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- PDB-2obp: Crystal structure of a putative dna-binding protein (reut_b4095) ... -

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Basic information

Entry
Database: PDB / ID: 2obp
TitleCrystal structure of a putative dna-binding protein (reut_b4095) from ralstonia eutropha jmp134 at 1.70 A resolution
ComponentsPutative DNA-binding protein
KeywordsDNA BINDING PROTEIN / Structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homologyWinged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / DNA binding / Orthogonal Bundle / Mainly Alpha / NITRATE ION / Putative DNA-binding protein
Function and homology information
Biological speciesRalstonia eutropha (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.7 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of putative DNA-binding protein (YP_298295.1) from Ralstonia eutropha JMP134 at 1.70 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionDec 19, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 16, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Jan 25, 2023Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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
Revision 1.5Nov 13, 2024Group: Data collection / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id
Remark 999SEQUENCE 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, FOLLOWED BY THE TARGET SEQUENCE.
Remark 300BIOMOLECULE: 1, 2 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 ...BIOMOLECULE: 1, 2 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). SIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING SUPPORTS THE ASSIGNMENT OF A MONOMER AS A SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative DNA-binding protein
B: Putative DNA-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,3024
Polymers20,2042
Non-polymers972
Water2,990166
1
A: Putative DNA-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,1642
Polymers10,1021
Non-polymers621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Putative DNA-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,1382
Polymers10,1021
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)76.580, 76.580, 137.860
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11A-104-

HOH

21A-122-

HOH

31A-178-

HOH

41B-106-

HOH

51B-127-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31A
41B

NCS domain segments:

Ens-ID: 1 / Refine code: 5

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASPASPGLUGLUAA14 - 7015 - 71
21ASPASPGLUGLUBB14 - 7015 - 71
32HISHISPROPROAA76 - 9277 - 93
42HISHISPROPROBB76 - 9277 - 93

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Components

#1: Protein Putative DNA-binding protein


Mass: 10102.067 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ralstonia eutropha (bacteria) / Species: Cupriavidus necator / Strain: JMP134 / Gene: YP_298295.1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q46TT3
#2: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO3
#3: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 166 / 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: 2.89 Å3/Da / Density % sol: 57.38 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop, nanodrop / pH: 5.8
Details: 0.2M MgNO3, 20.0% PEG-3350, No Buffer pH 5.8, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.91837, 0.97932, 0.97910
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Dec 3, 2006 / 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
20.979321
30.97911
ReflectionResolution: 1.7→29.412 Å / Num. obs: 26996 / % possible obs: 98.2 % / Biso Wilson estimate: 30.103 Å2 / Rmerge(I) obs: 0.063 / Net I/σ(I): 19.02
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique all% possible all
1.7-1.760.6283.133318447990.9
1.76-1.830.507437113488598
1.83-1.910.4244.935967473398.1
1.91-2.020.2867.240849537598.3
2.02-2.140.18810.735721469999.2
2.14-2.310.12815.438710508799.4
2.31-2.540.08720.937811493199.6
2.54-2.90.06627.837532490099.6
2.90.04241.338859506199.7

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
SHELXphasing
REFMAC5.2.0019refinement
XSCALEdata scaling
PDB_EXTRACT2data extraction
XDSdata reduction
SHELXDphasing
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.7→29.412 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.931 / SU B: 3.327 / SU ML: 0.057 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.086 / ESU R Free: 0.09
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 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4. CHLORIDE AND NO3 ARE MODELED BASED ON THE CRYSTALLIZATION CONDITIONS. 5. THERE ARE SOME UNINTERPRETED BLOBS OF DENSITY NEAR THE PROTEIN SURFACE. 6. A26,A30,A66 AND A/B70 SIDE CHAINS ARE MODELLED AS PARTIAL OCCUPANCY.
RfactorNum. reflection% reflectionSelection details
Rfree0.219 1351 5 %RANDOM
Rwork0.186 ---
obs0.188 26956 99.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 20.67 Å2
Baniso -1Baniso -2Baniso -3
1-1.06 Å20.53 Å20 Å2
2--1.06 Å20 Å2
3----1.59 Å2
Refinement stepCycle: LAST / Resolution: 1.7→29.412 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1177 0 5 166 1348
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0221289
X-RAY DIFFRACTIONr_bond_other_d0.0030.02863
X-RAY DIFFRACTIONr_angle_refined_deg1.5111.991769
X-RAY DIFFRACTIONr_angle_other_deg1.00932135
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.555185
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.26624.08249
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.01815217
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1841511
X-RAY DIFFRACTIONr_chiral_restr0.0970.2214
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021470
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02235
X-RAY DIFFRACTIONr_nbd_refined0.2210.2287
X-RAY DIFFRACTIONr_nbd_other0.1950.2863
X-RAY DIFFRACTIONr_nbtor_refined0.1730.2631
X-RAY DIFFRACTIONr_nbtor_other0.0880.2638
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2080.2116
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.2250.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2020.24
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1980.219
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2180.217
X-RAY DIFFRACTIONr_mcbond_it1.92731050
X-RAY DIFFRACTIONr_mcbond_other0.6363345
X-RAY DIFFRACTIONr_mcangle_it2.39751370
X-RAY DIFFRACTIONr_scbond_it4.3358461
X-RAY DIFFRACTIONr_scangle_it5.66511389
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
427MEDIUM POSITIONAL0.190.5
425LOOSE POSITIONAL0.455
427MEDIUM THERMAL1.162
425LOOSE THERMAL1.9310
LS refinement shellResolution: 1.701→1.745 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.262 91 -
Rwork0.236 1840 -
obs-1931 98.42 %
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)
11.11660.5196-0.03262.1143-0.85861.5481-0.02750.09570.1486-0.1190.13120.1555-0.0597-0.2161-0.1037-0.00780.00520.0258-0.02320.04520.000729.400238.210926.9115
21.14540.0898-0.39141.431-0.91241.7047-0.0388-0.0663-0.11310.0508-0.0386-0.03150.16-0.02050.0774-0.0127-0.00440.0219-0.06320.0203-0.032538.989648.16387.8771
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL / Auth seq-ID: 12 - 92 / Label seq-ID: 13 - 93

IDRefine TLS-IDAuth asym-IDLabel asym-ID
11AA
22BB

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