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- PDB-4fb5: Crystal structure of a probable oxidoreduxtase protein -

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Basic information

Entry
Database: PDB / ID: 4fb5
TitleCrystal structure of a probable oxidoreduxtase protein
ComponentsProbable oxidoreductase protein
KeywordsOXIDOREDUCTASE / PSI-Biology / NYSGRC / Structural Genomics / New York Structural Genomics Research Consortium / GFO/IDH/MOCA family
Function / homology
Function and homology information


oxidoreductase activity / nucleotide binding
Similarity search - Function
: / : / GFO/IDH/MocA C-terminal domain / 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 ...: / : / GFO/IDH/MocA C-terminal domain / 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
Probable oxidoreductase protein
Similarity search - Component
Biological speciesRhizobium etli (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.61 Å
AuthorsEswaramoorthy, S. / Almo, S.C. / Swaminathan, S. / New York Structural Genomics Research Consortium (NYSGRC)
CitationJournal: To be Published
Title: Crystal structure of a probable oxidoreduxtase protein
Authors: Eswaramoorthy, S. / Chamala, S. / Evans, B. / Foti, R. / Gizzi, A. / Hillerich, B. / Kar, A. / Lafleur, J. / Seidel, R. / Villigas, G. / Zencheck, W. / Almo, S.C. / Swaminathan, S.
History
DepositionMay 22, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 15, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Probable oxidoreductase protein
B: Probable oxidoreductase protein


Theoretical massNumber of molelcules
Total (without water)88,6272
Polymers88,6272
Non-polymers00
Water1,08160
1
A: Probable oxidoreductase protein
B: Probable oxidoreductase protein

A: Probable oxidoreductase protein
B: Probable oxidoreductase protein


Theoretical massNumber of molelcules
Total (without water)177,2534
Polymers177,2534
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area15470 Å2
ΔGint-42 kcal/mol
Surface area46690 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3130 Å2
ΔGint-8 kcal/mol
Surface area27950 Å2
MethodPISA
3
A: Probable oxidoreductase protein

A: Probable oxidoreductase protein


Theoretical massNumber of molelcules
Total (without water)88,6272
Polymers88,6272
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area3510 Å2
ΔGint-7 kcal/mol
Surface area27560 Å2
MethodPISA
4
B: Probable oxidoreductase protein

B: Probable oxidoreductase protein


Theoretical massNumber of molelcules
Total (without water)88,6272
Polymers88,6272
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area3330 Å2
ΔGint-9 kcal/mol
Surface area27770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.342, 179.094, 127.824
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Probable oxidoreductase protein


Mass: 44313.254 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhizobium etli (bacteria) / Strain: CFN 42 / ATCC 51251 / Gene: RHE_CH01346 / Plasmid: PET3A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q2KAI6
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 60 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.82 Å3/Da / Density % sol: 56.38 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.9
Details: 0.49M Sodium phosphate monobasic, 0.91M Potassium phosphate dibasic, Sarcosine, pH 6.9, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 26, 2012
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. all: 30554 / Num. obs: 30554 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 14.7 % / Biso Wilson estimate: 58.357 Å2 / Rmerge(I) obs: 0.101 / Net I/σ(I): 13.7
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 15.1 % / Rmerge(I) obs: 0.46 / Num. unique all: 2990 / % possible all: 99.3

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Processing

Software
NameVersionClassification
CBASSdata collection
SHELXSphasing
REFMAC5.5.0110refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.61→50 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.91 / SU B: 11.471 / SU ML: 0.243 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.551 / ESU R Free: 0.318 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26636 1539 5.1 %RANDOM
Rwork0.20704 ---
all0.21008 28927 --
obs0.21008 28927 98.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 51.171 Å2
Baniso -1Baniso -2Baniso -3
1--4.23 Å20 Å20 Å2
2--5.13 Å20 Å2
3----0.9 Å2
Refinement stepCycle: LAST / Resolution: 2.61→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5707 0 0 60 5767
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0225850
X-RAY DIFFRACTIONr_angle_refined_deg1.8061.9477918
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5455730
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.63722.883274
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.08915948
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5221551
X-RAY DIFFRACTIONr_chiral_restr0.1150.2838
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0214529
X-RAY DIFFRACTIONr_mcbond_it0.8231.53634
X-RAY DIFFRACTIONr_mcangle_it1.62125782
X-RAY DIFFRACTIONr_scbond_it3.0632216
X-RAY DIFFRACTIONr_scangle_it4.8564.52136
LS refinement shellResolution: 2.611→2.679 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.438 100 -
Rwork0.311 1991 -
obs-100 94.02 %

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