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- PDB-3hnp: Crystal Structure of an Oxidoreductase from Bacillus cereus. Nort... -

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Basic information

Entry
Database: PDB / ID: 3hnp
TitleCrystal Structure of an Oxidoreductase from Bacillus cereus. Northeast Structural Genomics Consortium target id BcR251
ComponentsOxidoreductase
KeywordsOXIDOREDUCTASE / Bacillus cereus / Structural Genomics / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homology
Function and homology information


hydroxymethylglutaryl-CoA reductase (NADPH) activity / Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor
Similarity search - Function
HMGR, N-terminal domain / HMGR, N-terminal domain / Hydroxymethylglutaryl-CoA reductase, N-terminal / Gfo/Idh/MocA-like oxidoreductase, C-terminal / Oxidoreductase family, C-terminal alpha/beta domain / Gfo/Idh/MocA-like oxidoreductase, N-terminal / Oxidoreductase family, NAD-binding Rossmann fold / Dihydrodipicolinate Reductase; domain 2 / Dihydrodipicolinate Reductase; domain 2 / NAD(P)-binding Rossmann-like Domain ...HMGR, N-terminal domain / HMGR, N-terminal domain / Hydroxymethylglutaryl-CoA reductase, N-terminal / Gfo/Idh/MocA-like oxidoreductase, C-terminal / Oxidoreductase family, C-terminal alpha/beta domain / Gfo/Idh/MocA-like oxidoreductase, N-terminal / Oxidoreductase family, NAD-binding Rossmann fold / Dihydrodipicolinate Reductase; domain 2 / Dihydrodipicolinate Reductase; domain 2 / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesBacillus cereus ATCC 14579 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.6 Å
AuthorsSeetharaman, J. / Su, M. / Sahdev, S. / Janjua, H. / Xiao, R. / Ciccosanti, C. / Foote, E.L. / Acton, T.B. / Rost, B. / Montelione, G.T. ...Seetharaman, J. / Su, M. / Sahdev, S. / Janjua, H. / Xiao, R. / Ciccosanti, C. / Foote, E.L. / Acton, T.B. / Rost, B. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: TO BE PUBLISHED
Title: Crystal Structure of an Oxidoreductase from Bacillus cereus. Northeast Structural Genomics Consortium target id BcR251
Authors: Seetharaman, J. / Su, M. / Sahdev, S. / Janjua, H. / Xiao, R. / Ciccosanti, C. / Foote, E.L. / Acton, T.B. / Rost, B. / Montelione, G.T. / Tong, L. / Hunt, J.F.
History
DepositionMay 31, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 30, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Oxidoreductase
B: Oxidoreductase
C: Oxidoreductase
D: Oxidoreductase
E: Oxidoreductase
F: Oxidoreductase


Theoretical massNumber of molelcules
Total (without water)239,7436
Polymers239,7436
Non-polymers00
Water1,60389
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17170 Å2
ΔGint-31 kcal/mol
Surface area76870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.661, 149.510, 95.767
Angle α, β, γ (deg.)90.00, 92.13, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Oxidoreductase /


Mass: 39957.145 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cereus ATCC 14579 (bacteria) / Gene: BC_3406 / Production host: Escherichia coli (E. coli)
References: UniProt: Q81AZ1, Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 89 / 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: 2.74 Å3/Da / Density % sol: 55.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: PEG3350, 100 mM TrisHCL, MgCl2, pH 8, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 2, 2009 / Details: Mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. all: 157443 / Num. obs: 157443 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 42.2 Å2 / Rmerge(I) obs: 0.073 / Rsym value: 0.072 / Net I/σ(I): 23.9
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.45 / Num. unique all: 15818 / Rsym value: 0.44 / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SOLVEphasing
CNS1.2refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.6→43.79 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 156329.94 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.282 5891 4 %RANDOM
Rwork0.239 ---
obs0.239 147751 94.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 52.134 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 62.1 Å2
Baniso -1Baniso -2Baniso -3
1-9.28 Å20 Å27.95 Å2
2---9.04 Å20 Å2
3----0.23 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.48 Å0.39 Å
Luzzati d res low-5 Å
Luzzati sigma a0.55 Å0.45 Å
Refinement stepCycle: LAST / Resolution: 2.6→43.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15446 0 0 89 15535
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d24.1
X-RAY DIFFRACTIONc_improper_angle_d0.9
LS refinement shellResolution: 2.6→2.76 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.403 925 4.1 %
Rwork0.351 21590 -
obs--86.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top

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