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

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Basic information

Entry
Database: PDB / ID: 7lhr
TitleCrystal structure of adenosine-5'-phosphosulfate reductase from Mycobacterium tuberculosis
ComponentsPhosphoadenosine phosphosulfate reductase
KeywordsOXIDOREDUCTASE / holo / Fe-S cluster / tuberculosis / sulfate assimilation pathway
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
IRON/SULFUR CLUSTER / Adenosine 5'-phosphosulfate reductase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / 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 1.1Mar 6, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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)58,1446
Polymers57,0502
Non-polymers1,0944
Water1086
1
A: Phosphoadenosine phosphosulfate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0723
Polymers28,5251
Non-polymers5472
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Phosphoadenosine phosphosulfate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0723
Polymers28,5251
Non-polymers5472
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.414, 77.414, 204.352
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 41 or (resid 42...

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
12THRTHRPROPRO(chain A and ((resid 8 and (name N or name...AA5 - 2305 - 230
13THRTHRPROPRO(chain A and ((resid 8 and (name N or name...AA5 - 2305 - 230
14THRTHRPROPRO(chain A and ((resid 8 and (name N or name...AA5 - 2305 - 230
15THRTHRPROPRO(chain A and ((resid 8 and (name N or name...AA5 - 2305 - 230
21LEULEUGLYGLY(chain B and (resid 8 through 41 or (resid 42...BB8 - 418 - 41
22ASPASPTHRTHR(chain B and (resid 8 through 41 or (resid 42...BB42 - 5842 - 58
23LEULEUALAALA(chain B and (resid 8 through 41 or (resid 42...BB8 - 2318 - 231
24LEULEUALAALA(chain B and (resid 8 through 41 or (resid 42...BB8 - 2318 - 231
25LEULEUALAALA(chain B and (resid 8 through 41 or (resid 42...BB8 - 2318 - 231
26LEULEUALAALA(chain B and (resid 8 through 41 or (resid 42...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: isolated from a natural source / 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: 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: 2.79 Å3/Da / Density % sol: 55.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: 0.1 M MES, 10-12% (w/v) 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: 0.9792 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 30, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 3.1→50 Å / Num. obs: 11937 / % possible obs: 100 % / Redundancy: 23.3 % / Biso Wilson estimate: 110.02 Å2 / Rsym value: 0.134 / Net I/σ(I): 32.4
Reflection shellResolution: 3.1→3.15 Å / Num. unique obs: 568 / CC1/2: 0.616

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 3.11→48.25 Å / SU ML: 0.52 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 30.41 / Stereochemistry target values: ML
Details: Fe-SAD at a wavelength of 1.7389 A was used for phasing. Then the structure was refined against a data set collected with a wavelength of 0.9792 A.
RfactorNum. reflection% reflection
Rfree0.2492 592 4.99 %
Rwork0.2073 11272 -
obs0.2095 11864 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 185.36 Å2 / Biso mean: 106.4639 Å2 / Biso min: 55.19 Å2
Refinement stepCycle: final / Resolution: 3.11→48.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3117 0 40 6 3163
Biso mean--90.83 69.61 -
Num. residues----423
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033229
X-RAY DIFFRACTIONf_angle_d0.6064451
X-RAY DIFFRACTIONf_dihedral_angle_d25.703470
X-RAY DIFFRACTIONf_chiral_restr0.043537
X-RAY DIFFRACTIONf_plane_restr0.005573
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1272X-RAY DIFFRACTION10.651TORSIONAL
12B1272X-RAY DIFFRACTION10.651TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 4 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
3.11-3.420.40291420.309527332875
3.42-3.910.3081450.247627542899
3.91-4.930.23761480.201228002948
4.93-48.250.21791570.18329853142
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)
16.36860.80034.93.44364.40329.30640.16550.0081-0.62050.55060.0076-0.01440.27130.3416-0.18280.86790.04010.19420.5722-0.07910.712492.684921.7911209.9724
22.7866-2.1448-0.79897.39270.80523.1466-0.0986-0.15360.34830.43710.2621-0.2071-0.45330.0829-0.14791.0076-0.03660.10720.7345-0.010.875488.976143.0115218.892
34.7816-0.16240.1455.64812.1222.456-0.05510.0852-0.21750.7580.17310.23910.5288-0.5768-0.26850.9467-0.01170.22610.8020.05230.821983.042131.1263217.8672
49.3366-6.2088-0.94274.803-1.88419.2062-0.01790.66351.2504-0.893-0.27350.34560.2663-2.76150.1360.9271-0.15030.06111.2722-0.01660.991173.620245.4537223.2779
50.5373-0.8974-0.85148.23765.99724.4401-0.01670.7862-0.8319-2.10630.4734-0.5518-3.0373-0.8511-0.2131.66160.30980.21360.97040.0420.994777.08665.1886228.7548
65.10780.4093-1.74741.3622-0.99834.88410.36090.0880.591-1.2055-0.0594-0.0397-1.0296-0.387-0.31171.62790.22640.00860.7509-0.30011.20275.638862.1594243.4797
73.56860.81520.29255.3952-0.21126.25830.0068-0.36640.5196-0.210.3040.2888-0.726-0.777-0.28540.87250.17320.04460.9689-0.14810.871965.325744.9806245.1808
87.06036.64531.49547.21193.44627.1601-0.4334-0.00811.0729-0.1922-0.10121.9589-1.1269-0.04740.4731.32510.1521-0.13711.0458-0.16140.814369.700653.8825237.7933
98.0587-4.3023-2.27785.5909-1.44132.74991.00170.6770.0788-1.0529-0.91290.7464-0.30820.1605-0.11861.33730.19540.12821.0998-0.20891.050781.169753.1428236.9456
107.31614.02820.45349.87980.19595.1339-0.0646-0.69150.19061.1706-0.3469-0.1975-0.56930.32520.36140.9130.0807-0.02650.8642-0.13830.828579.443443.6362253.598
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 39 )A5 - 39
2X-RAY DIFFRACTION2chain 'A' and (resid 40 through 144 )A40 - 144
3X-RAY DIFFRACTION3chain 'A' and (resid 145 through 215 )A145 - 215
4X-RAY DIFFRACTION4chain 'A' and (resid 216 through 230 )A216 - 230
5X-RAY DIFFRACTION5chain 'B' and (resid 8 through 23 )B8 - 23
6X-RAY DIFFRACTION6chain 'B' and (resid 24 through 70 )B24 - 70
7X-RAY DIFFRACTION7chain 'B' and (resid 71 through 145 )B71 - 145
8X-RAY DIFFRACTION8chain 'B' and (resid 146 through 164 )B146 - 164
9X-RAY DIFFRACTION9chain 'B' and (resid 165 through 195 )B165 - 195
10X-RAY DIFFRACTION10chain 'B' and (resid 196 through 231 )B196 - 231

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