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- PDB-3mep: Crystal Structure of ECA2234 protein from Erwinia carotovora, Nor... -

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Basic information

Entry
Database: PDB / ID: 3mep
TitleCrystal Structure of ECA2234 protein from Erwinia carotovora, Northeast Structural Genomics Consortium Target EwR44
Componentsuncharacterized protein ECA2234
Keywordsstructural genomics / unknown function / all beta protein / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homologyProtein of unknown function DUF1349 / Uncharacterised conserved protein UCP022704 / Protein of unknown function (DUF1349) / Jelly Rolls - #200 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta / Regulation of enolase protein 1
Function and homology information
Biological speciesPectobacterium atrosepticum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsSeetharaman, J. / Abashidze, M. / Forouhar, F. / Mao, M. / Xiao, R. / Ciccosanti, C. / Wang, D. / Everett, J.K. / Nair, R. / Acton, T.B. ...Seetharaman, J. / Abashidze, M. / Forouhar, F. / Mao, M. / Xiao, R. / Ciccosanti, C. / Wang, D. / Everett, J.K. / Nair, R. / Acton, T.B. / Rost, B. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Northeast Structural Genomics Consortium Target EwR44
Authors: Seetharaman, J. / Abashidze, M. / Forouhar, F. / Mao, M. / Xiao, R. / Ciccosanti, C. / Wang, D. / Everett, J.K. / Nair, R. / Acton, T.B. / Rost, B. / Montelione, G.T. / Tong, L. / Hunt, J.F.
History
DepositionMar 31, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 14, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 17, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.contact_author / _software.contact_author_email ..._software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: uncharacterized protein ECA2234
B: uncharacterized protein ECA2234
C: uncharacterized protein ECA2234


Theoretical massNumber of molelcules
Total (without water)68,2743
Polymers68,2743
Non-polymers00
Water5,278293
1
A: uncharacterized protein ECA2234

A: uncharacterized protein ECA2234


Theoretical massNumber of molelcules
Total (without water)45,5162
Polymers45,5162
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area1800 Å2
ΔGint-7 kcal/mol
Surface area15170 Å2
MethodPISA
2
B: uncharacterized protein ECA2234
C: uncharacterized protein ECA2234


Theoretical massNumber of molelcules
Total (without water)45,5162
Polymers45,5162
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1800 Å2
ΔGint-7 kcal/mol
Surface area14990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.179, 41.930, 148.639
Angle α, β, γ (deg.)90.000, 105.620, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein uncharacterized protein ECA2234


Mass: 22757.896 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pectobacterium atrosepticum (bacteria) / Strain: SCRI1043 / Gene: ECA2234 / Plasmid: pET 21-23C / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+ Magic / References: UniProt: Q6D507
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 293 / 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: 2.2 Å3/Da / Density % sol: 44.14 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Protein solution: 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl (pH 7.5) . Reservoir solution: 0.1M Hepes (pH 7), 16% PEG 8k, and 0.2M sodium nitrate., VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.97853 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Feb 11, 2010 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2.3→36.18 Å / Num. all: 53055 / Num. obs: 51199 / % possible obs: 96.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.1 % / Biso Wilson estimate: 19.1 Å2 / Rmerge(I) obs: 0.082 / Rsym value: 0.069 / Net I/σ(I): 17.3
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.369 / Mean I/σ(I) obs: 3.05 / Rsym value: 0.3 / % possible all: 82.4

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Processing

Software
NameVersionClassificationNB
CNS1.2refinement
PDB_EXTRACT3data extraction
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
SHELXfollowed by SOLVE/RESOLVEphasing
REFMACrefinement
RefinementMethod to determine structure: SAD / Resolution: 2.3→36.18 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 87013.344 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.264 4311 10 %RANDOM
Rwork0.22 ---
all0.224 51739 --
obs0.222 43254 83.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 26.601 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 31.4 Å2
Baniso -1Baniso -2Baniso -3
1-10.87 Å20 Å2-11.06 Å2
2---4.29 Å20 Å2
3----6.58 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.45 Å0.41 Å
Refinement stepCycle: LAST / Resolution: 2.3→36.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4282 0 0 293 4575
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d26.7
X-RAY DIFFRACTIONc_improper_angle_d0.83
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.346 621 10.6 %
Rwork0.317 5222 -
obs-5843 67.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top

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