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- PDB-3dka: Crystal structure of a dinb-like protein (yjoa, bsu12410) from ba... -

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Basic information

Entry
Database: PDB / ID: 3dka
TitleCrystal structure of a dinb-like protein (yjoa, bsu12410) from bacillus subtilis at 2.30 A resolution
ComponentsDinB-like Protein
KeywordsUNKNOWN FUNCTION / Dinb/yfit-like putative metalloenzyme fold / 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 / metal ion binding / Uncharacterized protein YjoA
Function and homology information
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a DinB-like Protein (NP_389123.1) from BACILLUS SUBTILIS at 2.30 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJun 24, 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: Refinement description / Category: 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 / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DinB-like Protein
B: DinB-like Protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,2553
Polymers36,2192
Non-polymers351
Water1,76598
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1880 Å2
ΔGint-11 kcal/mol
Surface area14180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.690, 63.340, 82.060
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31A
41B
51A
61B

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
112AA5 - 675 - 67
212BB5 - 675 - 67
324AA68 - 6968 - 69
424BB68 - 6968 - 69
532AA70 - 15270 - 152
632BB70 - 15270 - 152

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Components

#1: Protein DinB-like Protein


Mass: 18109.627 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: NP_389123.1, yjoA, BSU12410 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: O34334
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 98 / Source method: isolated from a natural source / Formula: H2O
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: 2.07 Å3/Da / Density % sol: 40.57 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.2000M NH4OAc, 30.0000% PEG-4000, 0.1M Citrate pH 5.6, NANODROP, 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: 0.91837,0.97956,0.97904
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 14, 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
20.979561
30.979041
ReflectionResolution: 2.3→29.566 Å / Num. obs: 13596 / % possible obs: 95.9 % / Observed criterion σ(I): -3 / Redundancy: 3.63 % / Biso Wilson estimate: 34.972 Å2 / Rmerge(I) obs: 0.097 / Net I/σ(I): 7.3
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
2.3-2.380.5711.5845482313190.5
2.38-2.480.4621.952032619196.1
2.48-2.590.3782.448122441196.4
2.59-2.730.28350692554196
2.73-2.90.2143.948852460196
2.9-3.120.163548732468197.2
3.12-3.430.1077.649732501196.8
3.43-3.930.061249942523196.4
3.93-4.930.0416.649552499197.1
4.93-29.570.03518.550512562196.5

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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: 2.3→29.566 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.893 / SU B: 15.654 / SU ML: 0.193 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.437 / ESU R Free: 0.273
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. 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 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.269 677 5 %RANDOM
Rwork0.217 ---
obs0.219 13568 97.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.26 Å2
Baniso -1Baniso -2Baniso -3
1-2.39 Å20 Å20 Å2
2---0.47 Å20 Å2
3----1.92 Å2
Refinement stepCycle: LAST / Resolution: 2.3→29.566 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2288 0 1 98 2387
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0212343
X-RAY DIFFRACTIONr_bond_other_d0.0060.021532
X-RAY DIFFRACTIONr_angle_refined_deg1.0731.9453168
X-RAY DIFFRACTIONr_angle_other_deg0.83933763
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.5575286
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.95925.043117
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.5515418
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.103159
X-RAY DIFFRACTIONr_chiral_restr0.0650.2364
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022587
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02450
X-RAY DIFFRACTIONr_nbd_refined0.1920.2519
X-RAY DIFFRACTIONr_nbd_other0.170.21538
X-RAY DIFFRACTIONr_nbtor_refined0.1720.21131
X-RAY DIFFRACTIONr_nbtor_other0.0870.21140
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1420.289
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1050.216
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2250.218
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2430.25
X-RAY DIFFRACTIONr_mcbond_it1.30431511
X-RAY DIFFRACTIONr_mcbond_other0.2113577
X-RAY DIFFRACTIONr_mcangle_it2.08252308
X-RAY DIFFRACTIONr_scbond_it3.4028953
X-RAY DIFFRACTIONr_scangle_it4.63211858
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
798TIGHT POSITIONAL0.070.1
1007MEDIUM POSITIONAL0.250.4
798TIGHT THERMAL0.070.5
1007MEDIUM THERMAL0.281
LS refinement shellResolution: 2.299→2.38 Å / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rfree0.289 58 -
Rwork0.263 1225 -
all-1283 -
obs--96.03 %
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)
10.73320.2212-0.2771.022-0.47262.4037-0.04810.01440.0834-0.06170.08220.1071-0.1075-0.1458-0.0341-0.06560.0059-0.0026-0.0319-0.0036-0.022317.797836.270918.3858
21.3254-0.3565-1.52790.2585-0.01982.9029-0.0561-0.01410.05280.10190.0465-0.13250.00320.09790.0096-0.0432-0.0303-0.0031-0.0686-0.0216-0.010537.808537.565528.0478
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA5 - 1546 - 155
2X-RAY DIFFRACTION2BB5 - 1536 - 154

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