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- PDB-5zsr: NifS from Hydrogenimonas thermophila, soaked with L-cysteine for 8 min -

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Basic information

Entry
Database: PDB / ID: 5zsr
TitleNifS from Hydrogenimonas thermophila, soaked with L-cysteine for 8 min
ComponentsCysteine desulfurase
KeywordsBIOSYNTHETIC PROTEIN / Cysteine desulfurase
Function / homology
Function and homology information


cysteine desulfurase / cysteine desulfurase activity / cysteine metabolic process / 2 iron, 2 sulfur cluster binding / metal ion binding
Similarity search - Function
Cysteine desulfurase NifS, proteobacteria / Cysteine desulfurase / Aminotransferase class-V, pyridoxal-phosphate binding site / Aminotransferases class-V pyridoxal-phosphate attachment site. / 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) ...Cysteine desulfurase NifS, proteobacteria / Cysteine desulfurase / Aminotransferase class-V, pyridoxal-phosphate binding site / Aminotransferases class-V pyridoxal-phosphate attachment site. / 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
Similarity search - Component
Biological speciesHydrogenimonas thermophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.61 Å
AuthorsNakamura, R. / Fujishiro, T. / Takahashi, Y.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science17K14510 Japan
Japan Society for the Promotion of Science15H04472 Japan
CitationJournal: to be published
Title: X-ray snapshots of two classes of cysteine desulfurase enzymes NifS and SufS
Authors: Fujishiro, T. / Nakamura, R. / Takahashi, Y.
History
DepositionApr 29, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 1, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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

Downloads & links

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Assembly

Deposited unit
A: Cysteine desulfurase
B: Cysteine desulfurase


Theoretical massNumber of molelcules
Total (without water)92,5782
Polymers92,5782
Non-polymers00
Water2,576143
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5000 Å2
ΔGint-33 kcal/mol
Surface area28630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)135.900, 135.900, 98.600
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 0 through 310 or resid 312 through 385))
21(chain B and (resid 0 through 310 or resid 312 through 385))

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
11HISHISLEULEU(chain A and (resid 0 through 310 or resid 312 through 385))AA0 - 3103 - 313
12ASPASPTYRTYR(chain A and (resid 0 through 310 or resid 312 through 385))AA312 - 385315 - 388
21HISHISLEULEU(chain B and (resid 0 through 310 or resid 312 through 385))BB0 - 3103 - 313
22ASPASPTYRTYR(chain B and (resid 0 through 310 or resid 312 through 385))BB312 - 385315 - 388

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Components

#1: Protein Cysteine desulfurase / NifS


Mass: 46289.031 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hydrogenimonas thermophila (bacteria) / Gene: SAMN05216234_11013 / Production host: Escherichia coli (E. coli) / Strain (production host): C41(DE3) / References: UniProt: A0A1I5NEH3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 143 / 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: 3.06 Å3/Da / Density % sol: 59.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2M Magnesium chloride, 0.1M Tris-HCl, 20% (w/v) PEG 8000, 5mM L-cysteine

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Dec 24, 2017
RadiationMonochromator: Numerical link type Si(111) double crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.61→45.472 Å / Num. obs: 31566 / % possible obs: 99.5 % / Redundancy: 5.88 % / Biso Wilson estimate: 48.33 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.132 / Rrim(I) all: 0.145 / Χ2: 0.993 / Net I/σ(I): 13.73 / Num. measured all: 362267 / Scaling rejects: 26
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.61-2.715.8510.9822.1765370.7231.07899.2
2.71-35.8990.5843.45144620.8830.6499.3
3-45.8760.17210.52234660.990.18999.6
4-65.9020.0626.68120730.9980.06599.8
6-105.870.03838.3339960.9990.04199.9
10-45.4725.6440.02755.0310810.9990.0399.1

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
XSCALEdata scaling
PDB_EXTRACT3.24data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1EG5

