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- PDB-3pg5: Crystal structure of protein DIP2308 from Corynebacterium diphthe... -

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Basic information

Entry
Database: PDB / ID: 3pg5
TitleCrystal structure of protein DIP2308 from Corynebacterium diphtheriae, Northeast Structural Genomics Consortium Target CdR78
ComponentsUncharacterized protein
KeywordsStructural genomics / Unknown function / PSI-Biology / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG / alpha-beta p-loop containing protein / ATP-binding protein
Function / homology: / AAA domain / AAA domain / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta / AAA domain-containing protein
Function and homology information
Biological speciesCorynebacterium diphtheriae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.3 Å
AuthorsForouhar, F. / Lew, S. / Seetharaman, J. / Lee, D. / Ciccosanti, C. / Sahdev, S. / Nair, R. / Rost, B. / Acton, T.B. / Xiao, R. ...Forouhar, F. / Lew, S. / Seetharaman, J. / Lee, D. / Ciccosanti, C. / Sahdev, S. / Nair, R. / Rost, B. / Acton, T.B. / Xiao, R. / Everett, J.K. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Crystal structure of protein DIP2308 from Corynebacterium diphtheriae, Northeast Structural Genomics Consortium Target CdR78
Authors: Forouhar, F. / Lew, S. / Seetharaman, J. / Lee, D. / Ciccosanti, C. / Sahdev, S. / Nair, R. / Rost, B. / Acton, T.B. / Xiao, R. / Everett, J.K. / Montelione, G.T. / Hunt, J.F. / Tong, L.
History
DepositionOct 30, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 22, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 22, 2012Group: Structure summary
Revision 1.3Oct 25, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.4Oct 9, 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
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uncharacterized protein
B: Uncharacterized protein
C: Uncharacterized protein
D: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)164,2504
Polymers164,2504
Non-polymers00
Water37821
1
A: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)41,0631
Polymers41,0631
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)41,0631
Polymers41,0631
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)41,0631
Polymers41,0631
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)41,0631
Polymers41,0631
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
A: Uncharacterized protein
C: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)82,1252
Polymers82,1252
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2820 Å2
ΔGint-6 kcal/mol
Surface area25210 Å2
MethodPISA
6
B: Uncharacterized protein
D: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)82,1252
Polymers82,1252
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2640 Å2
ΔGint-8 kcal/mol
Surface area24870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)199.963, 199.963, 106.580
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212
DetailsDIMER IN THE CRYSTAL, WHEREAS LIGHT SCATTERING DATA SHOWS MONOMERIC PROTEIN IN SOLUTION.

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Components

#1: Protein
Uncharacterized protein


Mass: 41062.555 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium diphtheriae (bacteria) / Strain: NCTC 13129 / Gene: DIP2308 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+Magic / References: UniProt: Q6NEG6
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 21 / 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: 3.24 Å3/Da / Density % sol: 62.07 %
Crystal growTemperature: 277 K / Method: micro batch under oil / pH: 9
Details: Protein solution: 10 mM Tris (pH 7.5), 100 mM sodium chloride, and 5 mM DTT. Reservoir solution: 0.1 M TAPS (pH 9), 40% PEG400, and 0.1 M magnesium nitrate, micro batch under oil, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.97908 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Oct 12, 2010 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97908 Å / Relative weight: 1
ReflectionResolution: 3.3→30 Å / Num. all: 62028 / Num. obs: 62028 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13.6 % / Biso Wilson estimate: 55.2 Å2 / Rmerge(I) obs: 0.23 / Rsym value: 0.187 / Net I/σ(I): 13.47
Reflection shellResolution: 3.3→3.42 Å / Redundancy: 11 % / Rmerge(I) obs: 0.814 / Mean I/σ(I) obs: 2.56 / Num. unique all: 6231 / Rsym value: 0.738 / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SHELXthen SOLVE/RESOLVEmodel building
CNS1.2 & XtalViewrefinement
HKL-2000data reduction
SCALEPACKdata scaling
SHELXthen SOLVE/RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 3.3→20 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 166084.6 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1 / σ(I): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.235 5408 9.9 %RANDOM
Rwork0.187 ---
all0.19 61882 --
obs0.187 54766 88.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 13.3223 Å2 / ksol: 0.3 e/Å3
Displacement parametersBiso mean: 56.6 Å2
Baniso -1Baniso -2Baniso -3
1--5.68 Å20 Å20 Å2
2---5.68 Å20 Å2
3---11.35 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.41 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.51 Å0.45 Å
Refinement stepCycle: LAST / Resolution: 3.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9592 0 0 21 9613
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d22.3
X-RAY DIFFRACTIONc_improper_angle_d0.84
Refine LS restraints NCSNCS model details: NONE
LS refinement shellResolution: 3.3→3.42 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.287 439 10.7 %
Rwork0.244 3673 -
obs-3673 66.3 %

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