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- PDB-3bo9: Crystal structure of putative nitroalkan dioxygenase (TM0800) fro... -

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Basic information

Entry
Database: PDB / ID: 3bo9
TitleCrystal structure of putative nitroalkan dioxygenase (TM0800) from Thermotoga maritima at 2.71 A resolution
ComponentsPutative nitroalkan dioxygenase
KeywordsOXIDOREDUCTASE / TM0800 / putative nitroalkan dioxygenase / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


nitronate monooxygenase activity
Similarity search - Function
Enoyl-(acyl-carrier-protein) reductase II, putative / Nitronate monooxygenase / Nitronate monooxygenase / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Nitronate monooxygenase domain-containing protein
Similarity search - Component
Biological speciesThermotoga maritima MSB8 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.71 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of putative nitroalkan dioxygenase (TM0800) from Thermotoga maritima at 2.71 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionDec 17, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 25, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Jan 25, 2023Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999 SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHH FOLLOWED BY THE TARGET SEQUENCE.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative nitroalkan dioxygenase
B: Putative nitroalkan dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,13120
Polymers71,5732
Non-polymers4,55918
Water45025
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.058, 128.058, 161.678
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg label comp-ID: HIS / End label comp-ID: GLU / Refine code: 2 / Auth seq-ID: 0 - 313 / Label seq-ID: 12 - 325

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Putative nitroalkan dioxygenase


Mass: 35786.305 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima MSB8 (bacteria) / Species: Thermotoga maritima / Strain: MSB8 / DSM 3109 / JCM 10099 / Gene: TM0800 / Plasmid: MH1 / Production host: Escherichia coli (E. coli) / Strain (production host): DL41
References: UniProt: Q9WZQ7, enoyl-[acyl-carrier-protein] reductase (NADH)

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Non-polymers , 5 types, 43 molecules

#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-2PE / NONAETHYLENE GLYCOL / Polyethylene glycol


Mass: 414.488 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C18H38O10 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 25 / 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: 4.63 Å3/Da / Density % sol: 73.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.67
Details: NANODROP, 44.0% PEG 400, 0.2M Lithium sulfate, 0.1M Tris-HCl pH 8.67, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.91840, 0.97939, 0.97953
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 27, 2007 / Details: Adjustable focusing mirrors in K-B geometry
RadiationMonochromator: Si(111) Double crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.91841
20.979391
30.979531
ReflectionResolution: 2.71→29.761 Å / Num. obs: 37210 / % possible obs: 99.9 % / Redundancy: 7.3 % / Biso Wilson estimate: 67.24 Å2 / Rmerge(I) obs: 0.171 / Rsym value: 0.171 / Net I/σ(I): 3.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.71-2.787.41.5550.42015927251.555100
2.78-2.867.41.1620.61954826321.162100
2.86-2.947.40.8950.81904525580.895100
2.94-3.037.40.7320.91847724860.732100
3.03-3.137.40.5211.41800624320.521100
3.13-3.247.40.4081.71734523370.408100
3.24-3.367.40.3182.31680322680.318100
3.36-3.57.40.2331617221960.23100
3.5-3.657.40.1833.71536920890.183100
3.65-3.837.30.1494.61471720110.149100
3.83-4.047.30.13451399319280.134100
4.04-4.287.20.1185.31299918120.118100
4.28-4.587.10.10661235317330.106100
4.58-4.957.10.0966.71138015980.096100
4.95-5.427.20.0867.31071014900.086100
5.42-6.067.10.0857.5969413660.085100
6.06-770.0867.2851712100.086100
7-8.576.90.0747.7713310400.074100
8.57-12.126.60.0677.255338330.067100
12.12-29.7615.90.0755.527504660.07593.5

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PHENIXrefinement
SOLVEphasing
MolProbity3beta29model building
SCALAdata scaling
PDB_EXTRACT3data extraction
MAR345CCDdata collection
MOSFLMdata reduction
RefinementMethod to determine structure: MAD / Resolution: 2.71→29.761 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.935 / SU B: 15.515 / SU ML: 0.147 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.288 / ESU R Free: 0.216
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 4. PEG 400 (2PE) FRAGMENTS, ETHYLENE GLYCOL (EDO) AND SULFATE IONS ARE MODELED BASED ON CRYSTALLIZATION/CRYO CONDITIONS. 5. THE TWO PHOSPHATES MODELED IN THE ACTIVE SITE ARE LIKELY PART OF MONONUCLEOTIDE FMN (BY SIMILARITY TO 2GJN). HOWEVER, THE DENSITY FOR FULL FMN IS TOO WEAK TO ALLOW RELIABLE REFINEMENT.
RfactorNum. reflection% reflectionSelection details
Rfree0.211 1854 5 %RANDOM
Rwork0.189 ---
obs0.19 37145 99.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.802 Å2
Baniso -1Baniso -2Baniso -3
1--0.36 Å20 Å20 Å2
2---0.36 Å20 Å2
3---0.72 Å2
Refinement stepCycle: LAST / Resolution: 2.71→29.761 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4663 0 152 25 4840
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0224875
X-RAY DIFFRACTIONr_bond_other_d0.0020.023361
X-RAY DIFFRACTIONr_angle_refined_deg1.3121.9996555
X-RAY DIFFRACTIONr_angle_other_deg0.89438244
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.6635630
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.21723.864176
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.24115837
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.7461536
X-RAY DIFFRACTIONr_chiral_restr0.0730.2760
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.025282
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02894
X-RAY DIFFRACTIONr_nbd_refined0.2160.21016
X-RAY DIFFRACTIONr_nbd_other0.1880.23447
X-RAY DIFFRACTIONr_nbtor_refined0.1770.22424
X-RAY DIFFRACTIONr_nbtor_other0.0860.22521
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1890.2102
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1420.25
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2230.227
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0960.23
X-RAY DIFFRACTIONr_mcbond_it1.57233260
X-RAY DIFFRACTIONr_mcbond_other0.28231290
X-RAY DIFFRACTIONr_mcangle_it2.19255003
X-RAY DIFFRACTIONr_scbond_it4.5781857
X-RAY DIFFRACTIONr_scangle_it6.594111550
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
1840TIGHT POSITIONAL0.040.06
2084MEDIUM POSITIONAL0.310.5
1840TIGHT THERMAL0.241.2
2084MEDIUM THERMAL0.753
LS refinement shellResolution: 2.71→2.78 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.395 138 -
Rwork0.361 2581 -
all-2719 -
obs--99.93 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
11.10790.3324-0.24331.71350.10191.24330.03570.02720.0383-0.0087-0.04780.0683-0.07970.00720.0121-0.13540.0169-0.0086-0.10390.0433-0.103821.367178.126349.1166
21.18950.18540.37021.5548-0.42262.1255-0.01030.1172-0.1813-0.194-0.0558-0.04060.51480.09660.06610.04180.01150.0711-0.07050.0192-0.050619.462646.210949.6695
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA0 - 31312 - 325
2X-RAY DIFFRACTION2BB0 - 31312 - 325

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