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- PDB-4q75: Crystal structure of Nfs2, the plastidial cysteine desulfurase fr... -

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Basic information

Entry
Database: PDB / ID: 4q75
TitleCrystal structure of Nfs2, the plastidial cysteine desulfurase from Arabidopsis thaliana
ComponentsCysteine desulfurase 2, chloroplastic
KeywordsTRANSFERASE / Cysteine desulfurase / AtSufE1 / Chloroplast
Function / homology
Function and homology information


selenium compound metabolic process / selenocysteine lyase / iron incorporation into metallo-sulfur cluster / selenocysteine lyase activity / sulfur compound metabolic process / cysteine desulfurase / cysteine desulfurase activity / response to selenium ion / cysteine metabolic process / chloroplast stroma ...selenium compound metabolic process / selenocysteine lyase / iron incorporation into metallo-sulfur cluster / selenocysteine lyase activity / sulfur compound metabolic process / cysteine desulfurase / cysteine desulfurase activity / response to selenium ion / cysteine metabolic process / chloroplast stroma / chloroplast / pyridoxal phosphate binding
Similarity search - Function
Cysteine desulfurase, SufS / Aminotransferase class V domain / Aminotransferase class-V / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase ...Cysteine desulfurase, SufS / Aminotransferase class V domain / Aminotransferase class-V / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Cysteine desulfurase 1, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.709 Å
AuthorsRoret, T. / Didierjean, C.
CitationJournal: Acta Crystallogr F Struct Biol Commun / Year: 2014
Title: X-ray structures of Nfs2, the plastidial cysteine desulfurase from Arabidopsis thaliana.
Authors: Roret, T. / Pegeot, H. / Couturier, J. / Mulliert, G. / Rouhier, N. / Didierjean, C.
History
DepositionApr 24, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 10, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 24, 2014Group: Database references
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_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_asym_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_ref_seq_dif.details
Revision 1.3Dec 6, 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

Downloads & links

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Assembly

Deposited unit
A: Cysteine desulfurase 2, chloroplastic
B: Cysteine desulfurase 2, chloroplastic


Theoretical massNumber of molelcules
Total (without water)94,4192
Polymers94,4192
Non-polymers00
Water15,385854
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7610 Å2
ΔGint-34 kcal/mol
Surface area27020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.567, 68.205, 87.066
Angle α, β, γ (deg.)90.00, 94.76, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Cysteine desulfurase 2, chloroplastic / NIFS-like protein / Plastid sufS-like protein / Protein AtCpNifS / Selenocysteine lyase


Mass: 47209.293 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: NFS2, NIFS, At1g08490, T27G7.17 / Production host: Escherichia coli (E. coli)
References: UniProt: Q93WX6, cysteine desulfurase, selenocysteine lyase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 854 / 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: 2.56 Å3/Da / Density % sol: 51.88 %
Crystal growTemperature: 278 K / Method: microbatch under oil / pH: 7.5
Details: 20% PEG3000, 0.2M sodium chloride and 0.1M HEPES pH 7.5, microbatch under oil, temperature 278K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.978542 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 12, 2012
RadiationMonochromator: 2Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978542 Å / Relative weight: 1
ReflectionResolution: 1.709→45.853 Å / Num. all: 97828 / Num. obs: 97823 / % possible obs: 95 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.71→1.8 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.187 / Mean I/σ(I) obs: 3.5 / Num. unique all: 11087 / % possible all: 75

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Processing

Software
NameVersionClassification
Xnemodata collection
MOLREPphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1T3I

