.5

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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: 1.902→61.805 Å / SU ML: 0.22 / σ(F): 1.17 / Phase error: 20.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2084 3100 5 %
Rwork0.1787 --
obs0.1802 33085 99.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.6 Å2
Baniso -1Baniso -2Baniso -3
1-5.3344 Å20 Å20 Å2
2---3.7407 Å20 Å2
3----1.5937 Å2
Refinement stepCycle: LAST / Resolution: 1.902→61.805 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2391 0 8 152 2551
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0132442
X-RAY DIFFRACTIONf_angle_d1.3753320
X-RAY DIFFRACTIONf_dihedral_angle_d14.08917
X-RAY DIFFRACTIONf_chiral_restr0.076376
X-RAY DIFFRACTIONf_plane_restr0.007448
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9021-1.93190.35511400.29912612X-RAY DIFFRACTION97
1.9319-1.96350.28121410.28082673X-RAY DIFFRACTION99
1.9635-1.99740.29821380.25972674X-RAY DIFFRACTION99
1.9974-2.03370.30521400.24712679X-RAY DIFFRACTION100
2.0337-2.07280.28791450.23282658X-RAY DIFFRACTION100
2.0728-2.11510.24861450.22382676X-RAY DIFFRACTION99
2.1151-2.16110.20471410.20532663X-RAY DIFFRACTION99
2.1611-2.21140.22761430.19662707X-RAY DIFFRACTION99
2.2114-2.26670.2221370.18652646X-RAY DIFFRACTION100
2.2667-2.3280.24241420.18082700X-RAY DIFFRACTION99
2.328-2.39650.22891410.17422674X-RAY DIFFRACTION100
2.3965-2.47390.20041390.172667X-RAY DIFFRACTION100
2.4739-2.56230.22731430.17842703X-RAY DIFFRACTION99
2.5623-2.66490.23331400.16542678X-RAY DIFFRACTION100
2.6649-2.78620.2181400.16662671X-RAY DIFFRACTION100
2.7862-2.93310.21181370.17382674X-RAY DIFFRACTION99
2.9331-3.11680.21191460.17012697X-RAY DIFFRACTION100
3.1168-3.35750.1961370.15782661X-RAY DIFFRACTION99
3.3575-3.69530.17211440.14962689X-RAY DIFFRACTION99
3.6953-4.22990.14931400.14192650X-RAY DIFFRACTION99
4.2299-5.32880.14041370.14082659X-RAY DIFFRACTION98
5.3288-61.83760.23261440.19742682X-RAY DIFFRACTION99

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