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- PDB-1td6: Crystal structure of the conserved hypothetical protein MP506/MPN... -

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Basic information

Entry
Database: PDB / ID: 1td6
TitleCrystal structure of the conserved hypothetical protein MP506/MPN330 (gi: 1674200)from Mycoplasma pneumoniae
ComponentsHypothetical protein MG237 homologHypothesis
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / ALPHA HELICAL / PSI / Protein Structure Initiative / Berkeley Structural Genomics Center / BSGC
Function / homology
Function and homology information


Hypothetical protein mg237 homolog; domain 3 / hypothetical protein mp506/mpn330, domain 1 / hypothetical protein mp506/mpn330, domain 2 / hypothetical protein mp506/mpn330, domain 2 / Uncharacterised protein MG237, central domain / Uncharacterised protein MG237, N-terminal / Protein of unknown function DUF3196 / Protein of unknown function (DUF3196) / hypothetical protein mp506/mpn330, domain 1 / Cyclin A; domain 1 ...Hypothetical protein mg237 homolog; domain 3 / hypothetical protein mp506/mpn330, domain 1 / hypothetical protein mp506/mpn330, domain 2 / hypothetical protein mp506/mpn330, domain 2 / Uncharacterised protein MG237, central domain / Uncharacterised protein MG237, N-terminal / Protein of unknown function DUF3196 / Protein of unknown function (DUF3196) / hypothetical protein mp506/mpn330, domain 1 / Cyclin A; domain 1 / Up-down Bundle / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Uncharacterized protein MG237 homolog
Similarity search - Component
Biological speciesMycoplasma pneumoniae (Filterable agent of primary atypical pneumonia)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å
AuthorsDas, D. / Oganesyan, N. / Yokota, H. / Jancarik, J. / Kim, R. / Kim, S.H. / Berkeley Structural Genomics Center (BSGC)
CitationJournal: Proteins / Year: 2004
Title: Crystal structure of the conserved hypothetical protein MPN330 (GI: 1674200) from Mycoplasma pneumoniae.
Authors: Das, D. / Oganesyan, N. / Yokota, H. / Pufan, R. / Kim, R. / Kim, S.H.
History
DepositionMay 21, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 7, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_related / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_related.db_name / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hypothetical protein MG237 homolog


Theoretical massNumber of molelcules
Total (without water)35,4201
Polymers35,4201
Non-polymers00
Water90150
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)82.840, 82.840, 225.040
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122

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Components

#1: Protein Hypothetical protein MG237 homolog / Hypothesis / F10_orf294


Mass: 35419.602 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycoplasma pneumoniae (Filterable agent of primary atypical pneumonia)
Gene: MPN330, MP506 / Plasmid: pLIC (pET21a derivative) / Production host: Escherichia coli (E. coli) / Strain (production host): B834 / References: UniProt: P75455
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 50 / 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: 2.96 Å3/Da / Density % sol: 58 %
Crystal growTemperature: 298 K
Method: vapor diffusion, sitting drop (hydra crystallization robot)
pH: 8.5
Details: 0.1 M Tris pH 8.5, 1.5 M Lithium Sulfate monohydrate, VAPOR DIFFUSION, SITTING DROP (HYDRA CRYSTALLIZATION ROBOT), temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 11, 2004
RadiationMonochromator: Double-crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.5→41.4 Å / Num. all: 25896 / Num. obs: 25029 / % possible obs: 96.7 % / Observed criterion σ(F): 0 / Biso Wilson estimate: 36.5 Å2 / Net I/σ(I): 28.2

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.5→41.4 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 106735.87 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.298 1197 4.8 %RANDOM
Rwork0.244 ---
obs0.244 25029 96.7 %-
all-25896 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 35.0881 Å2 / ksol: 0.353207 e/Å3
Displacement parametersBiso mean: 42.8 Å2
Baniso -1Baniso -2Baniso -3
1--1.56 Å20 Å20 Å2
2---1.56 Å20 Å2
3---3.11 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.43 Å0.35 Å
Luzzati d res low-5 Å
Luzzati sigma a0.37 Å0.31 Å
Refinement stepCycle: LAST / Resolution: 2.5→41.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2356 0 0 50 2406
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d20.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.01
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.35 191 4.9 %
Rwork0.31 3719 -
obs--90.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP

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