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

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Basic information

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


sulfate adenylyltransferase complex (ATP) / Sulfate assimilation / cellular response to sulfur starvation / sulfate assimilation via adenylyl sulfate reduction / adenylyl-sulfate kinase / sulfate adenylyltransferase / adenylylsulfate kinase activity / sulfate adenylyltransferase (ATP) activity / sulfate assimilation / hydrogen sulfide biosynthetic process ...sulfate adenylyltransferase complex (ATP) / Sulfate assimilation / cellular response to sulfur starvation / sulfate assimilation via adenylyl sulfate reduction / adenylyl-sulfate kinase / sulfate adenylyltransferase / adenylylsulfate kinase activity / sulfate adenylyltransferase (ATP) activity / sulfate assimilation / hydrogen sulfide biosynthetic process / cellular response to oxidative stress / GTPase activity / GTP binding / ATP binding / plasma membrane / cytosol
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 / Tr-type G domain, conserved site ...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 / ADENOSINE-5'-PHOSPHOSULFATE / CITRIC ACID / Bifunctional enzyme CysN/CysC / Bifunctional enzyme CysN/CysC
Similarity search - Component
Biological speciesMYCOBACTERIUM TUBERCULOSIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsPoyraz, O. / 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 13, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 8, 2015Group: Database references
Revision 1.2May 16, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_beamline
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 / struct_ncs_dom_lim / 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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _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)40,33310
Polymers38,1152
Non-polymers2,2178
Water1,06359
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3610 Å2
ΔGint-21.7 kcal/mol
Surface area15420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.930, 70.110, 79.280
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: PRO / Beg label comp-ID: PRO / End auth comp-ID: SER / End label comp-ID: SER / Refine code: _ / Auth seq-ID: 440 - 612 / Label seq-ID: 1 - 173

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein BIFUNCTIONAL ENZYME CYSN/CYSC / CYSC / SULFATE ADENYLYLTRANSFERASE SUBUNIT 1 / ATP-SULFURYLASE LARGE SUBUNIT / SULFATE ADENYLATE ...CYSC / SULFATE ADENYLYLTRANSFERASE SUBUNIT 1 / ATP-SULFURYLASE LARGE SUBUNIT / SULFATE ADENYLATE TRANSFERASE / SAT / ADENYLYL-SULFATE KINASE / APS KINASE / ATP ADENOSINE-5'-PHOSPHOSULFATE 3'-PHOSPHOTRANSFERASE


Mass: 19057.648 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: P9WNM5*PLUS, sulfate adenylyltransferase, adenylyl-sulfate kinase

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Non-polymers , 5 types, 67 molecules

#2: Chemical ChemComp-ADX / ADENOSINE-5'-PHOSPHOSULFATE


Type: RNA linking / Mass: 427.284 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O10PS
#3: 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
#4: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 59 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsAPS KINASE DOMAIN OF MYCOBACTERIUM TUBERCULOSIS CYSN

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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: 2.1 Å3/Da / Density % sol: 40.9 % / Description: NONE
Crystal growDetails: 0.1 MM CITRATE, PH 5.5, 20% PEG4000, 10% 2-PROPANOL, 0.8 MM CYSC, 1.9 MM APS, 2.3 MM ADP, 1.8 MM MGCL2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Type: ESRF / Wavelength: 1.00319
DetectorDate: Apr 11, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00319 Å / Relative weight: 1
ReflectionResolution: 2.1→34.51 Å / Num. obs: 21457 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 4.4 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 10
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.61 / Mean I/σ(I) obs: 2.3 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0071refinement
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4BZP

4bzp


Resolution: 2.1→52.52 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.928 / SU B: 12.12 / SU ML: 0.165 / Cross valid method: THROUGHOUT / ESU R: 0.243 / ESU R Free: 0.205 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25309 1102 5.1 %RANDOM
Rwork0.1962 ---
obs0.19895 20308 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Refinement stepCycle: LAST / Resolution: 2.1→52.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2678 0 142 59 2879
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0192919
X-RAY DIFFRACTIONr_bond_other_d0.0060.022732
X-RAY DIFFRACTIONr_angle_refined_deg1.8462.0323981
X-RAY DIFFRACTIONr_angle_other_deg1.16236298
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4455358
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.44423.101129
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.26215473
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.921528
X-RAY DIFFRACTIONr_chiral_restr0.0910.2439
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0213245
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02655
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_it2.1452.6581399
X-RAY DIFFRACTIONr_mcbond_other2.1432.6561398
X-RAY DIFFRACTIONr_mcangle_it3.2323.9711750
X-RAY DIFFRACTIONr_mcangle_other3.2313.9731751
X-RAY DIFFRACTIONr_scbond_it2.5883.0691520
X-RAY DIFFRACTIONr_scbond_other2.5863.0691520
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.8914.4942226
X-RAY DIFFRACTIONr_long_range_B_refined6.80225.82812406
X-RAY DIFFRACTIONr_long_range_B_other6.80225.82212396
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 10383 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.12 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3 85 -
Rwork0.281 1469 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.56820.1526-0.11241.0583-0.99073.3978-0.00340.00460.0190.00850.04490.0828-0.0334-0.088-0.04150.0028-0.00670.00150.0270.00220.038915.8306-2.9067-15.0336
21.50190.58470.6820.66960.3251.87630.02240.0363-0.0480.0150.0316-0.1263-0.1449-0.1656-0.05390.01910.01530.00330.08220.02950.057847.35563.4184-17.1141
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A440 - 612
2X-RAY DIFFRACTION2B440 - 612

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