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- PDB-3v7b: Dip2269 protein from corynebacterium diphtheriae -

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Basic information

Entry
Database: PDB / ID: 3v7b
TitleDip2269 protein from corynebacterium diphtheriae
ComponentsUncharacterized protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / PSI-BIOLOGY / PROTEIN STRUCTURE INITIATIVE / MIDWEST CENTER FOR STRUCTURAL GENOMICS / MCSG
Function / homologyDomain of unknown function DUF2020 / Domain of unknown function (DUF2020) / Mog1/PsbP, alpha/beta/alpha sandwich / Protein Transport Mog1p; Chain A / Mog1/PsbP, alpha/beta/alpha sandwich / 3-Layer(aba) Sandwich / Alpha Beta / DUF2020 domain-containing protein
Function and homology information
Biological speciesCorynebacterium diphtheriae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.743 Å
AuthorsOsipiuk, J. / Duggan, E. / Clancy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Dip2269 protein from corynebacterium diphtheriae.
Authors: Osipiuk, J. / Duggan, E. / Clancy, S. / Joachimiak, A.
History
DepositionDec 20, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 11, 2012Provider: repository / Type: Initial release
SupersessionJan 25, 2012ID: 2I8G
Revision 1.1Nov 8, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.2Oct 30, 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 / struct_site
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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized protein
B: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,6534
Polymers33,5292
Non-polymers1242
Water4,360242
1
A: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,8272
Polymers16,7651
Non-polymers621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,8272
Polymers16,7651
Non-polymers621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)54.002, 66.752, 70.287
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Uncharacterized protein


Mass: 16764.658 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium diphtheriae (bacteria) / Strain: NCTC13129 / Gene: DIP2269 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q6NEK4
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 242 / 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: 1.89 Å3/Da / Density % sol: 34.89 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 4% PEG 8000, PH 8.0, 20 mM HEPES buffer, 250 mM sodium chloride, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 8, 2005
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.75→36 Å / Num. all: 25734 / Num. obs: 25734 / % possible obs: 96.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 12 % / Biso Wilson estimate: 26 Å2 / Rmerge(I) obs: 0.173 / Χ2: 1.629 / Net I/σ(I): 6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
1.75-1.796.30.7041.8414481.10477.7
1.79-1.848.10.70416031.05686.6
1.84-1.99.20.63517821.12495.2
1.9-1.9610.70.53818401.16898.1
1.96-2.03120.42218351.26799.1
2.03-2.1112.90.40118831.28799.6
2.11-2.213.40.33618581.34599.9
2.2-2.3213.60.2818901.488100
2.32-2.4713.70.23618871.595100
2.47-2.6613.70.20718801.773100
2.66-2.9213.50.16719121.826100
2.92-3.3513.20.13619251.892100
3.35-4.2212.90.10419441.983100
4.22-40130.10820472.82599.8

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.6.0117refinement
PDB_EXTRACT3.1data extraction
SBC-Collectdata collection
HKL-2000data reduction
HKL-2000data scaling
SHELXDphasing
MLPHAREphasing
DMphasing
SOLVEphasing
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.743→36 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.945 / Occupancy max: 1 / Occupancy min: 0.35 / SU B: 6.262 / SU ML: 0.095 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.138 / ESU R Free: 0.135 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2279 1991 7.7 %RANDOM
Rwork0.1772 ---
all0.181 25697 --
obs0.181 25697 96.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 75.06 Å2 / Biso mean: 22.5423 Å2 / Biso min: 10.03 Å2
Baniso -1Baniso -2Baniso -3
1--0.54 Å20 Å20 Å2
2---1.98 Å20 Å2
3---2.52 Å2
Refinement stepCycle: LAST / Resolution: 1.743→36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2223 0 8 242 2473
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.022359
X-RAY DIFFRACTIONr_bond_other_d0.0010.021583
X-RAY DIFFRACTIONr_angle_refined_deg1.7631.9473236
X-RAY DIFFRACTIONr_angle_other_deg1.0013.0023864
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5225306
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.91224.912114
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.39515355
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.5041514
X-RAY DIFFRACTIONr_chiral_restr0.110.2339
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0212703
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02463
LS refinement shellResolution: 1.743→1.789 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.332 114 -
Rwork0.312 1256 -
all-1370 -
obs-1370 74.38 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.8557-0.0039-0.07881.1680.030.3031-0.03050.00540.02130.0240.0268-0.02470.0003-0.03660.00370.01970.00180.00320.00550.00070.016442.439816.46798.9707
21.05630.35310.23921.22420.29960.46250.0178-0.01660.0634-0.0681-0.02440.00370.0061-0.03250.00660.01510.00440.0080.00480.00120.019217.743417.442825.9923
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 148
2X-RAY DIFFRACTION2B2 - 148

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