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- PDB-7lhs: Crystal structure of adenosine-5'-phosphosulfate reductase from M... -

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Basic information

Entry
Database: PDB / ID: 7lhs
TitleCrystal structure of adenosine-5'-phosphosulfate reductase from Mycobacterium tuberculosis in a complex with substrate APS
ComponentsPhosphoadenosine phosphosulfate reductase
KeywordsOXIDOREDUCTASE / substrate / APS / adenosine-5'-phosphosulfate reductase / tuberculosis
Function / homology
Function and homology information


adenylyl-sulfate reductase (thioredoxin) / adenylyl-sulfate reductase (thioredoxin) activity / phosphoadenylyl-sulfate reductase (thioredoxin) activity / sulfate assimilation, phosphoadenylyl sulfate reduction by phosphoadenylyl-sulfate reductase (thioredoxin) / hydrogen sulfide biosynthetic process / cysteine biosynthetic process / 4 iron, 4 sulfur cluster binding / metal ion binding / cytoplasm
Similarity search - Function
Adenosine 5'-phosphosulphate reductase / Phosphoadenosine phosphosulphate/adenosine 5'-phosphosulphate reductase / Phosphoadenosine phosphosulphate reductase / Phosphoadenosine phosphosulfate reductase domain / HUPs / Rossmann-like alpha/beta/alpha sandwich fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-PHOSPHOSULFATE / IRON/SULFUR CLUSTER / Adenosine 5'-phosphosulfate reductase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.11 Å
AuthorsFeliciano, P.R. / Drennan, C.L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM126982 United States
CitationJournal: Acs Omega / Year: 2021
Title: Crystal Structure of the [4Fe-4S] Cluster-Containing Adenosine-5'-phosphosulfate Reductase from Mycobacterium tuberculosis .
Authors: Feliciano, P.R. / Carroll, K.S. / Drennan, C.L.
History
DepositionJan 26, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 7, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phosphoadenosine phosphosulfate reductase
B: Phosphoadenosine phosphosulfate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,9988
Polymers57,0502
Non-polymers1,9486
Water1086
1
A: Phosphoadenosine phosphosulfate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,4994
Polymers28,5251
Non-polymers9743
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Phosphoadenosine phosphosulfate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,4994
Polymers28,5251
Non-polymers9743
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.502, 77.502, 205.310
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and ((resid 8 and (name N or name...
21(chain B and (resid 8 through 37 or (resid 38...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LEULEULEULEU(chain A and ((resid 8 and (name N or name...AA88
12THRTHRALAALA(chain A and ((resid 8 and (name N or name...AA5 - 2315 - 231
13THRTHRALAALA(chain A and ((resid 8 and (name N or name...AA5 - 2315 - 231
14THRTHRALAALA(chain A and ((resid 8 and (name N or name...AA5 - 2315 - 231
15THRTHRALAALA(chain A and ((resid 8 and (name N or name...AA5 - 2315 - 231
21LEULEUASPASP(chain B and (resid 8 through 37 or (resid 38...BB8 - 378 - 37
22GLUGLUGLUGLU(chain B and (resid 8 through 37 or (resid 38...BB3838
23LEULEUALAALA(chain B and (resid 8 through 37 or (resid 38...BB8 - 2318 - 231
24LEULEUALAALA(chain B and (resid 8 through 37 or (resid 38...BB8 - 2318 - 231
25LEULEUALAALA(chain B and (resid 8 through 37 or (resid 38...BB8 - 2318 - 231
26LEULEUALAALA(chain B and (resid 8 through 37 or (resid 38...BB8 - 2318 - 231

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Components

#1: Protein Phosphoadenosine phosphosulfate reductase / 3'-phosphoadenylylsulfate reductase / PAPS reductase / thioredoxin dependent / PAPS ...3'-phosphoadenylylsulfate reductase / PAPS reductase / thioredoxin dependent / PAPS sulfotransferase / PAdoPS reductase / adenosine-5'-phosphosulfate reductase


Mass: 28525.068 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: cysH, MRA_2416 / Production host: Escherichia coli (E. coli)
References: UniProt: A5U586, phosphoadenylyl-sulfate reductase (thioredoxin)
#2: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4S4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#4: Chemical ChemComp-ADX / ADENOSINE-5'-PHOSPHOSULFATE


Type: RNA linking / Mass: 427.284 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C10H14N5O10PS / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 54.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: MES, PEG 20000 / PH range: 6-6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Aug 4, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 3.1→50 Å / Num. obs: 11945 / % possible obs: 99.5 % / Redundancy: 13.6 % / Biso Wilson estimate: 108.83 Å2 / CC1/2: 1 / Rsym value: 0.143 / Net I/σ(I): 23.6
Reflection shellResolution: 3.1→3.15 Å / Mean I/σ(I) obs: 0.9 / Num. unique obs: 537 / CC1/2: 0.597 / Rsym value: 1.685

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7LHR

7lhr


Resolution: 3.11→48.34 Å / SU ML: 0.43 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 30.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2639 593 5.01 %
Rwork0.219 11241 -
obs0.2213 11834 99.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 202.45 Å2 / Biso mean: 114.3499 Å2 / Biso min: 55.7 Å2
Refinement stepCycle: final / Resolution: 3.11→48.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3133 0 94 6 3233
Biso mean--110 72.85 -
Num. residues----420
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023303
X-RAY DIFFRACTIONf_angle_d0.5124560
X-RAY DIFFRACTIONf_dihedral_angle_d28.101488
X-RAY DIFFRACTIONf_chiral_restr0.04546
X-RAY DIFFRACTIONf_plane_restr0.004577
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1282X-RAY DIFFRACTION10.565TORSIONAL
12B1282X-RAY DIFFRACTION10.565TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.11-3.420.36611410.3222669281097
3.42-3.920.28961450.25227712916100
3.92-4.930.28351480.212228072955100
4.93-48.340.23161590.197129943153100
Refinement TLS params.Method: refined / Origin x: 79.9664 Å / Origin y: 42.974 Å / Origin z: 231.1241 Å
111213212223313233
T0.7468 Å2-0.0159 Å20.0512 Å2-0.5774 Å20.0104 Å2--0.6311 Å2
L1.8587 °2-0.2099 °2-1.6046 °2-0.992 °21.0918 °2--5.3246 °2
S-0.0564 Å °-0.0971 Å °0.2643 Å °0.0816 Å °0.1413 Å °-0.0191 Å °-0.3342 Å °-0.1806 Å °-0.0893 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA5 - 231
2X-RAY DIFFRACTION1allB8 - 231
3X-RAY DIFFRACTION1allC1 - 2
4X-RAY DIFFRACTION1allD1 - 6
5X-RAY DIFFRACTION1allE1 - 2
6X-RAY DIFFRACTION1allF1 - 2

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