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- PDB-3di5: Crystal structure of a dinb-like protein (bce_4655) from bacillus... -

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Basic information

Entry
Database: PDB / ID: 3di5
TitleCrystal structure of a dinb-like protein (bce_4655) from bacillus cereus atcc 10987 at 2.01 A resolution
ComponentsDinB-like Protein
KeywordsMETAL BINDING PROTEIN / Structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homologyDNA damage-inducible protein DinB / DinB family / dinb family like domain / DinB/YfiT-like putative metalloenzymes / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha / NICKEL (II) ION / DinB family protein
Function and homology information
Biological speciesBacillus cereus ATCC 10987 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.009 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a DinB-like Protein (NP_980948.1) from BACILLUS CEREUS ATCC 10987 at 2.01 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJun 19, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 19, 2008Provider: 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 1.4Feb 1, 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
Revision 1.5Nov 13, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DinB-like Protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,2162
Polymers19,1571
Non-polymers591
Water99155
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)78.120, 84.190, 50.320
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-169-

HOH

DetailsAUTHORS STATE THAT THE RESULTS FROM SIZE EXCLUSION CHROMATOGRAPHY SUPPORTS THE ASSIGNMENT OF A MONOMER AS A SIGNIFICANT OLIGOMERIZATION STATE.

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Components

#1: Protein DinB-like Protein


Mass: 19157.441 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cereus ATCC 10987 (bacteria) / Gene: NP_980948.1, BCE_4655 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q72ZL3
#2: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 55 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...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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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.16 Å3/Da / Density % sol: 43.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.57
Details: 0.2M magnesium chloride, 30.5% polyethylene glycol 4000, 0.1M TRIS pH 8.57, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.91837,0.97916,0.97860
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Apr 10, 2008 / Details: Flat mirror (vertical focusing)
RadiationMonochromator: Single crystal Si(111) bent monochromator (horizontal focusing)
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.979161
30.97861
ReflectionResolution: 2.009→28.63 Å / Num. obs: 11180 / % possible obs: 95.6 % / Observed criterion σ(I): -3 / Redundancy: 3.93 % / Biso Wilson estimate: 35.693 Å2 / Rmerge(I) obs: 0.034 / Net I/σ(I): 13.57
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
2-2.070.4132.6333541627177.6
2.07-2.150.2653.943262043197.3
2.15-2.250.1974.845932166198.3
2.25-2.370.1356.745642147196.7
2.37-2.520.18.845572134198
2.52-2.710.0741144592091198.5
2.71-2.990.04814.946722174198
2.99-3.420.03120.645392118198.8
3.42-4.30.0222844652089197
4.3-28.630.02132.144552093195.7

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3.004data extraction
XDSdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.009→28.63 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.935 / SU B: 12.715 / SU ML: 0.173 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.215 / ESU R Free: 0.185
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. 3.X-RAY FLUORESCENCE EXCITATION AND WAVELENGTH SCANS, ANOMALOUS DIFFERENCE FOURIERS AND COORDINATION GEOMETRY SUPPORT THE MODELING OF NI ION IN THE PUTATIVE ACTIVE SITE 4.THE DATA IS ANISOTROPIC ALONG THE B-DIRECTION.
RfactorNum. reflection% reflectionSelection details
Rfree0.266 534 4.8 %RANDOM
Rwork0.229 ---
obs0.231 11168 97.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.148 Å2
Baniso -1Baniso -2Baniso -3
1--4.4 Å20 Å20 Å2
2--5.29 Å20 Å2
3----0.88 Å2
Refinement stepCycle: LAST / Resolution: 2.009→28.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1146 0 1 55 1202
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0221189
X-RAY DIFFRACTIONr_bond_other_d0.0010.02753
X-RAY DIFFRACTIONr_angle_refined_deg1.2731.9361627
X-RAY DIFFRACTIONr_angle_other_deg0.92431850
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0355151
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.43424.34846
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.89215184
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.366153
X-RAY DIFFRACTIONr_chiral_restr0.0760.2189
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021324
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02235
X-RAY DIFFRACTIONr_nbd_refined0.2210.2280
X-RAY DIFFRACTIONr_nbd_other0.170.2718
X-RAY DIFFRACTIONr_nbtor_refined0.1810.2608
X-RAY DIFFRACTIONr_nbtor_other0.0880.2554
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.150.242
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1470.27
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1210.217
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0760.26
X-RAY DIFFRACTIONr_mcbond_it0.7641.5778
X-RAY DIFFRACTIONr_mcbond_other0.1541.5305
X-RAY DIFFRACTIONr_mcangle_it1.14721219
X-RAY DIFFRACTIONr_scbond_it1.6413489
X-RAY DIFFRACTIONr_scangle_it2.2594.5408
LS refinement shellResolution: 2.009→2.061 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.356 33 -
Rwork0.316 699 -
all-732 -
obs--87.56 %
Refinement TLS params.Method: refined / Origin x: 22.8597 Å / Origin y: 10.4516 Å / Origin z: 20.6285 Å
111213212223313233
T-0.0434 Å20.0047 Å20.0057 Å2--0.1881 Å2-0.0786 Å2---0.0932 Å2
L6.3896 °20.5926 °21.8195 °2-1.5532 °2-0.2248 °2--1.6438 °2
S0.0178 Å °-0.4297 Å °0.3764 Å °0.0133 Å °-0.1043 Å °0.1939 Å °-0.0313 Å °0.0527 Å °0.0865 Å °

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