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- PDB-4h6p: Crystal structure of a putative chromate reductase from Gluconace... -

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Basic information

Entry
Database: PDB / ID: 4h6p
TitleCrystal structure of a putative chromate reductase from Gluconacetobacter hansenii, Gh-ChrR, containing a R101A substitution.
ComponentsChromate reductase
KeywordsOXIDOREDUCTASE / triple-layered / a/b/a structure / NAD(P)H-dependent FMN reductase / FMN / NADH / NADPH
Function / homology
Function and homology information


FMN binding / oxidoreductase activity / cytosol
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: 2.556 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. / Robinson, H. / Zhang, Y.
History
DepositionSep 19, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 10, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 20, 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
E: Chromate reductase
F: Chromate reductase
G: Chromate reductase
H: Chromate reductase
I: Chromate reductase
J: Chromate reductase
K: Chromate reductase
L: Chromate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)260,46824
Polymers254,99212
Non-polymers5,47612
Water6,864381
1
A: Chromate reductase
B: Chromate reductase
hetero molecules

A: Chromate reductase
B: Chromate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,8238
Polymers84,9974
Non-polymers1,8254
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,-y,z1
Buried area13170 Å2
ΔGint-69 kcal/mol
Surface area25750 Å2
MethodPISA
2
C: Chromate reductase
D: Chromate reductase
hetero molecules

C: Chromate reductase
D: Chromate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,8238
Polymers84,9974
Non-polymers1,8254
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area13360 Å2
ΔGint-69 kcal/mol
Surface area25680 Å2
MethodPISA
3
E: Chromate reductase
F: Chromate reductase
G: Chromate reductase
L: Chromate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,8238
Polymers84,9974
Non-polymers1,8254
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13290 Å2
ΔGint-67 kcal/mol
Surface area25870 Å2
MethodPISA
4
H: Chromate reductase
I: Chromate reductase
J: Chromate reductase
K: Chromate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,8238
Polymers84,9974
Non-polymers1,8254
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13420 Å2
ΔGint-64 kcal/mol
Surface area26120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.918, 287.590, 91.362
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11B-306-

HOH

21D-352-

HOH

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Components

#1: Protein
Chromate reductase


Mass: 21249.316 Da / Num. of mol.: 12
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


Mass: 456.344 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 381 / 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: 2.45 Å3/Da / Density % sol: 49.7 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1:1 mixture of protein (~12 mg/mL) in 100 mM NaCl, 20 mM TrisHCl, 1 mM DTT, pH 7 and precipatant (Emerald BioSystems) 25% w/v PEG3350, 4% isopropanol, 0.1 M HEPES (pH 7.5) 0.1 M CaCl2, VAPOR ...Details: 1:1 mixture of protein (~12 mg/mL) in 100 mM NaCl, 20 mM TrisHCl, 1 mM DTT, pH 7 and precipatant (Emerald BioSystems) 25% w/v PEG3350, 4% isopropanol, 0.1 M HEPES (pH 7.5) 0.1 M CaCl2, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 19, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.556→49.191 Å / Num. all: 85635 / Num. obs: 85635 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.556→2.5865 Å / % possible all: 89

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.8_1069)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3S2Y

3s2y


Resolution: 2.556→49.191 Å / SU ML: 0.32 / σ(F): 1.34 / Phase error: 27.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2712 4089 5.01 %random
Rwork0.2328 ---
obs0.2348 81546 99.6 %-
all-85635 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.556→49.191 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16440 0 372 381 17193
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00717184
X-RAY DIFFRACTIONf_angle_d1.32923580
X-RAY DIFFRACTIONf_dihedral_angle_d17.6776120
X-RAY DIFFRACTIONf_chiral_restr0.0742808
X-RAY DIFFRACTIONf_plane_restr0.0073000
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5564-2.58650.32961250.29662362X-RAY DIFFRACTION89
2.5865-2.6180.34191510.27952621X-RAY DIFFRACTION100
2.618-2.65110.33181480.27332622X-RAY DIFFRACTION100
2.6511-2.6860.29141660.26582662X-RAY DIFFRACTION100
2.686-2.72280.30711500.26632609X-RAY DIFFRACTION100
2.7228-2.76170.29821260.26392653X-RAY DIFFRACTION100
2.7617-2.80290.33141300.25682684X-RAY DIFFRACTION100
2.8029-2.84670.27611180.25772657X-RAY DIFFRACTION100
2.8467-2.89340.30451310.2692637X-RAY DIFFRACTION100
2.8934-2.94330.28651270.27092696X-RAY DIFFRACTION100
2.9433-2.99680.3191560.272642X-RAY DIFFRACTION100
2.9968-3.05440.31551240.26792676X-RAY DIFFRACTION100
3.0544-3.11680.35331420.2752629X-RAY DIFFRACTION100
3.1168-3.18450.30361570.26852645X-RAY DIFFRACTION100
3.1845-3.25860.35721250.26942688X-RAY DIFFRACTION100
3.2586-3.34010.28111340.26532645X-RAY DIFFRACTION100
3.3401-3.43030.29991370.24652683X-RAY DIFFRACTION100
3.4303-3.53130.27031330.24092677X-RAY DIFFRACTION100
3.5313-3.64520.30061440.23572708X-RAY DIFFRACTION100
3.6452-3.77540.26471350.23392658X-RAY DIFFRACTION100
3.7754-3.92650.28051490.22762672X-RAY DIFFRACTION100
3.9265-4.10520.23531490.21752694X-RAY DIFFRACTION100
4.1052-4.32150.23821420.20512684X-RAY DIFFRACTION100
4.3215-4.5920.25791530.20012694X-RAY DIFFRACTION100
4.592-4.94630.2131310.1982708X-RAY DIFFRACTION100
4.9463-5.44350.25521360.22032746X-RAY DIFFRACTION100
5.4435-6.22980.26231440.23132729X-RAY DIFFRACTION100
6.2298-7.84380.2261650.21522770X-RAY DIFFRACTION100
7.8438-49.20020.23681610.19252906X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -18.6294 Å / Origin y: 32.2858 Å / Origin z: -8.3015 Å
111213212223313233
T0.1746 Å2-0.0731 Å2-0.0808 Å2-0.1573 Å20.0539 Å2--0.1559 Å2
L0.0389 °20.0013 °20.0169 °2-0.0741 °20.0096 °2--0.0559 °2
S-0.062 Å °-0.0168 Å °0.0486 Å °0.0035 Å °-0.0142 Å °0.0113 Å °-0.0843 Å °0.0627 Å °-0.089 Å °
Refinement TLS groupSelection details: all

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