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- PDB-6m9s: Crystal structure of SeMet SznF from Streptomyces achromogenes va... -

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Basic information

Entry
Database: PDB / ID: 6m9s
TitleCrystal structure of SeMet SznF from Streptomyces achromogenes var. streptozoticus NRRL 2697
ComponentsSznF
KeywordsOXIDOREDUCTASE / non-heme iron-dependent / cupin domain / helix bundle / monooxygenase / N-nitrosation / metal-bound / anaerobic / SeMet / selenemethionine
Function / homology
Function and homology information


Heme oxygenase-like / Heme Oxygenase; Chain A / Jelly Rolls / Jelly Rolls / Up-down Bundle / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
: / ISOPROPYL ALCOHOL
Similarity search - Component
Biological speciesStreptomyces achromogenes subsp. streptozoticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.08 Å
AuthorsRohac, R. / Mitchell, A.J. / Boal, A.K.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)119707 United States
CitationJournal: Nature / Year: 2019
Title: An N-nitrosating metalloenzyme constructs the pharmacophore of streptozotocin.
Authors: Ng, T.L. / Rohac, R. / Mitchell, A.J. / Boal, A.K. / Balskus, E.P.
History
DepositionAug 24, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 6, 2019Provider: repository / Type: Initial release
Revision 1.1Feb 13, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_id_ISSN / _citation.journal_volume ..._citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 13, 2019Group: Database references / Category: citation
Item: _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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_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: SznF
B: SznF
C: SznF
D: SznF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)226,25424
Polymers224,7464
Non-polymers1,50820
Water22,2851237
1
A: SznF
B: SznF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,12512
Polymers112,3732
Non-polymers75210
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7580 Å2
ΔGint-114 kcal/mol
Surface area34470 Å2
MethodPISA
2
C: SznF
D: SznF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,12912
Polymers112,3732
Non-polymers75610
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8180 Å2
ΔGint-130 kcal/mol
Surface area35210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.510, 109.460, 365.980
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: HIS / Beg label comp-ID: HIS / Refine code: _

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LEULEUAA3 - 47120 - 488
21LEULEUBB3 - 47120 - 488
12LEULEUAA3 - 47120 - 488
22LEULEUCC3 - 47120 - 488
13LEULEUAA3 - 47120 - 488
23LEULEUDD3 - 47120 - 488
14LEULEUBB3 - 47120 - 488
24LEULEUCC3 - 47120 - 488
15CYSCYSBB3 - 47020 - 487
25CYSCYSDD3 - 47020 - 487
16LEULEUCC3 - 47120 - 488
26LEULEUDD3 - 47120 - 488

NCS ensembles :
ID
1
2
3
4
5
6

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
SznF


Mass: 56186.496 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces achromogenes subsp. streptozoticus (bacteria)
Strain: NRRL 2697 / Gene: sznf / Plasmid: pET-29a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: Oxidoreductases

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Non-polymers , 5 types, 1257 molecules

