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- PDB-7mhv: Crystal Structure of Cysteine desulfurase NifS from Legionella pn... -

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Basic information

Entry
Database: PDB / ID: 7mhv
TitleCrystal Structure of Cysteine desulfurase NifS from Legionella pneumophila Philadelphia 1 in complex with pyridoxal 5'-phosphate
ComponentsCysteine desulfurase
KeywordsTRANSFERASE / SSGCID / Cysteine desulfurase / Legionella pneumophila / pyridoxal 5'-phosphate / aminotransferase / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


Lyases; Carbon-sulfur lyases / cysteine desulfurase activity / iron-sulfur cluster assembly / 2 iron, 2 sulfur cluster binding / lyase activity / metal ion binding
Similarity search - Function
Cysteine desulfurase / Aminotransferase class-V, pyridoxal-phosphate binding site / Aminotransferases class-V pyridoxal-phosphate attachment site. / Aminotransferase class V domain / Aminotransferase class-V / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase
Similarity search - Domain/homology
PHOSPHATE ION / Cysteine desulfurase NifS
Similarity search - Component
Biological speciesLegionella pneumophila subsp. pneumophila (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Crystal Structure of Cysteine desulfurase NifS from Legionella pneumophila Philadelphia 1 in complex with pyridoxal 5'-phosphate
Authors: Sidhu, R.S. / Abendroth, J. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E.
History
DepositionApr 15, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 26, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cysteine desulfurase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,8395
Polymers43,5241
Non-polymers3144
Water8,629479
1
A: Cysteine desulfurase
hetero molecules

A: Cysteine desulfurase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,67710
Polymers87,0492
Non-polymers6288
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_554-x,y,-z-11
Buried area5990 Å2
ΔGint-51 kcal/mol
Surface area26810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)129.010, 51.170, 74.260
Angle α, β, γ (deg.)90.000, 110.406, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11A-736-

HOH

21A-975-

HOH

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Components

#1: Protein Cysteine desulfurase


Mass: 43524.445 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513) (bacteria)
Strain: Philadelphia 1 / ATCC 33152 / DSM 7513 / Gene: iscS, lpg1746 / Plasmid: LepnA.00081.a.B1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q5ZUP7, cysteine desulfurase
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 479 / 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: 2.66 Å3/Da / Density % sol: 53.7 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: Anatrace/Calibre MCSG1 screen, condition F7: 1M NaH2PO4 / K2HPO4 pH 5.6: LepnA.00081.a.B1.PS38430 at 22.0mg/ml: tray: 300662 f7: cryo: 25% EG in 2 steps + 2.5mM PLP: puck: kdy1-15

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Mar 12, 2021 / Details: RIGAKU VARIMAX HF
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. obs: 45395 / % possible obs: 98.4 % / Redundancy: 7.491 % / Biso Wilson estimate: 27.051 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.064 / Rrim(I) all: 0.068 / Χ2: 0.937 / Net I/σ(I): 18.87
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.75-1.82.8350.5432.1228850.7670.65385.2
1.8-1.843.860.4333.2132500.8860.598.3
1.84-1.94.5440.3924.0232060.9180.44499.5
1.9-1.964.7450.2735.5531000.9530.307100
1.96-2.024.9980.1997.4530080.9760.22299.7
2.02-2.095.9630.17410.1129600.9820.19199.9
2.09-2.176.9380.14512.8727990.990.15799.6
2.17-2.267.4850.12415.0327150.9940.13499.5
2.26-2.367.8970.10816.7725860.9960.11599.7
2.36-2.478.4760.09719.0224980.9970.10399.2
2.47-2.619.4920.08722.523340.9970.09298.9
2.61-2.7710.9680.07526.1722510.9980.07899.6
2.77-2.9611.0260.06629.6921170.9990.06999.4
2.96-3.211.0380.05933.0119670.9990.06199.7
3.2-3.511.0020.04939.7218200.9990.05199.7
3.5-3.9111.010.04445.5816540.9990.04699.8
3.91-4.5211.0060.04347.9214580.9990.04599.5
4.52-5.5310.9530.04348.212570.9990.04599.7
5.53-7.8310.8090.04846.049690.9990.0599.4
7.83-509.9890.0549.735610.9990.05399.3

