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- PDB-5xhu: Crystal structure of ycgT from bacillus subtilis -

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Basic information

Entry
Database: PDB / ID: 5xhu
TitleCrystal structure of ycgT from bacillus subtilis
ComponentsFerredoxin--NADP reductase
KeywordsOXIDOREDUCTASE / ferredoxin-NADP+ oxidoreductase homolog
Function / homology
Function and homology information


ferredoxin-NADP+ reductase / ferredoxin-NADP+ reductase activity / cellular response to iron ion / NADP binding / flavin adenine dinucleotide binding
Similarity search - Function
Ferredoxin--NADP reductase, type 2 / Pyridine nucleotide-disulphide oxidoreductase / 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 / Ferredoxin--NADP reductase / Ferredoxin--NADP reductase 1
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsKomori, H.
CitationJournal: To Be Published
Title: Crystal structure of ycgT from bacillus subtilis
Authors: Komori, H.
History
DepositionApr 24, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 2, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ferredoxin--NADP reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,9622
Polymers36,1761
Non-polymers7861
Water1,69394
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1280 Å2
ΔGint-9 kcal/mol
Surface area15760 Å2
2
A: Ferredoxin--NADP reductase
hetero molecules

A: Ferredoxin--NADP reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,9244
Polymers72,3532
Non-polymers1,5712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_456-x-1,y,-z+11
Buried area6840 Å2
ΔGint-43 kcal/mol
Surface area27240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.371, 164.598, 76.576
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number21
Space group name H-MC222
Components on special symmetry positions
IDModelComponents
11A-1163-

HOH

21A-1164-

HOH

31A-1191-

HOH

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Components

#1: Protein Ferredoxin--NADP reductase / Fd-NADP(+) reductase


Mass: 36176.301 Da / Num. of mol.: 1 / Fragment: UNP residues 6-334
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: B4417_2052 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A164V7W7, UniProt: O31475*PLUS, ferredoxin-NADP+ reductase
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 94 / 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: 3.15 Å3/Da / Density % sol: 60.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1M Tris buffer pH 8.6, 0.2 M tri-Sodium citrate, and 40% PEG400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: May 29, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 27133 / % possible obs: 100 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.085 / Rpim(I) all: 0.034 / Rrim(I) all: 0.092 / Χ2: 0.985 / Net I/σ(I): 8.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.1-2.147.30.830.8920.3280.8930.97499.9
2.14-2.187.30.8220.8510.3240.8841.012100
2.18-2.227.30.7040.8630.2780.7571.007100
2.22-2.267.40.6020.9290.2380.6481.015100
2.26-2.317.40.4960.9320.1960.5340.969100
2.31-2.377.40.4540.9370.1790.4881.025100
2.37-2.427.30.3740.960.1480.4020.996100
2.42-2.497.40.3270.9670.1290.3521.02100
2.49-2.567.30.2750.9790.1090.2960.994100
2.56-2.657.30.2250.9810.0890.2420.982100
2.65-2.747.30.1820.9890.0720.1960.97799.9
2.74-2.857.30.1470.9910.0580.1580.955100
2.85-2.987.30.1190.9940.0470.1280.904100
2.98-3.147.30.0850.9970.0340.0920.841100
3.14-3.337.20.0660.9970.0260.0710.846100
3.33-3.597.30.0650.9970.0260.071.135100
3.59-3.957.20.0650.9950.0260.071.66100
3.95-4.527.10.0530.9970.0210.0571.511100
4.52-5.770.0270.9990.0110.0290.496100
5.7-506.40.0210.9990.0090.0230.3499.6

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Processing

Software
NameVersionClassification
HKL-2000data scaling
REFMAC5.7.0032refinement
PDB_EXTRACT3.22data extraction
PHASERphasing
HKLdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→43.72 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.924 / SU B: 8.863 / SU ML: 0.116 / SU R Cruickshank DPI: 0.1913 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.191 / ESU R Free: 0.167
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2341 1325 5.1 %RANDOM
Rwork0.2014 ---
obs0.203 24714 95.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 83.15 Å2 / Biso mean: 32.503 Å2 / Biso min: 14.89 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å2-0 Å2-0 Å2
2--0.09 Å2-0 Å2
3----0.06 Å2
Refinement stepCycle: final / Resolution: 2.1→43.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2539 0 53 94 2686
Biso mean--19.65 30.12 -
Num. residues----329
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0192642
X-RAY DIFFRACTIONr_bond_other_d0.0010.022537
X-RAY DIFFRACTIONr_angle_refined_deg1.4151.9953570
X-RAY DIFFRACTIONr_angle_other_deg0.75235854
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8465328
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.55224.248113
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.25215466
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0851516
X-RAY DIFFRACTIONr_chiral_restr0.0780.2394
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022945
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02572
LS refinement shellResolution: 2.1→2.155 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.255 70 -
Rwork0.239 1239 -
all-1309 -
obs--66.11 %
Refinement TLS params.Method: refined / Origin x: -38.6012 Å / Origin y: -19.6244 Å / Origin z: 18.6426 Å
111213212223313233
T0.0746 Å20.0386 Å2-0.036 Å2-0.0449 Å2-0.0215 Å2--0.0385 Å2
L0.6399 °2-0.2128 °20.4129 °2-0.7147 °2-0.7601 °2--1.3947 °2
S0.075 Å °0.0917 Å °-0.0501 Å °-0.0225 Å °-0.0173 Å °0.0285 Å °0.1867 Å °0.0569 Å °-0.0577 Å °

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