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- PDB-4huj: Crystal structure of a hypothetical protein SMa0349 from Sinorhiz... -

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Basic information

Entry
Database: PDB / ID: 4huj
TitleCrystal structure of a hypothetical protein SMa0349 from Sinorhizobium meliloti
ComponentsUncharacterized protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / PSI-Biology / NYSGRC / New York Structural Genomics Research Consortium / dinucleotide-binding / NAD(P)+ binding
Function / homologyPyrroline-5-carboxylate reductase, catalytic, N-terminal / NADP oxidoreductase coenzyme F420-dependent / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / F420_oxidored domain-containing protein
Function and homology information
Biological speciesSinorhizobium meliloti (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.77 Å
AuthorsRice, S. / Eswaramoorthy, S. / Chamala, S. / Evans, B. / Foti, F. / Gizzi, A. / Hillerich, B. / Kar, A. / LaFleur, J. / Seidel, R. ...Rice, S. / Eswaramoorthy, S. / Chamala, S. / Evans, B. / Foti, F. / Gizzi, A. / Hillerich, B. / Kar, A. / LaFleur, J. / Seidel, R. / Villigas, G. / Zencheck, W. / Almo, S.C. / Swaminathan, S. / New York Structural Genomics Research Consortium (NYSGRC)
CitationJournal: To be Published
Title: Crystal structure of a hypothetical protein SMa0349 from Sinorhizobium meliloti
Authors: Rice, S. / Eswaramoorthy, S. / Almo, S.C. / Swaminathan, S.
History
DepositionNov 2, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 12, 2012Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uncharacterized protein
B: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)45,9852
Polymers45,9852
Non-polymers00
Water3,207178
1
A: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)22,9931
Polymers22,9931
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)22,9931
Polymers22,9931
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Uncharacterized protein

B: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)45,9852
Polymers45,9852
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_575-x+1/2,-y+2,z+1/21
Buried area1480 Å2
ΔGint-11 kcal/mol
Surface area17790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.456, 79.487, 100.127
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 Uncharacterized protein


Mass: 22992.660 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sinorhizobium meliloti (bacteria) / Strain: 1021 / Gene: RA0188, SMa0349 / Plasmid: PET3A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q930K7
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 178 / 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: 2.53 Å3/Da / Density % sol: 51.37 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2M Lithium sulfate, 0.1M TRIS, 30% PEG4000 and tert-Butanol, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 16, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.77→50 Å / Num. all: 46300 / Num. obs: 46300 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 14.2 % / Biso Wilson estimate: 19.2 Å2 / Rmerge(I) obs: 0.063 / Net I/σ(I): 16.4
Reflection shellResolution: 1.77→1.82 Å / Redundancy: 13.7 % / Rmerge(I) obs: 0.335 / Num. unique all: 3763 / % possible all: 99.8

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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: 1.77→42.614 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.938 / SU B: 2.044 / SU ML: 0.067 / Cross valid method: THROUGHOUT / ESU R: 0.118 / ESU R Free: 0.113 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2337 2340 5.1 %RANDOM
Rwork0.20556 ---
all0.223 46126 --
obs0.20697 43786 99.21 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.322 Å2
Baniso -1Baniso -2Baniso -3
1--0.52 Å20 Å20 Å2
2--0.52 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.77→42.614 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2979 0 0 178 3157
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0223029
X-RAY DIFFRACTIONr_angle_refined_deg1.0591.9744131
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8995407
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.43724.643112
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.27315464
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.4221516
X-RAY DIFFRACTIONr_chiral_restr0.0670.2501
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212274
X-RAY DIFFRACTIONr_mcbond_it0.5531.52031
X-RAY DIFFRACTIONr_mcangle_it1.04823251
X-RAY DIFFRACTIONr_scbond_it1.6043998
X-RAY DIFFRACTIONr_scangle_it2.7694.5880
LS refinement shellResolution: 1.767→1.812 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.297 158 -
Rwork0.263 3050 -
obs-5491 96.25 %

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