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- PDB-3k6h: Crystal structure of a nitroreductase family protein from Agrobac... -

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Basic information

Entry
Database: PDB / ID: 3k6h
TitleCrystal structure of a nitroreductase family protein from Agrobacterium tumefaciens str. C58
ComponentsNitroreductase family protein
KeywordsOXIDOREDUCTASE / APC5990 / nitroreductase family / Agrobacterium tumefaciens str. C58 / structural genomics / PSI-2 / protein structure initiative / midwest center for structural genomics / MCSG
Function / homology
Function and homology information


Oxidoreductases / oxidoreductase activity / nucleotide binding
Similarity search - Function
Putative NAD(P)H nitroreductase YdjA-like / : / NADH Oxidase / NADH Oxidase / Nitroreductase / Nitroreductase family / Nitroreductase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / Putative NAD(P)H nitroreductase
Similarity search - Component
Biological speciesAgrobacterium tumefaciens str. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3.05 Å
AuthorsTan, K. / Xu, X. / Cui, H. / Savchenko, A. / Edwards, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal structure of a nitroreductase family protein from Agrobacterium tumefaciens str. C58
Authors: Tan, K. / Xu, X. / Cui, H. / Savchenko, A. / Edwards, A. / Joachimiak, A.
History
DepositionOct 8, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 27, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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_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: Nitroreductase family protein
B: Nitroreductase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,74711
Polymers44,1622
Non-polymers1,5859
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9980 Å2
ΔGint-165 kcal/mol
Surface area16670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.470, 127.470, 150.983
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422

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Components

#1: Protein Nitroreductase family protein


Mass: 22080.850 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agrobacterium tumefaciens str. (bacteria)
Strain: C58 / Gene: AGR_C_3200, Atu1744 / Plasmid: p15Tv lic / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: A9CIP6
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P
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: 3.47 Å3/Da / Density % sol: 64.57 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1M Bis-tris, 1.5M Ammonium sulphate, 1/80 trpsin, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97940, 0.97951
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 13, 2009 / Details: Mirror
RadiationMonochromator: Si 111 crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97941
20.979511
ReflectionResolution: 3.05→49 Å / Num. all: 12188 / Num. obs: 12188 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.2 % / Biso Wilson estimate: 75.4 Å2 / Rmerge(I) obs: 0.111 / Net I/σ(I): 23.4
Reflection shellResolution: 3.05→3.1 Å / Redundancy: 8.4 % / Rmerge(I) obs: 0.814 / Mean I/σ(I) obs: 2.86 / Num. unique all: 599 / % possible all: 100

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
SHELXDphasing
MLPHAREphasing
DMmodel building
RESOLVEmodel building
HKL-3000phasing
PHENIX(phenix.refine: 1.5_2)refinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing
RESOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 3.05→48.7 Å / SU ML: 0.5 / σ(F): 1.9 / σ(I): 0 / Phase error: 26.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2468 1094 4.84 %random
Rwork0.1918 ---
obs0.1944 22613 99.63 %-
all-0 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 48.106 Å2 / ksol: 0.311 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-11.8792 Å20 Å2-0 Å2
2--11.8792 Å20 Å2
3----23.7585 Å2
Refinement stepCycle: LAST / Resolution: 3.05→48.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3006 0 97 0 3103
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083174
X-RAY DIFFRACTIONf_angle_d1.2584342
X-RAY DIFFRACTIONf_dihedral_angle_d20.1391158
X-RAY DIFFRACTIONf_chiral_restr0.079474
X-RAY DIFFRACTIONf_plane_restr0.011550
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0504-3.18920.45741240.3252712X-RAY DIFFRACTION98
3.1892-3.35730.33931570.2362665X-RAY DIFFRACTION100
3.3573-3.56760.23361480.19662654X-RAY DIFFRACTION99
3.5676-3.84290.22061240.17112705X-RAY DIFFRACTION100
3.8429-4.22940.20351230.14732695X-RAY DIFFRACTION100
4.2294-4.8410.20491470.12342682X-RAY DIFFRACTION100
4.841-6.09730.22641350.15652701X-RAY DIFFRACTION100
6.0973-48.70590.22561360.19472705X-RAY DIFFRACTION100
Refinement TLS params.

Refine-ID: X-RAY DIFFRACTION

IDMethodL11 (°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)
1refined2.4841-0.4210.50061.190.03843.32120.26080.0428-0.37630.1167-0.00810.20040.90430.0757-0.23310.5851-0.0457-0.10040.3397-0.07920.504536.212536.258768.0701
21.24151.4151-0.12771.58140.47882.52980.03480.42280.0955-0.62370.2029-0.0660.47831.6507-0.28820.66540.00310.12340.6154-0.16450.5116
32.3519-0.15760.6268-0.8227-0.40082.2098-0.1010.07550.2683-0.1016-0.0020.0195-0.16690.14350.07590.5985-0.0048-0.01420.4212-0.12660.5615
42.3611.36650.48390.83050.55921.10640.5908-0.37510.46970.4087-0.73410.80.08520.23060.23150.2915-0.13960.06930.55820.01690.3473
Refinement TLS groupSelection details: chain B resid 174:195

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