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

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Basic information

Entry
Database: PDB / ID: 4bzx
TitleStructure of the Mycobacterium tuberculosis APS kinase CysC in complex with AMPPNP and APS
ComponentsBIFUNCTIONAL ENZYME CYSN/CYSC
KeywordsTRANSFERASE / SULFUR ASSIMILATION
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 ...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'-PHOSPHOSULFATE / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / CITRIC ACID / DI(HYDROXYETHYL)ETHER / Bifunctional enzyme CysN/CysC / Bifunctional enzyme CysN/CysC
Similarity search - Component
Biological speciesMYCOBACTERIUM TUBERCULOSIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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 30, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 13, 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 / pdbx_struct_conn_angle / struct_conn / 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 / _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.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.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.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_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

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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)41,32824
Polymers38,1152
Non-polymers3,21322
Water3,117173
1
A: BIFUNCTIONAL ENZYME CYSN/CYSC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,74813
Polymers19,0581
Non-polymers1,69112
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: BIFUNCTIONAL ENZYME CYSN/CYSC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,58011
Polymers19,0581
Non-polymers1,52210
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)63.820, 69.430, 79.370
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 / APS KINASE / ATP ADENOSINE-5-PHOSPHOSULFATE 3-PHOSPHOTRANSFERASE / CYSC


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, adenylyl-sulfate kinase

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Non-polymers , 7 types, 195 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-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7
#7: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 173 / 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: 2.06 Å3/Da / Density % sol: 40.23 % / Description: NONE
Crystal growDetails: 0.1 M CITRATE, PH 5.3 20% PEG4, 10% 2- PROPANOL, 1.9 MM APS, 2.3 MM AMPPNP, 1.8 MM MGCL2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9793
DetectorDate: Apr 11, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.7→49.74 Å / Num. obs: 38074 / % possible obs: 96.6 % / Observed criterion σ(I): 2 / Redundancy: 4.3 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 11.3
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 2.3 / % possible all: 83.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4BZP

4bzp


Resolution: 1.7→52.26 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.95 / SU B: 4.685 / SU ML: 0.081 / Cross valid method: THROUGHOUT / ESU R: 0.112 / ESU R Free: 0.112 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21599 1930 5.1 %RANDOM
Rwork0.17415 ---
obs0.17619 36095 96.3 %-
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: 1.7→52.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2678 0 203 173 3054
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0193041
X-RAY DIFFRACTIONr_bond_other_d0.0070.022899
X-RAY DIFFRACTIONr_angle_refined_deg2.0322.0464141
X-RAY DIFFRACTIONr_angle_other_deg1.29436691
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.345378
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.73623.077130
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.99615496
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.8431528
X-RAY DIFFRACTIONr_chiral_restr0.1070.2457
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0213347
X-RAY DIFFRACTIONr_gen_planes_other0.0070.02673
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_it2.0182.0171427
X-RAY DIFFRACTIONr_mcbond_other2.0152.0151426
X-RAY DIFFRACTIONr_mcangle_it2.7433.0111793
X-RAY DIFFRACTIONr_mcangle_other2.7453.0131794
X-RAY DIFFRACTIONr_scbond_it3.1832.5881614
X-RAY DIFFRACTIONr_scbond_other3.1812.5861612
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.5893.7142333
X-RAY DIFFRACTIONr_long_range_B_refined6.42620.47912788
X-RAY DIFFRACTIONr_long_range_B_other6.39220.33112701
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 10569 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.1 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.371 108 -
Rwork0.321 2065 -
obs--75.61 %
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)
10.71860.0040.19481.4528-1.28684.4490.0467-0.02720.01540.00590.03570.1441-0.0564-0.0394-0.08230.0135-0.00630.00360.00440.00420.075315.8351-2.9199-14.8877
21.71690.56020.27040.99220.5253.12980.04530.05580.031-0.05340.0372-0.1199-0.2508-0.1661-0.08250.0401-0.00350.01380.0490.03350.110947.31083.2916-17.0175
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A440 - 612
2X-RAY DIFFRACTION2B440 - 612

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