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- PDB-3fz4: The crystal structure of a possible arsenate reductase from Strep... -

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Basic information

Entry
Database: PDB / ID: 3fz4
TitleThe crystal structure of a possible arsenate reductase from Streptococcus mutans UA159
ComponentsPutative arsenate reductase
KeywordsOXIDOREDUCTASE / APC61768 / arsenate reductase / Streptococcus mutans UA159 / structural genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


Transcriptional regulator Spx/MgsR / Arsenate reductase-like / ArsC family / ArsC family profile. / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FORMIC ACID / Arsenate reductase
Similarity search - Component
Biological speciesStreptococcus mutans UA159 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.38 Å
AuthorsTan, K. / Hatzos, C. / Shackelford, G. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of a possible arsenate reductase from Streptococcus mutans UA159.
Authors: Tan, K. / Hatzos, C. / Shackelford, G. / Joachimiak, A.
History
DepositionJan 23, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 10, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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
Revision 1.3Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative arsenate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0157
Polymers13,7451
Non-polymers2696
Water2,342130
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)31.857, 41.357, 76.795
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsAUTHORS STATE THAT THE BIOLOGICAL UNIT IS EXPERIMENTALLY UNKNOWN. IT IS PREDICTED TO BE A MONOMERIC.

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Components

#1: Protein Putative arsenate reductase


Mass: 13745.392 Da / Num. of mol.: 1 / Mutation: D101G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus mutans UA159 (bacteria) / Strain: UA159, serotype c. / Gene: SMU_1651 / Plasmid: pMCSG19 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q8DSV8
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CH2O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 130 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsD101G IS A PCR MUTATION.

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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: 1.84 Å3/Da / Density % sol: 33.16 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 0.2M Zn(OAc)2, 0.1M Acetate, 10% w/v PEG 3000, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97857 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 8, 2008 / Details: mirror
RadiationMonochromator: Si(111) crystal / Protocol: SAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 1.38→24.51 Å / Num. all: 21569 / Num. obs: 21569 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.2 % / Rmerge(I) obs: 0.073 / Net I/σ(I): 41
Reflection shellResolution: 1.38→1.4 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.625 / Mean I/σ(I) obs: 2.62 / Num. unique all: 1034 / % possible all: 99.5

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
SHELXDphasing
MLPHAREphasing
DMmodel building
RESOLVEmodel building
HKL-3000phasing
REFMAC5.5.0054refinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.38→24.51 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.954 / SU B: 2.168 / SU ML: 0.041 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.085 / ESU R Free: 0.072 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20786 1098 5.1 %RANDOM
Rwork0.16661 ---
all0.1688 20334 --
obs0.1688 20334 99.26 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.487 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å20 Å20 Å2
2---0.07 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.38→24.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1068 0 5 142 1215
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0221119
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3931.9981531
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1015155
X-RAY DIFFRACTIONr_dihedral_angle_2_deg43.12124.72755
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.67615225
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.212158
X-RAY DIFFRACTIONr_chiral_restr0.0860.2169
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021854
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.5131.5664
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.38821072
X-RAY DIFFRACTIONr_scbond_it3.0883455
X-RAY DIFFRACTIONr_scangle_it4.5034.5438
X-RAY DIFFRACTIONr_rigid_bond_restr1.76731119
X-RAY DIFFRACTIONr_sphericity_free6.8663135
X-RAY DIFFRACTIONr_sphericity_bonded4.46531084
LS refinement shellResolution: 1.38→1.41 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.303 65 -
Rwork0.216 1407 -
obs-1472 96.4 %

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