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- PDB-3h3z: Crystal structure of a putative cyclic nucleotide binding protein... -

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Basic information

Entry
Database: PDB / ID: 3h3z
TitleCrystal structure of a putative cyclic nucleotide binding protein (spoa0323) from ruegeria pomeroyi dss-3 at 2.35 A resolution
ComponentsCyclic nucleotide-binding protein
KeywordscNMP-BINDING PROTEIN / cyclic nucleotide-binding domain / structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


DNA-binding transcription factor activity / DNA binding / cytosol
Similarity search - Function
: / Crp-like helix-turn-helix domain / Crp-type HTH domain profile. / Crp-type HTH domain / Cyclic nucleotide-monophosphate binding domain / Cyclic nucleotide-binding domain / cAMP/cGMP binding motif profile. / Cyclic nucleotide-binding domain / Cyclic nucleotide-binding domain superfamily / Jelly Rolls ...: / Crp-like helix-turn-helix domain / Crp-type HTH domain profile. / Crp-type HTH domain / Cyclic nucleotide-monophosphate binding domain / Cyclic nucleotide-binding domain / cAMP/cGMP binding motif profile. / Cyclic nucleotide-binding domain / Cyclic nucleotide-binding domain superfamily / Jelly Rolls / RmlC-like jelly roll fold / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Jelly Rolls / Winged helix-like DNA-binding domain superfamily / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Cyclic nucleotide-binding protein
Similarity search - Component
Biological speciesRuegeria pomeroyi DSS-3 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.35 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of PUTATIVE CAMP-BINDING REGULATORY PROTEIN (YP_165150.1) from SILICIBACTER POMEROYI DSS-3 at 2.35 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionApr 17, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 5, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: 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 27, 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

Downloads & links

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Assembly

Deposited unit
A: Cyclic nucleotide-binding protein
B: Cyclic nucleotide-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,4514
Polymers52,3802
Non-polymers712
Water1,76598
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4200 Å2
ΔGint-47 kcal/mol
Surface area21450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)137.052, 137.052, 94.937
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1115A1 - 143
2115B1 - 143
1215A155 - 223
2215B155 - 223
DetailsTHE RESULTS FROM SIZE EXCLUSION CHROMATOGRAPHY SUPPORTS THE ASSIGNMENT OF A DIMER AS A SIGNIFICANT OLIGOMERIZATION STATE.

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Components

#1: Protein Cyclic nucleotide-binding protein / PUTATIVE CAMP-BINDING REGULATORY PROTEIN


Mass: 26190.061 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ruegeria pomeroyi DSS-3 (bacteria) / Gene: SPOA0323, YP_165150.1 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q5LKQ8
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 98 / 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: 2

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
13.2862.45
2
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 1.2600M (NH4)2SO4, 0.1M Cacodylate pH 6.5, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K, VAPOR DIFFUSION, SITTING DROP

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSSRL BL9-210.97946
SYNCHROTRONAPS 23-ID-B20.97967,0.94645
Detector
TypeIDDetectorDateDetails
MARMOSAIC 325 mm CCD1CCDJan 19, 2009Flat collimating mirror, toroid focusing mirror
MARMOSAIC 300 mm CCD2CCDOct 12, 2008Adjustable focusing mirrors in K-B geometry
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Double crystal monochromatorSINGLE WAVELENGTHMx-ray1
2Si(111) Double Crystal MonochrometerMADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.979461
20.979671
30.946451
ReflectionResolution: 2.35→28.724 Å / Num. obs: 27604 / % possible obs: 98.2 % / Observed criterion σ(I): -3 / Redundancy: 3.82 % / Biso Wilson estimate: 56.796 Å2 / Rmerge(I) obs: 0.047 / Net I/σ(I): 11.09
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.35-2.430.6031.49841513696
2.43-2.530.4531.910868563599
2.53-2.650.3292.611033570099
2.65-2.790.2353.610560544799.1
2.79-2.960.1435.710375534899.2
2.96-3.190.0868.910695551598.9
3.19-3.510.05114.210581545598.7
3.51-4.010.03419.810483539298.5
4.01-5.040.02625.510538543197.7
5.04-28.7240.02627.710432538696

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3.006data extraction
XDSdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.35→28.724 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.927 / Occupancy max: 1 / Occupancy min: 0.25 / SU B: 13.698 / SU ML: 0.159 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.267 / ESU R Free: 0.209
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.CHLORIDE IONS FROM CRYSTALLIZATION ARE MODELED IN THE STRUCTURE.
RfactorNum. reflection% reflectionSelection details
Rfree0.236 1409 5.1 %RANDOM
Rwork0.202 ---
obs0.204 27596 99.83 %-
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 max: 128.15 Å2 / Biso mean: 71.309 Å2 / Biso min: 38.36 Å2
Baniso -1Baniso -2Baniso -3
1--0.62 Å2-0.31 Å20 Å2
2---0.62 Å20 Å2
3---0.94 Å2
Refinement stepCycle: LAST / Resolution: 2.35→28.724 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3391 0 2 98 3491
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0223565
X-RAY DIFFRACTIONr_bond_other_d0.0030.022339
X-RAY DIFFRACTIONr_angle_refined_deg1.7251.9594863
X-RAY DIFFRACTIONr_angle_other_deg1.0553.0015729
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.5345473
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.13423.696138
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.22315578
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.2711524
X-RAY DIFFRACTIONr_chiral_restr0.0640.2572
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024043
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02706
X-RAY DIFFRACTIONr_nbd_refined0.2140.3780
X-RAY DIFFRACTIONr_nbd_other0.1760.32407
X-RAY DIFFRACTIONr_nbtor_refined0.180.51737
X-RAY DIFFRACTIONr_nbtor_other0.0940.51811
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1630.5193
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0110.51
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1350.315
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3170.335
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1580.54
X-RAY DIFFRACTIONr_mcbond_it2.09432437
X-RAY DIFFRACTIONr_mcbond_other0.6853930
X-RAY DIFFRACTIONr_mcangle_it3.41753741
X-RAY DIFFRACTIONr_scbond_it6.01381322
X-RAY DIFFRACTIONr_scangle_it8.009111122
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
1227MEDIUM POSITIONAL0.240.5
1331LOOSE POSITIONAL0.545
1227MEDIUM THERMAL1.592
1331LOOSE THERMAL3.6710
LS refinement shellResolution: 2.351→2.412 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.287 109 -
Rwork0.254 1919 -
all-2028 -
obs--99.66 %

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