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- PDB-2q62: Crystal Structure of ArsH from Sinorhizobium meliloti -

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Basic information

Entry
Database: PDB / ID: 2q62
TitleCrystal Structure of ArsH from Sinorhizobium meliloti
ComponentsarsH
KeywordsFLAVOPROTEIN / alpha/beta
Function / homology
Function and homology information


FMN reductase (NADPH) activity / : / Oxidoreductases / response to metal ion / FMN binding / protein homotetramerization
Similarity search - Function
Arsenate resistance ArsH / NADPH-dependent FMN reductase-like / NADPH-dependent FMN reductase / Flavodoxin domain / Flavoprotein-like superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NADPH-dependent FMN reductase ArsH
Similarity search - Component
Biological speciesSinorhizobium meliloti (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIR / Resolution: 1.8 Å
AuthorsYe, J. / Yang, H. / Bhattacharjee, H. / Rosen, B.P.
CitationJournal: FEBS Lett. / Year: 2007
Title: Crystal structure of the flavoprotein ArsH from Sinorhizobium meliloti
Authors: Ye, J. / Yang, H. / Rosen, B.P. / Bhattacharjee, H.
History
DepositionJun 4, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 11, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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: arsH
B: arsH
C: arsH
D: arsH
E: arsH
F: arsH
G: arsH
H: arsH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)224,23915
Polymers223,5668
Non-polymers6727
Water30,3011682
1
A: arsH
B: arsH
C: arsH
D: arsH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,1678
Polymers111,7834
Non-polymers3844
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17880 Å2
ΔGint-162 kcal/mol
Surface area31980 Å2
MethodPISA, PQS
2
E: arsH
F: arsH
G: arsH
H: arsH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,0717
Polymers111,7834
Non-polymers2883
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17270 Å2
ΔGint-151 kcal/mol
Surface area30420 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)158.534, 158.534, 87.953
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number77
Space group name H-MP42
DetailsThe asymmetric unit contains two biological units.

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Components

#1: Protein
arsH


Mass: 27945.811 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sinorhizobium meliloti (bacteria) / Gene: arsH / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q92R45
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1682 / 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: 2.47 Å3/Da / Density % sol: 50.24 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 17% PEG 6000, 0.1 M calcium acetate, 0.1 M cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 296K

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 32-ID / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jul 26, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→39.633 Å / Num. obs: 176155 / % possible obs: 92.1 % / Redundancy: 11.4 % / Rmerge(I) obs: 0.088 / Rsym value: 0.088 / Net I/σ(I): 5.7
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 9.3 % / Rmerge(I) obs: 0.532 / Mean I/σ(I) obs: 1.5 / Num. measured all: 227608 / Num. unique all: 24428 / Rsym value: 0.532 / % possible all: 83.5

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
REFMAC5.2.0005refinement
PDB_EXTRACT2data extraction
MOSFLMdata reduction
SnBphasing
RefinementMethod to determine structure: SIR / Resolution: 1.8→39.63 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.942 / SU B: 5.156 / SU ML: 0.083 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.122 / ESU R Free: 0.12 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.212 9123 4.9 %RANDOM
Rwork0.173 ---
obs0.175 176155 91.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.939 Å2
Baniso -1Baniso -2Baniso -3
1--0.67 Å20 Å20 Å2
2---0.67 Å20 Å2
3---1.34 Å2
Refinement stepCycle: LAST / Resolution: 1.8→39.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14072 0 35 1682 15789
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.02214415
X-RAY DIFFRACTIONr_angle_refined_deg1.6521.97119529
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.11551770
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.64422.5640
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.86152516
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.59415153
X-RAY DIFFRACTIONr_chiral_restr0.2260.22151
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0210897
X-RAY DIFFRACTIONr_nbd_refined0.2060.27281
X-RAY DIFFRACTIONr_nbtor_refined0.3070.29872
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1310.21225
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1970.277
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1690.220
X-RAY DIFFRACTIONr_mcbond_it0.8711.59190
X-RAY DIFFRACTIONr_mcangle_it1.273214399
X-RAY DIFFRACTIONr_scbond_it2.41735975
X-RAY DIFFRACTIONr_scangle_it3.6034.55130
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.324 599 -
Rwork0.253 11812 -
obs-12411 83.6 %
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)
10.65320.23240.71911.03210.33761.75140.14490.2589-0.13070.03620.1178-0.10950.36630.5775-0.2627-0.07290.1546-0.08850.0577-0.1472-0.152440.8157.9786.112
20.9121-0.59690.43231.0793-0.17381.43380.1687-0.1229-0.2642-0.06330.03840.18360.33-0.0217-0.2071-0.01140.0209-0.0833-0.1596-0.0231-0.147623.15-0.97430.618
30.7904-0.04940.21360.77970.15471.31750.023-0.10.00470.07-0.00880.0324-0.0077-0.0758-0.0142-0.13960.01460.004-0.1357-0.0267-0.240421.14720.43735.631
40.64830.13320.39830.7168-0.13741.49440.03790.1723-0.0020.04550.047-0.0629-0.030.4432-0.0849-0.1547-0.026-0.00910.0089-0.0464-0.180944.2627.3415.399
50.7755-0.06080.14511.4164-0.16990.6871-0.014-0.0161-0.0268-0.0378-0.0155-0.08140.1828-0.0520.0294-0.0239-0.04320.0285-0.1859-0.0043-0.22534.87651.63555.966
61.0385-0.33090.57361.2872-0.60521.2803-0.1073-0.09570.12790.0625-0.0473-0.26170.00830.04540.1546-0.11570.0052-0.0531-0.1490.0331-0.108357.30458.34676.561
70.8401-0.70330.20081.6837-0.56260.9802-0.1672-0.05470.36520.2028-0.0564-0.488-0.18610.08060.2236-0.0413-0.0189-0.1363-0.16650.03120.039254.02879.81172.024
80.61330.2273-0.05251.8872-0.44380.9879-0.0280.07070.0728-0.1579-0.0707-0.18960.0333-0.0520.0987-0.06830.00630.0342-0.18460.0333-0.173639.18670.92446.064
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA8 - 2278 - 227
2X-RAY DIFFRACTION2BB8 - 2298 - 229
3X-RAY DIFFRACTION3CC9 - 2299 - 229
4X-RAY DIFFRACTION4DD8 - 2428 - 242
5X-RAY DIFFRACTION5EE9 - 2299 - 229
6X-RAY DIFFRACTION6FF9 - 2279 - 227
7X-RAY DIFFRACTION7GG8 - 2268 - 226
8X-RAY DIFFRACTION8HH9 - 2299 - 229

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