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- PDB-1vkw: Crystal structure of a putative nitroreductase (tm1586) from ther... -

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Basic information

Entry
Database: PDB / ID: 1vkw
TitleCrystal structure of a putative nitroreductase (tm1586) from thermotoga maritima msb8 at 2.00 A resolution
Componentsputative nitroreductase
KeywordsOXIDOREDUCTASE / Structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI
Function / homology
Function and homology information


oxidoreductase activity
Similarity search - Function
putative nitroreductase (tm1586), domain 2 / Putative nitroreductase TM1586 / Putative TM nitroreductase / NADH Oxidase / NADH Oxidase / Nitroreductase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
TM1586_NiRdase domain-containing protein
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of Putative Nitroreductase (TM1586) from Thermotoga maritima at 2.00 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJun 24, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 21, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.3Jan 25, 2023Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / 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_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: putative nitroreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,9883
Polymers25,7961
Non-polymers1922
Water1,71195
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.299, 45.299, 192.752
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein putative nitroreductase /


Mass: 25796.008 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Strain: MSB8 / Gene: TM1586 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9X1S2
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 95 / 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: 2.2 Å3/Da / Density % sol: 43.58 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop, nanodrop / pH: 4.6
Details: Acetate pH 4.6, 0.2M (NH4)2SO4, 20% Glycerol, 25% PEG-4000 , VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
1,21
Diffraction source
SourceSiteBeamlineIDWavelengthWavelength (Å)
SYNCHROTRONSSRL BL9-210.979029
SYNCHROTRONSSRL BL9-220.979029, 0.918370,0.978835
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 4, 2004
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1double crystal monochromatorSINGLE WAVELENGTHMx-ray1
2MADMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.9790291
20.918371
30.9788351
ReflectionResolution: 2→39.23 Å / Num. obs: 15922 / % possible obs: 97.1 % / Redundancy: 5.7 % / Biso Wilson estimate: 41.38 Å2 / Rsym value: 0.059 / Net I/σ(I): 18
Reflection shellResolution: 2→2.05 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 3.2 / Num. unique all: 969 / Rsym value: 0.229 / % possible all: 82.3

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALA4.2)data scaling
SOLVEphasing
SHARPphasing
REFMAC5.2.0001refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MAD / Resolution: 2→39.23 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.927 / SU B: 7.734 / SU ML: 0.114 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.205 / ESU R Free: 0.171
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24281 827 5.1 %RANDOM
Rwork0.21022 ---
obs0.2118 15544 99.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 32.938 Å2
Baniso -1Baniso -2Baniso -3
1-0.29 Å20.15 Å20 Å2
2--0.29 Å20 Å2
3----0.44 Å2
Refinement stepCycle: LAST / Resolution: 2→39.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1751 0 10 95 1856
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0221807
X-RAY DIFFRACTIONr_bond_other_d0.0010.021639
X-RAY DIFFRACTIONr_angle_refined_deg1.131.9462455
X-RAY DIFFRACTIONr_angle_other_deg0.73933803
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9445216
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.55823.21484
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.70415305
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.2221513
X-RAY DIFFRACTIONr_chiral_restr0.070.2267
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021980
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02374
X-RAY DIFFRACTIONr_nbd_refined0.1920.2345
X-RAY DIFFRACTIONr_nbd_other0.1770.21632
X-RAY DIFFRACTIONr_nbtor_other0.080.21008
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1390.282
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2040.227
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1960.260
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1390.221
X-RAY DIFFRACTIONr_mcbond_it1.52931170
X-RAY DIFFRACTIONr_mcbond_other0.2973432
X-RAY DIFFRACTIONr_mcangle_it2.21951768
X-RAY DIFFRACTIONr_scbond_it3.7968786
X-RAY DIFFRACTIONr_scangle_it4.96711687
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.232 72 6.08 %
Rwork0.211 1112 -
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)
12.4481-0.07260.0343.84930.01353.78310.19080.6166-0.0887-0.98330.0484-0.61870.09370.4477-0.23910.1951-0.03350.15830.1402-0.09290.051333.25814.223411.1637
22.7395-0.69420.57482.89040.48312.22060.0412-0.05520.0653-0.09280.1182-0.13160.0382-0.0499-0.1593-0.1374-0.06580.0261-0.0875-0.0109-0.075624.87338.512928.7287
Refinement TLS group

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

IDRefine TLS-IDAuth seq-IDLabel seq-ID
111 - 11313 - 125
22114 - 206126 - 218

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