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- PDB-3d7n: The crystal structure of the flavodoxin, WrbA-like protein from A... -

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Basic information

Entry
Database: PDB / ID: 3d7n
TitleThe crystal structure of the flavodoxin, WrbA-like protein from Agrobacterium tumefaciens
ComponentsFlavodoxin, WrbA-like protein
KeywordsELECTRON TRANSPORT / flavodoxin / WrbA-like protein / structural genomics / PSI / MCSG / Protein Structure Initiative / Midwest Center for Structural Genomics
Function / homology
Function and homology information


NAD(P)H dehydrogenase (quinone) activity / FMN binding / electron transfer activity / membrane
Similarity search - Function
NADPH-dependent FMN reductase-like / NADPH-dependent FMN reductase / Flavodoxin, conserved site / Flavodoxin signature. / Flavodoxin domain / Flavodoxin-like domain profile. / Flavodoxin/nitric oxide synthase / Flavoprotein-like superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Flavodoxin, WrbA-like protein
Similarity search - Component
Biological speciesAgrobacterium tumefaciens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsZhang, R. / Xu, X. / Gu, J. / Savchenko, A. / Edwards, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published / Year: 2008
Title: The crystal structure of the flavodoxin, WrbA-like protein from Agrobacterium tumefaciens
Authors: Zhang, R. / Xu, X. / Gu, J. / Savchenko, A. / Edwards, A. / Joachimiak, A.
History
DepositionMay 21, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 15, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.2Oct 16, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Flavodoxin, WrbA-like protein


Theoretical massNumber of molelcules
Total (without water)20,9441
Polymers20,9441
Non-polymers00
Water48627
1
A: Flavodoxin, WrbA-like protein

A: Flavodoxin, WrbA-like protein

A: Flavodoxin, WrbA-like protein

A: Flavodoxin, WrbA-like protein


Theoretical massNumber of molelcules
Total (without water)83,7774
Polymers83,7774
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_655-x+1,-y,z1
crystal symmetry operation8_556x-y,-y,-z+11
crystal symmetry operation11_656-x+y+1,y,-z+11
Buried area8910 Å2
ΔGint-55 kcal/mol
Surface area21570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.948, 73.948, 144.488
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222
DetailsThis protein exists as tetramer. The rest part of the biological assembly is generated by the operations:x-y,-y,-z+1; -x+1,-y,z; -x+y+1,y,-z+1

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Components

#1: Protein Flavodoxin, WrbA-like protein


Mass: 20944.268 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agrobacterium tumefaciens (bacteria) / Strain: str. C58 / Gene: AGR_L_1309, Atu4201 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: A9CG77
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / Source method: isolated from a natural source / Formula: H2O
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: 2.72 Å3/Da / Density % sol: 54.82 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M Hepes, 0.2M NaCl, 25%PEG3350, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9794 Å
DetectorType: SBC-2 / Detector: CCD / Date: Nov 22, 2006 / Details: mirrors
RadiationMonochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.3→58.52 Å / Num. all: 10480 / Num. obs: 10224 / % possible obs: 97.56 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 24.7 % / Biso Wilson estimate: 48.1 Å2 / Rmerge(I) obs: 0.097 / Net I/σ(I): 35
Reflection shellResolution: 2.3→2.36 Å / Redundancy: 17.3 % / Rmerge(I) obs: 0.65 / Mean I/σ(I) obs: 1.45 / Num. unique all: 781 / % possible all: 92.32

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
SBC-Collectdata collection
HKL-2000data reduction
HKL-2000data scaling
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 2.3→58.52 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.94 / SU B: 14.067 / SU ML: 0.155 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.233 / ESU R Free: 0.206
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25378 514 4.8 %RANDOM
Rwork0.20748 ---
obs0.20954 10224 97.56 %-
all-10480 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 47.774 Å2
Baniso -1Baniso -2Baniso -3
1-2.56 Å21.28 Å20 Å2
2--2.56 Å20 Å2
3----3.84 Å2
Refinement stepCycle: LAST / Resolution: 2.3→58.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1187 0 0 27 1214
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0211217
X-RAY DIFFRACTIONr_bond_other_d0.0010.02785
X-RAY DIFFRACTIONr_angle_refined_deg1.7661.9161649
X-RAY DIFFRACTIONr_angle_other_deg1.05531906
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.4115154
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.04624.25954
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.40315181
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.624154
X-RAY DIFFRACTIONr_chiral_restr0.1130.2175
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021386
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02257
X-RAY DIFFRACTIONr_nbd_refined0.2360.2289
X-RAY DIFFRACTIONr_nbd_other0.2020.2768
X-RAY DIFFRACTIONr_nbtor_refined0.1890.2591
X-RAY DIFFRACTIONr_nbtor_other0.0980.2595
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2270.239
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0270.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.170.215
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2570.236
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1150.25
X-RAY DIFFRACTIONr_mcbond_it1.411.5926
X-RAY DIFFRACTIONr_mcbond_other0.2221.5326
X-RAY DIFFRACTIONr_mcangle_it1.86421207
X-RAY DIFFRACTIONr_scbond_it2.3973533
X-RAY DIFFRACTIONr_scangle_it3.4534.5442
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.324 43 -
Rwork0.262 678 -
obs-721 92.32 %
Refinement TLS params.Method: refined / Origin x: 25.2885 Å / Origin y: 12.5357 Å / Origin z: 77.9606 Å
111213212223313233
T-0.1034 Å20.1429 Å20.0199 Å2--0.1079 Å2-0.0486 Å2---0.1892 Å2
L2.5222 °20.1778 °2-0.166 °2-4.7107 °20.7441 °2--4.6193 °2
S-0.0271 Å °-0.1721 Å °0.1378 Å °0.1716 Å °-0.1032 Å °0.4234 Å °-0.5385 Å °-0.5156 Å °0.1302 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA7 - 407 - 40
2X-RAY DIFFRACTION1AA41 - 8041 - 80
3X-RAY DIFFRACTION1AA81 - 12981 - 129
4X-RAY DIFFRACTION1AA149 - 156149 - 156
5X-RAY DIFFRACTION1AA165 - 187165 - 187

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