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- PDB-3e82: Crystal structure of a putative oxidoreductase from Klebsiella pn... -

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Basic information

Entry
Database: PDB / ID: 3.0E+82
TitleCrystal structure of a putative oxidoreductase from Klebsiella pneumoniae
ComponentsPutative oxidoreductase
KeywordsOXIDOREDUCTASE / NAD / GFO/IDH/MOCA family / PSI-2 / NYSGXRC / 11136f / Structural Genomics / Protein Structure Initiative / New York SGX Research Center for Structural Genomics
Function / homology
Function and homology information


oxidoreductase activity
Similarity search - Function
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 ...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 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Putative oxidoreductase
Similarity search - Component
Biological speciesKlebsiella pneumoniae subsp. pneumoniae MGH 78578 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.04 Å
AuthorsEswaramoorthy, S. / Mohammad, M.B. / Thomas, C.A. / Brown, A.C. / Burley, S.K. / Swaminathan, S. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal structure of a putative oxidoreductase from Klebsiella pneumoniae
Authors: Eswaramoorthy, S. / Mohammad, M.B. / Thomas, C.A. / Brown, A.C. / Burley, S.K. / Swaminathan, S.
History
DepositionAug 19, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 26, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 10, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / struct_conn / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_conn.pdbx_leaving_atom_flag / _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: Putative oxidoreductase
B: Putative oxidoreductase
D: Putative oxidoreductase
E: Putative oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)161,7048
Polymers161,5634
Non-polymers1424
Water12,322684
1
A: Putative oxidoreductase
B: Putative oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,8524
Polymers80,7812
Non-polymers712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3250 Å2
ΔGint-44 kcal/mol
Surface area27430 Å2
MethodPISA
2
D: Putative oxidoreductase
E: Putative oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,8524
Polymers80,7812
Non-polymers712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3220 Å2
ΔGint-41 kcal/mol
Surface area28470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.910, 79.750, 209.144
Angle α, β, γ (deg.)90.00, 94.00, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Putative oxidoreductase /


Mass: 40390.641 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae subsp. pneumoniae MGH 78578 (bacteria)
Gene: KPN78578_13420, KPN_01371 / Plasmid: BC-PSGX3(BC), TOP10-INVITROGEN / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3)-CODON+RIL-STRATAGENE / References: UniProt: A6T882
#2: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 684 / 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: 2.72 Å3/Da / Density % sol: 54.85 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 25% PEG3350, 0.1M Bis-Tris, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 30, 2008 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.04→50 Å / Num. all: 109371 / Num. obs: 109371 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.5 % / Biso Wilson estimate: 16.4 Å2 / Rsym value: 0.096 / Net I/σ(I): 13
Reflection shellResolution: 2.04→2.11 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.56 / Num. unique all: 10624 / % possible all: 97.1

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Processing

Software
NameVersionClassification
CBASSdata collection
SHELX& SHARPmodel building
CNS1.1refinement
DENZOdata reduction
HKL-2000data scaling
SHELX& SHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 2.04→35.87 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.232 4166 -RANDOM
Rwork0.209 ---
all0.224 103973 --
obs0.224 103973 94 %-
Displacement parametersBiso mean: 28.9 Å2
Baniso -1Baniso -2Baniso -3
1-1.3 Å20 Å21.39 Å2
2--4.66 Å20 Å2
3----5.96 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.24 Å0.19 Å
Refinement stepCycle: LAST / Resolution: 2.04→35.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10670 0 4 684 11358
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_deg23.7
X-RAY DIFFRACTIONc_improper_angle_deg0.75
LS refinement shellResolution: 2.04→2.17 Å / Rfactor Rfree error: 0.012
RfactorNum. reflection% reflection
Rfree0.285 616 -
Rwork0.247 --
obs-15438 88 %

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