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- PDB-2qnl: CRYSTAL STRUCTURE OF A PUTATIVE DNA DAMAGE-INDUCIBLE PROTEIN (CHU... -

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Basic information

Entry
Database: PDB / ID: 2qnl
TitleCRYSTAL STRUCTURE OF A PUTATIVE DNA DAMAGE-INDUCIBLE PROTEIN (CHU_0679) FROM CYTOPHAGA HUTCHINSONII ATCC 33406 AT 1.50 A RESOLUTION
ComponentsUncharacterized protein
KeywordsSIGNALING PROTEIN / PUTATIVE DNA DAMAGE-INDUCIBLE PROTEIN / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-2
Function / homologyDinB-like domain / DinB superfamily / dinb family like domain / DinB/YfiT-like putative metalloenzymes / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha / DinB_2 domain-containing protein
Function and homology information
Biological speciesCytophaga hutchinsonii ATCC 33406 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.5 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of uncharacterized protein CHU_0679 (YP_677306.1) from Cytophaga hutchinsonii ATCC 33406 at 1.50 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJul 18, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 31, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_struct_assembly_auth_evidence / software / Item: _software.classification / _software.name
Revision 1.3Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Jan 25, 2023Group: Database references / Derived calculations / Category: database_2 / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 300 BIOMOLECULE: 1 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND PROGRAM GENERATED ASSEMBLY INFORMATION ... BIOMOLECULE: 1 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND PROGRAM GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON BURIED SURFACE AREA. SIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING SUPPORT THE ASSIGNMENT OF A DIMER AS A SIGNIFICANT OLIGOMERIZATION STATE.
Remark 999 SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ... SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,2189
Polymers18,5911
Non-polymers6278
Water4,504250
1
A: Uncharacterized protein
hetero molecules

A: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,43618
Polymers37,1812
Non-polymers1,25516
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_555x,x-y,-z+1/61
Buried area6530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.800, 64.800, 148.870
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
DetailsSIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING SUPPORTS THE ASSIGNMENT OF A DIMER AS A SIGNIFICANT OLIGOMERIZATION STATE.

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Components

#1: Protein Uncharacterized protein


Mass: 18590.635 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cytophaga hutchinsonii ATCC 33406 (bacteria)
Species: Cytophaga hutchinsonii / Strain: NCIMB 9469 / Gene: YP_677306.1, CHU_0679 / Plasmid: speedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q11XA0
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 250 / 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: 2.43 Å3/Da / Density % sol: 49.31 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: NANODROP, 1.6M (NH4)2SO4, 10.0% Dioxane, 0.1M MES pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97895 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 2, 2007 / Details: Flat mirror (vertical focusing)
RadiationMonochromator: Single crystal Si(111) bent (horizontal focusing)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97895 Å / Relative weight: 1
ReflectionResolution: 1.5→28.061 Å / Num. obs: 29769 / % possible obs: 97 % / Observed criterion σ(I): -3 / Redundancy: 11.33 % / Biso Wilson estimate: 14.54 Å2 / Rmerge(I) obs: 0.029 / Net I/σ(I): 34.13
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.5-1.550.1615.697794223180.5
1.55-1.620.1487.7201056057195.5
1.62-1.690.12211.4241735188198.6
1.69-1.780.09917.6382195630199.9
1.78-1.890.07324.64117355411100
1.89-2.040.0533.6423115746199.9
2.04-2.240.03544.4398675437199.7
2.24-2.560.02953.2399595510199.3
2.56-3.230.02362.8409385593198.5
3.23-28.0610.01975.1407395520197.6

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PHENIXrefinement
SOLVEphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3data extraction
MAR345CCDdata collection
XDSdata reduction
RefinementMethod to determine structure: SAD / Resolution: 1.5→28.061 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.954 / SU B: 1.967 / SU ML: 0.038 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.068 / ESU R Free: 0.069
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4. TWO CHLORIDE IONS, ONE SULFATE ION AND FIVE GLYCEROL MOLECULES WERE MODELED.
RfactorNum. reflection% reflectionSelection details
Rfree0.185 1519 5.1 %RANDOM
Rwork0.159 ---
obs0.161 29702 98.32 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.67 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å2-0.02 Å20 Å2
2---0.04 Å20 Å2
3---0.06 Å2
Refinement stepCycle: LAST / Resolution: 1.5→28.061 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1281 0 37 250 1568
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0211431
X-RAY DIFFRACTIONr_bond_other_d0.0060.02955
X-RAY DIFFRACTIONr_angle_refined_deg1.6441.9681955
X-RAY DIFFRACTIONr_angle_other_deg1.13432337
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.3055181
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.04224.55968
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.14415233
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.356158
X-RAY DIFFRACTIONr_chiral_restr0.0860.2213
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021619
X-RAY DIFFRACTIONr_gen_planes_other0.0120.02282
X-RAY DIFFRACTIONr_nbd_refined0.2350.3368
X-RAY DIFFRACTIONr_nbd_other0.1940.31049
X-RAY DIFFRACTIONr_nbtor_refined0.1880.5730
X-RAY DIFFRACTIONr_nbtor_other0.0940.5665
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2080.5308
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3090.326
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2680.367
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.240.547
X-RAY DIFFRACTIONr_mcbond_it1.9743933
X-RAY DIFFRACTIONr_mcbond_other0.4723341
X-RAY DIFFRACTIONr_mcangle_it2.5551406
X-RAY DIFFRACTIONr_scbond_it4.8868614
X-RAY DIFFRACTIONr_scangle_it6.18611548
LS refinement shellResolution: 1.5→1.54 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.174 98 -
Rwork0.162 1835 -
obs-1933 89 %
Refinement TLS params.Method: refined / Origin x: 19.391 Å / Origin y: 24.279 Å / Origin z: 10.572 Å
111213212223313233
T-0.0367 Å20.0029 Å2-0.0034 Å2--0.01 Å20.0087 Å2---0.0189 Å2
L0.9891 °20.1913 °20.0071 °2-0.3292 °2-0.0228 °2--0.4614 °2
S0.038 Å °-0.0879 Å °-0.0032 Å °-0.0067 Å °-0.0291 Å °0.0165 Å °-0.0182 Å °0.0055 Å °-0.0089 Å °

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