1eg5


Resolution: 2.61→45.472 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 24.53
RfactorNum. reflection% reflection
Rfree0.2408 1579 5 %
Rwork0.1935 --
obs0.1958 31561 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 121.85 Å2 / Biso mean: 57.7083 Å2 / Biso min: 23.64 Å2
Refinement stepCycle: final / Resolution: 2.61→45.472 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6022 0 0 143 6165
Biso mean---45.26 -
Num. residues----774
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2345X-RAY DIFFRACTION8.928TORSIONAL
12B2345X-RAY DIFFRACTION8.928TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.61-2.69430.33671430.281627032846
2.6943-2.79050.32111430.257927162859
2.7905-2.90230.30221430.248927202863
2.9023-3.03430.27461420.245426952837
3.0343-3.19420.29011430.239527212864
3.1942-3.39430.25061430.210827232866
3.3943-3.65630.2521440.203127362880
3.6563-4.0240.22741420.175827002842
4.024-4.60580.21721440.158127392883
4.6058-5.8010.21631450.165627552900
5.801-45.47860.19551470.166527742921
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)
11.79923.1323-1.09917.788-3.15112.59030.1487-0.0917-0.12060.4495-0.1870.0114-0.2388-0.13660.0420.30640.0396-0.00490.3714-0.04530.197-14.748860.38712.8231
23.8902-0.03370.56964.3193-2.46255.49830.02490.45590.1352-0.21860.1610.74150.0731-0.8637-0.16440.2890.0393-0.01060.4994-0.05050.4318-32.524572.7838-7.3992
35.08421.86862.61982.5214-1.99355.8594-0.04050.13230.33680.12770.11690.4095-0.3703-0.5765-0.04250.33520.08110.05220.3446-0.06180.3513-25.579376.13052.0409
47.5689-8.14661.93782.0165-0.44059.0115-0.2565-0.585-0.87330.83420.23341.52650.3946-0.9745-0.03860.4499-0.15410.13060.55310.01170.6831-32.915858.63154.873
56.90896.9854-6.51297.6058-5.67817.44470.6153-0.48530.54520.6763-0.34090.4986-0.7970.2852-0.28710.35390.0847-0.03410.3182-0.0460.3047-10.105178.63778.951
69.02863.3113-6.3328.2285-4.01518.97340.13250.52110.5226-0.15210.04940.1463-0.6633-0.5787-0.19920.41060.0525-0.07870.2643-0.00420.3175-7.513887.9059-8.0414
75.9948-4.61457.75115.127-5.57472.07760.45620.68610.5354-0.4405-0.2612-0.3192-0.1560.1137-0.02510.57010.14310.11080.5924-0.02040.3118-2.853978.5484-12.4998
85.8458-3.72343.97739.3653-6.91995.4248-0.39530.25180.34090.21370.62080.0316-0.8478-0.78-0.2350.44630.09160.09260.4614-0.00530.3598-11.268784.7337-10.0213
99.46942.0306-8.99328.4822-4.70772.01520.15620.14430.4828-0.2405-0.2907-0.2223-0.63780.92020.13250.4066-0.0507-0.02760.29-0.02030.34895.825484.3578-10.2868
102.26581.3872-0.16422.7235-0.20941.1707-0.27340.4501-0.399-0.40480.19340.09610.4034-0.26410.08260.4334-0.04710.07480.4544-0.12520.4468-23.64443.2926-5.5198
116.1374-0.764.56713.221-0.37646.3661-0.07430.7346-0.1879-0.40220.1908-0.21580.4511-0.1908-0.0680.3637-0.02730.12810.4345-0.09050.3743-19.508751.7125-6.8496
126.71118.0125-6.98579.8578-8.58437.7892-0.5986-0.1922-1.3964-0.6652-0.4498-1.15611.09040.42490.99550.62340.00070.08650.4054-0.0710.6839-12.009133.0316.6475
138.93386.2045-6.87188.7252-6.69052.0328-0.50210.5752-0.7698-0.19590.29650.07610.7369-0.76170.21010.6643-0.13510.19340.5155-0.16520.6868-29.010424.914813.4267
147.72174.02821.73642.26370.1374.29350.2428-0.0663-0.42190.3106-0.17730.1290.3848-0.6932-0.06690.5470.00840.11050.3311-0.04550.5794-31.496931.315114.8128
159.69995.6019-9.22599.8504-2.30992.0592-0.3511-0.9335-1.68980.7609-0.4272-0.0787-0.03730.37390.84860.6238-0.0030.09450.60770.11930.6162-26.251227.392726.7539
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid -1 through 57 )A-1 - 57
2X-RAY DIFFRACTION2chain 'A' and (resid 58 through 147 )A58 - 147
3X-RAY DIFFRACTION3chain 'A' and (resid 148 through 216 )A148 - 216
4X-RAY DIFFRACTION4chain 'A' and (resid 217 through 241 )A217 - 241
5X-RAY DIFFRACTION5chain 'A' and (resid 242 through 278 )A242 - 278
6X-RAY DIFFRACTION6chain 'A' and (resid 279 through 305 )A279 - 305
7X-RAY DIFFRACTION7chain 'A' and (resid 306 through 329 )A306 - 329
8X-RAY DIFFRACTION8chain 'A' and (resid 330 through 360 )A330 - 360
9X-RAY DIFFRACTION9chain 'A' and (resid 361 through 386 )A361 - 386
10X-RAY DIFFRACTION10chain 'B' and (resid 0 through 201 )B0 - 201
11X-RAY DIFFRACTION11chain 'B' and (resid 202 through 241 )B202 - 241
12X-RAY DIFFRACTION12chain 'B' and (resid 242 through 278 )B242 - 278
13X-RAY DIFFRACTION13chain 'B' and (resid 279 through 305 )B279 - 305
14X-RAY DIFFRACTION14chain 'B' and (resid 306 through 360 )B306 - 360
15X-RAY DIFFRACTION15chain 'B' and (resid 361 through 385 )B361 - 385

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