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIX1.18refinement
PDB_EXTRACT3.27data extraction
MoRDaphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3lvm

3lvm


Resolution: 1.75→47.12 Å / SU ML: 0.1513 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.0294
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.1792 2033 4.48 %0
Rwork0.1583 43352 --
obs0.1592 45385 98.53 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.8 Å2
Refinement stepCycle: LAST / Resolution: 1.75→47.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2852 0 18 479 3349
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00812969
X-RAY DIFFRACTIONf_angle_d0.93394035
X-RAY DIFFRACTIONf_chiral_restr0.0613464
X-RAY DIFFRACTIONf_plane_restr0.0061524
X-RAY DIFFRACTIONf_dihedral_angle_d19.9911437
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.790.24721210.2452460X-RAY DIFFRACTION84.68
1.79-1.840.22531270.22692840X-RAY DIFFRACTION97.12
1.84-1.890.27441530.21522900X-RAY DIFFRACTION99.71
1.89-1.940.20661400.18422877X-RAY DIFFRACTION99.74
1.94-20.1921400.16422914X-RAY DIFFRACTION99.93
2-2.070.19221510.15962880X-RAY DIFFRACTION100
2.07-2.160.20131230.15822940X-RAY DIFFRACTION99.77
2.16-2.260.1721340.16182940X-RAY DIFFRACTION99.64
2.26-2.380.20931550.1642876X-RAY DIFFRACTION99.67
2.38-2.520.19811280.16942900X-RAY DIFFRACTION99.28
2.52-2.720.18341390.16152912X-RAY DIFFRACTION99.48
2.72-2.990.18221350.15872961X-RAY DIFFRACTION99.42
2.99-3.420.18081430.14922919X-RAY DIFFRACTION99.87
3.43-4.310.13391160.12552988X-RAY DIFFRACTION99.84
4.32-47.120.14341280.15163045X-RAY DIFFRACTION99.84
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)
12.01038678966-0.276522606036-0.3199144228470.513143048799-0.0326815787320.7698966590990.03660303281090.225038492338-0.191902852496-0.0609776211031-0.02632614290110.01666457356360.07673664026940.0378594279074-0.001109387471670.105563446052-0.0100590812166-0.00770760786910.0938020471215-0.03510142145510.09660098114977.9666224226612.1722769818-44.9956974907
21.3443953922-0.321612884049-0.02107747429421.216165959350.1959465684291.1018646099-0.0631256471992-0.05753361353910.2012673869620.03858124135810.0229546904436-0.0642468063787-0.184873443365-0.0367501602470.03594750988430.1101267702220.007195092917-0.01463690876980.0739360887113-0.00384769696760.12268062934-4.9409897712836.4973842991-30.7006593683
31.63059943367-0.9711007539270.04177389202541.70302146660.1228261926180.756243848980.04503923332670.1164924557020.155744191538-0.125291089557-0.0508319128676-0.0584773138393-0.0611952681590.002475330881820.0009154163891130.0951996447137-0.00979493891410.003895057808580.0881900691010.00894860375870.1116598616660.20312802672825.869011897-39.886706762
40.9046794453910.01450065682520.1399333766121.050006140210.01572465729081.52961934964-0.0284369912967-0.370548926607-0.07974495126380.21700239510.01247421936130.0552436003158-0.0230885005282-0.1043027014940.02273795040990.133972992786-0.002647358248990.02437187295990.244480047430.03962157954970.13805463074-9.8135832115314.2993686843-15.3415186096
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 12 through 71 )12 - 719 - 76
22chain 'A' and (resid 72 through 171 )72 - 17177 - 180
33chain 'A' and (resid 172 through 254 )172 - 254181 - 263
44chain 'A' and (resid 255 through 385 )255 - 385264 - 387

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