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- PDB-4bgb: Nucleotide-bound closed form of a putative sugar kinase MK0840 fr... -

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Basic information

Entry
Database: PDB / ID: 4bgb
TitleNucleotide-bound closed form of a putative sugar kinase MK0840 from Methanopyrus kandleri
ComponentsPUTATIVE SUGAR KINASE MK0840
KeywordsTRANSFERASE / 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
ADENOSINE-5'-DIPHOSPHATE / : / Predicted molecular chaperone distantly related to HSP70-fold metalloproteases
Similarity search - Component
Biological speciesMETHANOPYRUS KANDLERI (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.34 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 4, 2013Group: Derived calculations
Revision 1.2Dec 18, 2013Group: Database references
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_alt_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_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_alt_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_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.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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

Downloads & links

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Assembly

Deposited unit
A: PUTATIVE SUGAR KINASE MK0840
B: PUTATIVE SUGAR KINASE MK0840
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,91220
Polymers70,1192
Non-polymers1,79318
Water9,350519
1
A: PUTATIVE SUGAR KINASE MK0840
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,9069
Polymers35,0601
Non-polymers8468
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: PUTATIVE SUGAR KINASE MK0840
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,00611
Polymers35,0601
Non-polymers94710
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)54.790, 108.540, 117.350
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein PUTATIVE SUGAR KINASE MK0840


Mass: 35059.656 Da / Num. of mol.: 2 / 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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Non-polymers , 6 types, 537 molecules

#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 519 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer detailsGLYCEROL (GOL): GOL7 ONLY PARTIALLY OCCUPIED
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: 2.3 Å3/Da / Density % sol: 46.5 %
Description: PARTIAL MODEL SOLVED BY MR. MODEL FOR SECOND PROTOMER - CLOSED FORM - BUILD BY WEB-BASED ARPWARP. MERGED DATASET FROM LOW-RESOLUTION AND HIGH-RESOLUTION PASS.
Crystal growpH: 4.6
Details: 0.14 M CACL2, 0.07 M SODIUM ACETATE PH 4.6, 10 % ISOPROPANOL AND 28% GLYCEROL

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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: Nov 8, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.34→45.2 Å / Num. obs: 154630 / % possible obs: 98.3 % / Observed criterion σ(I): 2 / Redundancy: 4.5 % / Biso Wilson estimate: 14.8 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 21.12
Reflection shellResolution: 1.34→1.37 Å / Redundancy: 4 % / Rmerge(I) obs: 0.65 / Mean I/σ(I) obs: 2.61 / % possible all: 93.2

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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 4BGA CHAIN A

4bga


Resolution: 1.34→45.147 Å / SU ML: 0.13 / σ(F): 1.99 / Phase error: 20.02 / 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
Rfree0.1828 7732 5 %
Rwork0.1576 --
obs0.1588 154611 98.34 %
Solvent computationShrinkage radii: 1.1 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.413 Å2 / ksol: 0.362 e/Å3
Displacement parametersBiso mean: 27.09 Å2
Baniso -1Baniso -2Baniso -3
1--5.1011 Å20 Å20 Å2
2---2.3404 Å20 Å2
3---7.4415 Å2
Refinement stepCycle: LAST / Resolution: 1.34→45.147 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4798 0 105 519 5422
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0125291
X-RAY DIFFRACTIONf_angle_d1.4827222
X-RAY DIFFRACTIONf_dihedral_angle_d12.4992020
X-RAY DIFFRACTIONf_chiral_restr0.077800
X-RAY DIFFRACTIONf_plane_restr0.006968
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3402-1.35540.32252270.28434315X-RAY DIFFRACTION88
1.3554-1.37140.2852530.25424797X-RAY DIFFRACTION97
1.3714-1.38810.28522510.2464767X-RAY DIFFRACTION97
1.3881-1.40570.27682560.23634875X-RAY DIFFRACTION98
1.4057-1.42410.26342520.21974769X-RAY DIFFRACTION98
1.4241-1.44370.24232550.20724856X-RAY DIFFRACTION98
1.4437-1.46430.24242510.19044769X-RAY DIFFRACTION98
1.4643-1.48610.23652580.19014890X-RAY DIFFRACTION98
1.4861-1.50940.22722540.1714830X-RAY DIFFRACTION98
1.5094-1.53410.21192540.16174827X-RAY DIFFRACTION98
1.5341-1.56060.19712570.15324891X-RAY DIFFRACTION98
1.5606-1.58890.20262550.15294838X-RAY DIFFRACTION98
1.5889-1.61950.18182570.14684876X-RAY DIFFRACTION98
1.6195-1.65260.19582570.14184882X-RAY DIFFRACTION99
1.6526-1.68850.17032570.14214883X-RAY DIFFRACTION99
1.6885-1.72780.18772580.14294902X-RAY DIFFRACTION99
1.7278-1.7710.19082590.14374916X-RAY DIFFRACTION99
1.771-1.81890.16652580.13314905X-RAY DIFFRACTION99
1.8189-1.87240.15992580.13414915X-RAY DIFFRACTION99
1.8724-1.93280.17362600.13794923X-RAY DIFFRACTION99
1.9328-2.00190.17862590.13914935X-RAY DIFFRACTION99
2.0019-2.08210.15612610.13944945X-RAY DIFFRACTION99
2.0821-2.17680.16632610.14214965X-RAY DIFFRACTION99
2.1768-2.29160.16822610.14274970X-RAY DIFFRACTION99
2.2916-2.43520.17782620.14834979X-RAY DIFFRACTION99
2.4352-2.62320.17132640.16324999X-RAY DIFFRACTION100
2.6232-2.88710.17962640.16585015X-RAY DIFFRACTION99
2.8871-3.30480.17252660.1615053X-RAY DIFFRACTION100
3.3048-4.16320.17282680.1465107X-RAY DIFFRACTION100
4.1632-45.17260.1762790.16575285X-RAY DIFFRACTION99

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