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- PDB-4hs4: Crystal structure of a putative chromate reductase from Gluconace... -

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Basic information

Entry
Database: PDB / ID: 4hs4
TitleCrystal structure of a putative chromate reductase from Gluconacetobacter hansenii, Gh-ChrR, containing a Y129N substitution.
ComponentsChromate reductase
KeywordsOXIDOREDUCTASE / TRIPLE-LAYERED / A/B/A STRUCTURE / NAD(P)H-DEPENDENT FMN 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: 2.1 Å
AuthorsZhang, Y. / Robinson, H. / Buchko, G.W.
CitationJournal: To be Published
Title: Mechanistic insights of chromate and uranyl reduction by the NADPH-dependent FMN reductase, ChrR, from Gluconacetobacter hansenii
Authors: Buchko, G.W. / Zhang, Y. / Robinson, H.
History
DepositionOct 29, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 26, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 28, 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: Chromate reductase
B: Chromate reductase
C: Chromate reductase
D: Chromate reductase
E: Chromate reductase
F: Chromate reductase
G: Chromate reductase
H: Chromate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)171,66011
Polymers170,2918
Non-polymers1,3693
Water11,133618
1
G: Chromate reductase
H: Chromate reductase
hetero molecules

A: Chromate reductase
B: Chromate reductase
hetero molecules

C: Chromate reductase
D: Chromate reductase
E: Chromate reductase
F: Chromate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)171,66011
Polymers170,2918
Non-polymers1,3693
Water1448
TypeNameSymmetry operationNumber
crystal symmetry operation1_455x-1,y,z1
crystal symmetry operation3_455-x-1,y+1/2,-z+1/21
identity operation1_555x,y,z1
Buried area19740 Å2
ΔGint-53 kcal/mol
Surface area53570 Å2
MethodPISA
2
A: Chromate reductase

E: Chromate reductase


Theoretical massNumber of molelcules
Total (without water)42,5732
Polymers42,5732
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_445-x-1,y-1/2,-z+1/21
Buried area2590 Å2
ΔGint-10 kcal/mol
Surface area15740 Å2
MethodPISA
3
B: Chromate reductase
hetero molecules

F: Chromate reductase


Theoretical massNumber of molelcules
Total (without water)43,0293
Polymers42,5732
Non-polymers4561
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_445-x-1,y-1/2,-z+1/21
Buried area2560 Å2
ΔGint-9 kcal/mol
Surface area15790 Å2
MethodPISA
4
C: Chromate reductase
D: Chromate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,0293
Polymers42,5732
Non-polymers4561
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2540 Å2
ΔGint-8 kcal/mol
Surface area15730 Å2
MethodPISA
5
G: Chromate reductase
H: Chromate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,0293
Polymers42,5732
Non-polymers4561
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2570 Å2
ΔGint-9 kcal/mol
Surface area15780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.422, 92.146, 188.013
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Chromate reductase


Mass: 21286.361 Da / Num. of mol.: 8
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(DE3) / References: UniProt: D5QFC5
#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE / Flavin mononucleotide


Mass: 456.344 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 618 / 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: 2.3 Å3/Da / Density % sol: 46.52 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 1.5 uL protein at 16 mg/mL (300 mM NaCl, 50 mM NaPO4, 250 mM imidazole, pH 8) plus 1.5 uL precipatant (20% (w/v) PEG3350, 200 mM magnesium formate), VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 27, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.1→44.96 Å / Num. all: 93997 / Num. obs: 91997 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIXmodel building
PHENIX(phenix.refine: 1.8.1_1161)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→44.96 Å / SU ML: 0.23 / σ(F): 1.34 / Phase error: 24.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2317 2000 2.17 %Random
Rwork0.2078 ---
obs0.2083 91997 99.64 %-
all-93997 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→44.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10976 0 93 618 11687
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00811299
X-RAY DIFFRACTIONf_angle_d1.18615470
X-RAY DIFFRACTIONf_dihedral_angle_d13.5864077
X-RAY DIFFRACTIONf_chiral_restr0.0711857
X-RAY DIFFRACTIONf_plane_restr0.0062003
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0998-2.15230.28161400.23516303X-RAY DIFFRACTION99
2.1523-2.21050.27791440.24266310X-RAY DIFFRACTION99
2.2105-2.27550.27381420.24286322X-RAY DIFFRACTION100
2.2755-2.3490.29491370.2346365X-RAY DIFFRACTION100
2.349-2.43290.27531420.23126378X-RAY DIFFRACTION100
2.4329-2.53030.25331460.22956383X-RAY DIFFRACTION100
2.5303-2.64550.25241380.23176394X-RAY DIFFRACTION100
2.6455-2.7850.2641410.23036392X-RAY DIFFRACTION100
2.785-2.95940.25411450.23496416X-RAY DIFFRACTION100
2.9594-3.18780.2441440.22946433X-RAY DIFFRACTION100
3.1878-3.50850.25081390.22876490X-RAY DIFFRACTION100
3.5085-4.0160.20371440.19166506X-RAY DIFFRACTION100
4.016-5.05860.18971440.17146547X-RAY DIFFRACTION100
5.0586-44.97120.21571540.18866758X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -32.0167 Å / Origin y: 20.167 Å / Origin z: 52.0941 Å
111213212223313233
T0.1987 Å2-0.0208 Å20.0039 Å2-0.2019 Å20.0167 Å2--0.1926 Å2
L0.106 °2-0.1103 °2-0.0721 °2-0.1366 °20.125 °2--0.0545 °2
S-0.0637 Å °-0.0299 Å °0.0045 Å °0.0178 Å °0.0675 Å °-0.0167 Å °-0.0096 Å °0.0494 Å °0 Å °
Refinement TLS groupSelection details: all

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