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- PDB-4bzp: Structure of the Mycobacterium tuberculosis APS kinase CysC in co... -

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Basic information

Entry
Database: PDB / ID: 4bzp
TitleStructure of the Mycobacterium tuberculosis APS kinase CysC in complex with ADP
ComponentsBIFUNCTIONAL ENZYME CYSN/CYSC
KeywordsTRANSFERASE / SULFUR ASSIMILATION
Function / homology
Function and homology information


adenylyl-sulfate kinase / sulfate adenylyltransferase / adenylylsulfate kinase activity / sulfate adenylyltransferase (ATP) activity / sulfate assimilation / hydrogen sulfide biosynthetic process / GTPase activity / GTP binding / ATP binding
Similarity search - Function
Sulphate adenylyltransferase, large subunit / Sulfate adenylyltransferase subunit CysN, GTP-binding domain / Sulfate adenylyltransferase subunit CysN, Domain II / Sulfate adenylyltransferase subunit CysN, Domain III / Adenylyl-sulfate kinase / Adenylylsulphate kinase / : / GTP-eEF1A C-terminal domain-like / : / Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal ...Sulphate adenylyltransferase, large subunit / Sulfate adenylyltransferase subunit CysN, GTP-binding domain / Sulfate adenylyltransferase subunit CysN, Domain II / Sulfate adenylyltransferase subunit CysN, Domain III / Adenylyl-sulfate kinase / Adenylylsulphate kinase / : / GTP-eEF1A C-terminal domain-like / : / Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal / Tr-type G domain, conserved site / Translational (tr)-type guanine nucleotide-binding (G) domain signature. / Translational (tr)-type GTP-binding domain / Elongation factor Tu GTP binding domain / Translational (tr)-type guanine nucleotide-binding (G) domain profile. / Translation protein, beta-barrel domain superfamily / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Multifunctional fusion protein / Bifunctional enzyme CysN/CysC
Similarity search - Component
Biological speciesMYCOBACTERIUM TUBERCULOSIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.47 Å
AuthorsPoyraz, O. / Lohkamp, B. / Schnell, R. / Schneider, G.
CitationJournal: Plos One / Year: 2015
Title: Crystal Structures of the Kinase Domain of the Sulfate-Activating Complex in Mycobacterium Tuberculosis.
Authors: Poyraz, O. / Brunner, K. / Lohkamp, B. / Axelsson, H. / Hammarstrom, L.G.J. / Schnell, R. / Schneider, G.
History
DepositionJul 29, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 6, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 8, 2015Group: Database references
Revision 1.2Dec 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 / 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 / _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: BIFUNCTIONAL ENZYME CYSN/CYSC
B: BIFUNCTIONAL ENZYME CYSN/CYSC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,3928
Polymers38,2892
Non-polymers1,1036
Water8,035446
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3310 Å2
ΔGint-14.9 kcal/mol
Surface area16650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.630, 66.330, 61.760
Angle α, β, γ (deg.)90.00, 103.59, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein BIFUNCTIONAL ENZYME CYSN/CYSC / ADENYLYL-SULFATE KINASE / APS KINASE / ATP ADENOSINE-5'-PHOSPHOSULFATE 3'-PHOSPHOTRANSFERASE


Mass: 19144.729 Da / Num. of mol.: 2 / Fragment: RESIDUES 440-612
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q10600, UniProt: A5U1Y4*PLUS, adenylyl-sulfate kinase
#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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 446 / 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: 1.89 Å3/Da / Density % sol: 34.9 % / Description: NONE
Crystal growDetails: 0.2 M NH4NO3 24 % PEG 3,350 25 % ETHYLENE GLYCOL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9334
DetectorDate: Jun 19, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9334 Å / Relative weight: 1
ReflectionResolution: 1.47→26.12 Å / Num. obs: 55519 / % possible obs: 96 % / Observed criterion σ(I): 2 / Redundancy: 2.1 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 9.1
Reflection shellResolution: 1.47→1.55 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.07 / Mean I/σ(I) obs: 9.1 / % possible all: 96

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2PEY

2pey


Resolution: 1.47→22.26 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.955 / SU B: 1.052 / SU ML: 0.041 / Cross valid method: THROUGHOUT / ESU R: 0.072 / ESU R Free: 0.071 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.18187 2821 5.1 %RANDOM
Rwork0.15836 ---
obs0.15954 52650 95.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.559 Å2
Baniso -1Baniso -2Baniso -3
1-0.42 Å20 Å2-0.1 Å2
2---0.25 Å20 Å2
3----0.13 Å2
Refinement stepCycle: LAST / Resolution: 1.47→22.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2678 0 70 446 3194
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0193106
X-RAY DIFFRACTIONr_bond_other_d0.0060.022943
X-RAY DIFFRACTIONr_angle_refined_deg1.9112.024258
X-RAY DIFFRACTIONr_angle_other_deg1.22836805
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.135403
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.94822.778144
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.31615526
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2951534
X-RAY DIFFRACTIONr_chiral_restr0.0950.2466
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0213513
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02725
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3541.1611474
X-RAY DIFFRACTIONr_mcbond_other1.3481.1591473
X-RAY DIFFRACTIONr_mcangle_it2.1371.7311861
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.9751.3611632
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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: 1.472→1.51 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.206 221 -
Rwork0.182 3625 -
obs--90.01 %

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