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- PDB-3s2y: Crystal structure of a chromate/uranium reductase from Gluconacet... -

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Basic information

Entry
Database: PDB / ID: 3s2y
TitleCrystal structure of a chromate/uranium reductase from Gluconacetobacter hansenii
ComponentsChromate reductase
KeywordsOXIDOREDUCTASE / chromate reductase / uranium reductase
Function / homology
Function and homology information


oxidoreductase activity / nucleotide binding
Similarity search - Function
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
FLAVIN MONONUCLEOTIDE / Chromate reductase
Similarity search - Component
Biological speciesGluconacetobacter hansenii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.244 Å
AuthorsJin, H. / Zhang, Y. / Buchko, G.W. / Li, P. / Squier, T.C. / Robinson, H. / Varnum, S.M. / Long, P.E.
CitationJournal: Plos One / Year: 2012
Title: Structure Determination and Functional Analysis of a Chromate Reductase from Gluconacetobacter hansenii.
Authors: Jin, H. / Zhang, Y. / Buchko, G.W. / Varnum, S.M. / Robinson, H. / Squier, T.C. / Long, P.E.
History
DepositionMay 17, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 30, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 22, 2012Group: Database references
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

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Assembly

Deposited unit
A: Chromate reductase
B: Chromate reductase
C: Chromate reductase
D: Chromate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,46812
Polymers85,3424
Non-polymers2,1268
Water5,909328
1
A: Chromate reductase
hetero molecules

A: Chromate reductase
hetero molecules

D: Chromate reductase
hetero molecules

D: Chromate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,23810
Polymers85,3424
Non-polymers1,8966
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
crystal symmetry operation1_565x,y+1,z1
crystal symmetry operation2_566-x,y+1,-z+11
Buried area13620 Å2
ΔGint-79 kcal/mol
Surface area25270 Å2
MethodPISA
2
A: Chromate reductase
hetero molecules

A: Chromate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,6546
Polymers42,6712
Non-polymers9844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area4850 Å2
ΔGint-37 kcal/mol
Surface area15030 Å2
MethodPISA
3
B: Chromate reductase
C: Chromate reductase
hetero molecules

B: Chromate reductase
C: Chromate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,69714
Polymers85,3424
Non-polymers2,35610
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area14450 Å2
ΔGint-77 kcal/mol
Surface area25240 Å2
MethodPISA
4
B: Chromate reductase
C: Chromate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,8497
Polymers42,6712
Non-polymers1,1785
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5270 Å2
ΔGint-30 kcal/mol
Surface area14580 Å2
MethodPISA
5
D: Chromate reductase
hetero molecules

D: Chromate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,5844
Polymers42,6712
Non-polymers9132
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area4560 Å2
ΔGint-22 kcal/mol
Surface area14440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.677, 90.051, 95.234
Angle α, β, γ (deg.)90.00, 119.61, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-260-

HOH

21D-232-

HOH

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Components

#1: Protein
Chromate reductase


Mass: 21335.434 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gluconacetobacter hansenii (bacteria) / Strain: ATCC 23769 / Gene: GXY_09224 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: D5QFC5
#2: Chemical
ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE / Flavin mononucleotide


Mass: 456.344 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 328 / 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: 2.61 Å3/Da / Density % sol: 52.94 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7.5
Details: 20% PEG4000, 10% isopropanol, hepes 7.5, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 2, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionLowest resolution: 50 Å / Num. all: 43812 / Num. obs: 41698 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

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Processing

Software
NameVersionClassification
HKL-2000data collection
AMoREphasing
PHENIX(phenix.refine: 1.7_650)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1RTT

1rtt


Resolution: 2.244→45.822 Å / SU ML: 0.33 / σ(F): 1.34 / Phase error: 25.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2383 2114 5.07 %
Rwork0.1934 --
obs0.1958 41698 99.03 %
all-43812 -
Solvent computationShrinkage radii: 1.06 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 47.153 Å2 / ksol: 0.335 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.0714 Å2-0 Å2-0.0661 Å2
2--0.0348 Å2-0 Å2
3----0.1061 Å2
Refinement stepCycle: LAST / Resolution: 2.244→45.822 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5460 0 140 328 5928
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085724
X-RAY DIFFRACTIONf_angle_d1.1317842
X-RAY DIFFRACTIONf_dihedral_angle_d14.6872056
X-RAY DIFFRACTIONf_chiral_restr0.071928
X-RAY DIFFRACTIONf_plane_restr0.006995
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2445-2.29670.33791340.2662353X-RAY DIFFRACTION89
2.2967-2.35410.33151520.25472557X-RAY DIFFRACTION98
2.3541-2.41780.31921460.24722631X-RAY DIFFRACTION99
2.4178-2.48890.33881280.24652675X-RAY DIFFRACTION100
2.4889-2.56920.29611320.22312684X-RAY DIFFRACTION100
2.5692-2.6610.27261260.19422641X-RAY DIFFRACTION100
2.661-2.76760.23511720.19812609X-RAY DIFFRACTION100
2.7676-2.89350.30121190.18812720X-RAY DIFFRACTION100
2.8935-3.0460.25991380.19622627X-RAY DIFFRACTION100
3.046-3.23680.23191370.18742690X-RAY DIFFRACTION100
3.2368-3.48670.23781400.1842646X-RAY DIFFRACTION100
3.4867-3.83740.241400.18372680X-RAY DIFFRACTION100
3.8374-4.39230.21821440.16292684X-RAY DIFFRACTION100
4.3923-5.53230.18161560.17822652X-RAY DIFFRACTION100
5.5323-45.83120.20241500.19552735X-RAY DIFFRACTION100

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