1t3i


Resolution: 1.709→45.853 Å / SU ML: 0.23 / σ(F): 1.34 / Phase error: 21.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2326 4892 5 %Scaling input intensities via French-Wilson Method
Rwork0.2025 ---
all0.204 97828 --
obs0.204 97823 94.77 %-
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.645 Å2 / ksol: 0.407 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.8666 Å20 Å2-0.7462 Å2
2---0.4169 Å2-0 Å2
3---1.2835 Å2
Refinement stepCycle: LAST / Resolution: 1.709→45.853 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6444 0 0 854 7298
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076658
X-RAY DIFFRACTIONf_angle_d1.1279065
X-RAY DIFFRACTIONf_dihedral_angle_d13.0852389
X-RAY DIFFRACTIONf_chiral_restr0.0761019
X-RAY DIFFRACTIONf_plane_restr0.0051168
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7088-1.72830.3411120.29672026X-RAY DIFFRACTION63
1.7283-1.74860.32141180.26472339X-RAY DIFFRACTION71
1.7486-1.76990.30321180.27112426X-RAY DIFFRACTION75
1.7699-1.79230.27481420.25172654X-RAY DIFFRACTION82
1.7923-1.81590.27031520.24172918X-RAY DIFFRACTION89
1.8159-1.84080.27261630.2353112X-RAY DIFFRACTION96
1.8408-1.86710.25341420.22983118X-RAY DIFFRACTION96
1.8671-1.8950.29651580.23173141X-RAY DIFFRACTION95
1.895-1.92460.25151790.22343114X-RAY DIFFRACTION97
1.9246-1.95610.24931610.21753120X-RAY DIFFRACTION96
1.9561-1.98990.23141820.22413143X-RAY DIFFRACTION97
1.9899-2.0260.25721860.2113134X-RAY DIFFRACTION97
2.026-2.0650.24921540.21333175X-RAY DIFFRACTION98
2.065-2.10720.24351680.20953189X-RAY DIFFRACTION99
2.1072-2.1530.23221940.20433227X-RAY DIFFRACTION99
2.153-2.20310.23351850.20343219X-RAY DIFFRACTION99
2.2031-2.25810.2571820.20243250X-RAY DIFFRACTION100
2.2581-2.31920.2151850.19513196X-RAY DIFFRACTION100
2.3192-2.38740.2361640.20133265X-RAY DIFFRACTION100
2.3874-2.46450.25041710.20243249X-RAY DIFFRACTION100
2.4645-2.55260.2371590.21073298X-RAY DIFFRACTION100
2.5526-2.65480.23691650.2043287X-RAY DIFFRACTION100
2.6548-2.77560.22621730.19633255X-RAY DIFFRACTION100
2.7756-2.92190.23591830.19253262X-RAY DIFFRACTION100
2.9219-3.10490.19261710.18523290X-RAY DIFFRACTION100
3.1049-3.34460.25131630.19383281X-RAY DIFFRACTION100
3.3446-3.6810.2131560.18723312X-RAY DIFFRACTION100
3.681-4.21340.17541640.1653290X-RAY DIFFRACTION100
4.2134-5.30710.18511740.17143314X-RAY DIFFRACTION100
5.3071-45.86970.28521680.2513270X-RAY DIFFRACTION96
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)
10.8605-0.2943-0.06081.1460.90911.77930.03-0.05120.01790.1016-0.0384-0.08430.09120.01850.00690.0808-0.00220.00070.07080.02480.095631.1322-0.908425.6249
20.8810.1737-0.07290.2882-0.24690.7-0.0550.0222-0.11880.161-0.1150.1150.2669-0.12280.1020.1819-0.04570.03690.0966-0.02530.148620.5478-12.433625.3563
30.18670.04950.06150.41880.24710.2178-0.0152-0.1153-0.08080.17-0.31150.48460.2201-0.4687-0.04870.108-0.13080.12120.287-0.13860.26485.5277-3.72633.8664
40.18-0.00520.04070.68490.26940.1102-0.055-0.15330.01670.3562-0.0730.14490.2112-0.0128-0.03650.2419-0.01610.03360.1475-0.00780.084223.7613.395645.3333
51.28310.2435-0.15781.95760.38031.55170.0294-0.04540.2797-0.0904-0.07440.3644-0.2778-0.09090.04480.1856-0.0006-0.02230.1802-0.08240.178722.061723.468242.4202
60.7784-0.1733-0.19511.25960.25180.86750.014-0.07880.15950.0741-0.12410.1473-0.0903-0.07060.09460.1236-0.01-0.01630.1443-0.05820.114722.838318.604543.1735
70.8020.25540.27150.68920.49261.3774-0.0041-0.01540.0991-0.1215-0.0504-0.0506-0.2099-0.01010.06860.10190.0035-0.00950.07430.01750.101729.53077.208317.8096
80.3971-0.095-0.04020.53390.25630.4822-0.0510.24720.0249-0.4564-0.18760.2911-0.3783-0.3063-0.20160.12780.1487-0.14170.138-0.04320.126313.0792.32222.9534
90.6206-0.41210.13731.03680.29010.7385-0.00850.1153-0.1441-0.0936-0.09120.17380.069-0.01840.05740.11870.00660.01550.1286-0.0450.140426.4381-19.7833-1.8414
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and ( resseq 37:71 )A37 - 71
2X-RAY DIFFRACTION2chain 'A' and ( resseq 72:114 )A72 - 114
3X-RAY DIFFRACTION3chain 'A' and ( resseq 115:290 )A115 - 290
4X-RAY DIFFRACTION4chain 'A' and ( resseq 291:352 )A291 - 352
5X-RAY DIFFRACTION5chain 'A' and ( resseq 353:372 )A353 - 372
6X-RAY DIFFRACTION6chain 'A' and ( resseq 373:429 )A373 - 429
7X-RAY DIFFRACTION7chain 'B' and ( resseq 37:94 )B37 - 94
8X-RAY DIFFRACTION8chain 'B' and ( resseq 95:353 )B95 - 353
9X-RAY DIFFRACTION9chain 'B' and ( resseq 354:429 )B354 - 429

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