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- PDB-3tpc: Crystal structure of a hypothtical protein SMa1452 from Sinorhizo... -

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Basic information

Entry
Database: PDB / ID: 3tpc
TitleCrystal structure of a hypothtical protein SMa1452 from Sinorhizobium meliloti 1021
ComponentsShort chain alcohol dehydrogenase-related dehydrogenase
KeywordsOXIDOREDUCTASE / Structural Genomics / PSI-Biology / New York Structural Genomics Research Consortium / NYSGRC
Function / homology
Function and homology information


oxidoreductase activity
Similarity search - Function
short chain dehydrogenase / Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Short chain alcohol dehydrogenase-related dehydrogenase
Similarity search - Component
Biological speciesSinorhizobium meliloti (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.34 Å
AuthorsAgarwal, R. / Chamala, S. / Evans, B. / Foti, R. / Gizzi, A. / Hillerich, B. / Kar, A. / LaFleur, J. / Seidel, R. / Villigas, G. ...Agarwal, R. / 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. / New York Structural Genomics Research Consortium (NYSGRC)
CitationJournal: To be Published
Title: Crystal structure of a hypothtical protein SMa1452 from Sinorhizobium meliloti 1021
Authors: Agarwal, R. / Almo, S.C. / Swaminathan, S.
History
DepositionSep 7, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 28, 2011Provider: repository / Type: Initial release
Revision 1.1Dec 21, 2011Group: Other
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Sep 13, 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_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_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.4Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Short chain alcohol dehydrogenase-related dehydrogenase
B: Short chain alcohol dehydrogenase-related dehydrogenase
C: Short chain alcohol dehydrogenase-related dehydrogenase
D: Short chain alcohol dehydrogenase-related dehydrogenase
E: Short chain alcohol dehydrogenase-related dehydrogenase
F: Short chain alcohol dehydrogenase-related dehydrogenase
G: Short chain alcohol dehydrogenase-related dehydrogenase
H: Short chain alcohol dehydrogenase-related dehydrogenase


Theoretical massNumber of molelcules
Total (without water)216,4368
Polymers216,4368
Non-polymers00
Water4,738263
1
A: Short chain alcohol dehydrogenase-related dehydrogenase
B: Short chain alcohol dehydrogenase-related dehydrogenase
C: Short chain alcohol dehydrogenase-related dehydrogenase
D: Short chain alcohol dehydrogenase-related dehydrogenase


Theoretical massNumber of molelcules
Total (without water)108,2184
Polymers108,2184
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13360 Å2
ΔGint-101 kcal/mol
Surface area30220 Å2
MethodPISA
2
F: Short chain alcohol dehydrogenase-related dehydrogenase

H: Short chain alcohol dehydrogenase-related dehydrogenase

E: Short chain alcohol dehydrogenase-related dehydrogenase
G: Short chain alcohol dehydrogenase-related dehydrogenase


Theoretical massNumber of molelcules
Total (without water)108,2184
Polymers108,2184
Non-polymers00
Water724
TypeNameSymmetry operationNumber
crystal symmetry operation1_666x+1,y+1,z+11
crystal symmetry operation1_556x,y,z+11
identity operation1_555x,y,z1
Buried area13330 Å2
ΔGint-100 kcal/mol
Surface area29660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.147, 69.375, 121.850
Angle α, β, γ (deg.)98.36, 92.72, 113.01
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Short chain alcohol dehydrogenase-related dehydrogenase


Mass: 27054.453 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sinorhizobium meliloti (bacteria) / Strain: 1021 / Gene: RA0792, SMa1452 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIPL / References: UniProt: Q92YS1
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 263 / 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: 2.44 Å3/Da / Density % sol: 49.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.2M Ammonium acetate, 0.1M Na-citrate pH 5.6, 30% PEG 4000, 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: Aug 26, 2011 / Details: mirrors
RadiationMonochromator: SI-III / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.34→50 Å / Num. all: 83792 / Num. obs: 83792 / % possible obs: 97.5 % / Observed criterion σ(I): 0 / Redundancy: 5.2 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 8.3
Reflection shellResolution: 2.34→2.42 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.496 / Mean I/σ(I) obs: 3 / Num. unique all: 8235 / % possible all: 95.7

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Processing

Software
NameVersionClassification
CBASSdata collection
PHASERphasing
CCP4model building
ARP/wARPmodel building
Cootmodel building
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1UAY

1uay


Resolution: 2.34→46.2 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.892 / SU B: 8.263 / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(I): 0 / ESU R: 0.35 / ESU R Free: 0.262 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26988 4193 5 %RANDOM
Rwork0.21206 ---
obs0.21497 79595 97.44 %-
all-83792 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.463 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0.01 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.34→46.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12752 0 0 263 13015
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.02212909
X-RAY DIFFRACTIONr_angle_refined_deg1.8521.96317512
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.64251764
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.25722.969485
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.113151908
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.80415108
X-RAY DIFFRACTIONr_chiral_restr0.1270.22093
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0219753
X-RAY DIFFRACTIONr_mcbond_it0.9381.58787
X-RAY DIFFRACTIONr_mcangle_it1.703213830
X-RAY DIFFRACTIONr_scbond_it2.77134122
X-RAY DIFFRACTIONr_scangle_it4.5084.53682
LS refinement shellResolution: 2.344→2.405 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.325 305 -
Rwork0.254 5730 -
obs--94.39 %

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