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- PDB-3fbs: The crystal structure of the oxidoreductase from Agrobacterium tu... -

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Basic information

Entry
Database: PDB / ID: 3fbs
TitleThe crystal structure of the oxidoreductase from Agrobacterium tumefaciens
ComponentsOxidoreductase
KeywordsOXIDOREDUCTASE / structural genomics / PSI2 / MCSG / Protein Structure Initiative / Midwest Center for Structural Genomics
Function / homology
Function and homology information


oxidoreductase activity / nucleotide binding
Similarity search - Function
FAD/NAD(P)-binding domain / Pyridine nucleotide-disulphide oxidoreductase / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / Oxidoreductase
Similarity search - Component
Biological speciesAgrobacterium tumefaciens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.15 Å
AuthorsZhang, R. / Xu, X. / Zheng, H. / Savchenko, A. / Edwards, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published / Year: 2008
Title: The crystal structure of the oxidoreductase from Agrobacterium tumefaciens
Authors: Zhang, R. / Xu, X. / Zheng, H. / Savchenko, A. / Edwards, A. / Joachimiak, A.
History
DepositionNov 19, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 23, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description ...Advisory / Refinement description / Source and taxonomy / Version format compliance
Revision 1.2Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_special_symmetry / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Oxidoreductase
B: Oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,7119
Polymers63,8032
Non-polymers1,9087
Water5,855325
1
A: Oxidoreductase
hetero molecules

A: Oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,80710
Polymers63,8032
Non-polymers2,0048
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area8660 Å2
ΔGint-119 kcal/mol
Surface area22410 Å2
MethodPISA
2
B: Oxidoreductase
hetero molecules

B: Oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,6158
Polymers63,8032
Non-polymers1,8126
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area8110 Å2
ΔGint-77 kcal/mol
Surface area22930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.190, 95.190, 149.237
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-308-

HOH

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Components

#1: Protein Oxidoreductase /


Mass: 31901.516 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agrobacterium tumefaciens (bacteria) / Strain: str. C58 / Gene: AGR_C_405, Atu0238, GI:17934154 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: A9CKI7
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 325 / 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: 2.65 Å3/Da / Density % sol: 53.57 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M NaHepes, 0.1M NaCl, 1.6M (NH4)2SO4, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9794, 0.9796
DetectorType: SBC-2 / Detector: CCD / Date: Jan 31, 2008 / Details: mirrors
RadiationMonochromator: Si 111 channel / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97941
20.97961
ReflectionResolution: 2.15→80.32 Å / Num. all: 36135 / Num. obs: 36027 / % possible obs: 99.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 17.6 % / Biso Wilson estimate: 19 Å2 / Rmerge(I) obs: 0.137 / Net I/σ(I): 21.42
Reflection shellResolution: 2.15→2.206 Å / Redundancy: 16.9 % / Rmerge(I) obs: 0.772 / Mean I/σ(I) obs: 2.75 / Num. unique all: 2755 / % possible all: 99.71

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000phasing
REFMAC5.5.0054refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MAD / Resolution: 2.15→80.32 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.917 / SU B: 8.991 / SU ML: 0.117 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.225 / ESU R Free: 0.191
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23626 1896 5 %RANDOM
Rwork0.18755 ---
obs0.18996 36027 99.7 %-
all-36135 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.483 Å2
Baniso -1Baniso -2Baniso -3
1-0.11 Å20 Å20 Å2
2--0.11 Å20 Å2
3----0.22 Å2
Refinement stepCycle: LAST / Resolution: 2.15→80.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4431 0 123 325 4879
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0214661
X-RAY DIFFRACTIONr_bond_other_d0.0020.023143
X-RAY DIFFRACTIONr_angle_refined_deg1.9051.9836330
X-RAY DIFFRACTIONr_angle_other_deg1.1313.0017592
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6175590
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.47422.308195
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.61215731
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.0791546
X-RAY DIFFRACTIONr_chiral_restr0.1140.2692
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0215222
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02982
X-RAY DIFFRACTIONr_mcbond_it1.0971.52905
X-RAY DIFFRACTIONr_mcbond_other0.2891.51229
X-RAY DIFFRACTIONr_mcangle_it2.02924616
X-RAY DIFFRACTIONr_scbond_it3.39131756
X-RAY DIFFRACTIONr_scangle_it5.4894.51714
LS refinement shellResolution: 2.15→2.206 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.262 139 -
Rwork0.192 2609 -
obs-2748 99.71 %
Refinement TLS params.Method: refined / Origin x: 45.538 Å / Origin y: 53.447 Å / Origin z: 12.563 Å
111213212223313233
T0.1005 Å2-0.023 Å2-0.0147 Å2-0.0654 Å20.017 Å2--0.0104 Å2
L0.3856 °20.126 °2-0.0403 °2-0.4134 °20.0678 °2--0.1959 °2
S0.0199 Å °-0.042 Å °0.02 Å °0.1169 Å °-0.0438 Å °-0.0069 Å °-0.0762 Å °0.0288 Å °0.0239 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 50
2X-RAY DIFFRACTION1A51 - 100
3X-RAY DIFFRACTION1A101 - 150
4X-RAY DIFFRACTION1A151 - 200
5X-RAY DIFFRACTION1A201 - 250
6X-RAY DIFFRACTION1A251 - 294
7X-RAY DIFFRACTION1B1 - 50
8X-RAY DIFFRACTION1B51 - 100
9X-RAY DIFFRACTION1B101 - 150
10X-RAY DIFFRACTION1B151 - 200
11X-RAY DIFFRACTION1B201 - 250
12X-RAY DIFFRACTION1B251 - 295

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