#2: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Fe
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1237 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.76 Å3/Da / Density % sol: 55.43 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1 M Tris, pH 8.5, 0.1 M magnesium chloride, 15-30% w/v PEG4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.97934 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 8, 2016
RadiationMonochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.08→49.09 Å / Num. obs: 141875 / % possible obs: 99.85 % / Redundancy: 10.069 % / Biso Wilson estimate: 39.8 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.087 / Rrim(I) all: 0.092 / Χ2: 1.735 / Net I/σ(I): 16.95
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.08-2.217.850.9122.06471950.7540.97798.8
2.21-2.3610.5580.6023.81435740.9290.632100
2.36-2.5510.4470.3945.98404450.9680.414100
2.55-2.7910.6540.23610.21373530.9880.248100
2.79-3.1210.4490.14416.25336570.9940.152100
3.12-3.610.5850.07628.99297880.9980.08100
3.6-4.410.30.04843.47251290.9990.051100
4.4-6.210.5270.04250.05194450.9990.044100
6.2-49.08910.330.03458.411081310.03699.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
XSCALEVERSION Jan 26, 2018data scaling
XDSVERSION Jan 26, 2018data reduction
HKL2MapVersion 0.4.e-betaphasing
SHELXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.08→49.09 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.961 / SU B: 6.143 / SU ML: 0.084 / Cross valid method: THROUGHOUT / ESU R: 0.17 / ESU R Free: 0.135
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. Restrained refinement against unmerged SAD data directly, using 10 TLS refinement cycles with 3 TLS groups for molecules A & D and 4 groups ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. Restrained refinement against unmerged SAD data directly, using 10 TLS refinement cycles with 3 TLS groups for molecules A & D and 4 groups for molecules B & C (isotropic temperature factors) followed by 10 cycles of maximum likelihood restrained refinement using 0.04 weighting term and jelly-body refinement with sigma 0.025, plus automatically generated local NCS restraints.
RfactorNum. reflection% reflectionSelection details
Rfree0.18889 7469 5 %RANDOM
Rwork0.17433 ---
obs0.17506 141875 99.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 46.72 Å2
Baniso -1Baniso -2Baniso -3
1-1.11 Å20 Å20 Å2
2---0.67 Å20 Å2
3----0.44 Å2
Refinement stepCycle: 1 / Resolution: 2.08→49.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14639 0 71 1237 15947
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01915407
X-RAY DIFFRACTIONr_bond_other_d0.0040.0214144
X-RAY DIFFRACTIONr_angle_refined_deg1.1991.9620940
X-RAY DIFFRACTIONr_angle_other_deg1.056332483
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.13151874
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.88823.354805
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.071152381
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.69315125
X-RAY DIFFRACTIONr_chiral_restr0.0690.22214
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02117729
X-RAY DIFFRACTIONr_gen_planes_other0.0040.023792
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.383.2127443
X-RAY DIFFRACTIONr_mcbond_other1.383.2127442
X-RAY DIFFRACTIONr_mcangle_it2.2034.7979331
X-RAY DIFFRACTIONr_mcangle_other2.2034.7979332
X-RAY DIFFRACTIONr_scbond_it1.9083.4337964
X-RAY DIFFRACTIONr_scbond_other1.9083.4347965
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.0675.06111608
X-RAY DIFFRACTIONr_long_range_B_refined5.95130.6267606
X-RAY DIFFRACTIONr_long_range_B_other5.95130.62167607
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A273480.08
12B273480.08
21A275610.09
22C275610.09
31A275970.08
32D275970.08
41B274680.08
42C274680.08
51B272790.08
52D272790.08
61C277550.09
62D277550.09
LS refinement shellResolution: 2.08→2.134 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.249 540 -
Rwork0.245 10234 -
obs--98.24 %
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)
10.4707-0.0630.06340.5906-0.32181.0258-0.0136-0.01330.02480.00190.02880.00990.0609-0.126-0.01520.18040.0531-0.01720.03920.00060.0227-14.275221.1449-41.4654
20.1455-0.35570.34080.9038-0.83520.9021-0.02630.06330.07510.028-0.1641-0.18460.05210.22330.19040.16060.08150.01520.09150.06440.09296.687424.0756-47.0786
30.6508-0.57610.39620.866-0.50670.8663-0.00590.1196-0.0185-0.038-0.05240.03250.0730.00090.05830.19070.06750.02520.070.00080.0138-11.143528.3988-60.0832
40.5574-0.2477-0.13990.3934-0.40751.16860.0021-0.0724-0.0463-0.10670.01110.00950.1988-0.098-0.01320.21190.0215-0.02690.07690.02080.0223-11.7986.2262-22.9223
50.9782-0.20740.021.0573-1.4482.4285-0.0042-0.22320.1014-0.0462-0.2651-0.2467-0.01280.51390.26930.14-0.0026-0.04880.16170.03620.10844.947718.4442-12.7458
65.1003-2.8277-2.56631.57191.42041.3041-0.1075-0.42470.38890.05550.2566-0.22520.06160.2316-0.14910.1341-0.0288-0.03610.21830.03770.220715.405113.7342-21.8394
70.5109-0.62320.31880.8432-0.20921.657-0.0243-0.03520.1069-0.0364-0.0299-0.15780.07670.17020.05420.19240.048-0.03920.17520.06060.0695-3.20785.1449-7.3004
80.1319-0.11930.19870.4709-0.23511.0217-0.05940.0199-0.01470.02150.1050.0349-0.0236-0.1754-0.04560.08040.0270.01490.18250.04280.053115.5872-32.4458-67.8756
90.9897-0.62470.89730.7226-0.57340.9206-0.14940.24490.14590.0835-0.0032-0.2025-0.22780.29110.15250.1168-0.07060.00320.23420.05320.116135.4005-22.7689-75.9539
107.9625-8.08480.412512.6934-0.79710.0738-0.08970.06171.00470.2170.0882-0.3762-0.0880.00680.00150.2689-0.0153-0.00570.22650.05640.222939.326-18.3829-59.3274
110.2651-0.39090.01270.8558-0.49051.1633-0.0441-0.01630.06280.02720.0497-0.0962-0.11450.027-0.00570.0934-0.01310.00740.14220.0530.044521.801-22.5794-81.5238
121.123-0.0861-0.30941.09580.00131.0668-0.00110.06070.0052-0.00230.02640.0360.0664-0.0896-0.02530.07550.05290.00870.10330.03770.033422.7725-43.7646-49.4033
130.3982-0.4570.51170.8186-0.62191.3518-0.06760.03540.04560.1703-0.0445-0.1687-0.25290.09450.11220.14830.0416-0.05540.07850.01850.060934.8431-28.6009-38.656
140.9934-1.09440.60831.263-0.70961.4554-0.0705-0.06110.08130.11210.0162-0.1334-0.0833-0.05670.05430.15270.0599-0.02340.10920.0410.041527.4089-46.8346-29.2606
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 136
2X-RAY DIFFRACTION2A137 - 309
3X-RAY DIFFRACTION3A310 - 471
4X-RAY DIFFRACTION4B3 - 136
5X-RAY DIFFRACTION5B137 - 213
6X-RAY DIFFRACTION6B214 - 227
7X-RAY DIFFRACTION7B228 - 471
8X-RAY DIFFRACTION8C3 - 134
9X-RAY DIFFRACTION9C137 - 204
10X-RAY DIFFRACTION10C205 - 226
11X-RAY DIFFRACTION11C227 - 471
12X-RAY DIFFRACTION12D-1 - 136
13X-RAY DIFFRACTION13D137 - 309
14X-RAY DIFFRACTION14D310 - 471

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