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- PDB-3g0k: Crystal structure of a protein of unknown function with a cystati... -

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Basic information

Entry
Database: PDB / ID: 3g0k
TitleCrystal structure of a protein of unknown function with a cystatin-like fold (saro_2880) from novosphingobium aromaticivorans dsm at 1.30 A resolution
ComponentsPutative membrane protein
KeywordsCa-BINDING PROTEIN / Snoal-like polyketide cyclase / structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


polyketide metabolic process / metal ion binding
Similarity search - Function
Polyketide cyclase SnoaL-like / SnoaL-like domain / SnoaL-like domain / Nuclear Transport Factor 2; Chain: A, - #50 / NTF2-like domain superfamily / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Putative membrane protein
Similarity search - Component
Biological speciesNovosphingobium aromaticivorans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.3 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of protein of unknown function with a cystatin-like fold (YP_498150.1) from Novosphingobium aromaticivorans DSM 12444 at 1.30 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJan 28, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 10, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / 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 1.5Oct 9, 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: Putative membrane protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,6198
Polymers16,9881
Non-polymers6317
Water3,261181
1
A: Putative membrane protein
hetero molecules

A: Putative membrane protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,23816
Polymers33,9762
Non-polymers1,26214
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area2760 Å2
ΔGint-15.2 kcal/mol
Surface area12460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.343, 54.343, 93.947
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-130-

CA

DetailsSTATIC LIGHT SCATTERING SUPPORTS THE ASSIGNMENT OF A DIMER AS A SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION.

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Components

#1: Protein Putative membrane protein


Mass: 16988.010 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Novosphingobium aromaticivorans (bacteria)
Strain: DSM 12444 / Gene: Saro_2880, YP_498150.1 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q2G4A7
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 181 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHIS CONSTRUCT WAS EXPRESSED WITH THE N-TERMINAL PURIFICATION TAG MGSDKIHHHHHHENLYFQG.

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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: 2.36 Å3/Da / Density % sol: 47.82 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: NANODROP, 0.020M CaCl2, 30.0% MPD, 0.1M Acetate pH 4.6, 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: 0.97821 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Nov 15, 2008 / Details: Flat mirror (vertical focusing)
RadiationMonochromator: Single crystal Si(111) bent (horizontal focusing)
Protocol: SAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97821 Å / Relative weight: 1
ReflectionResolution: 1.3→26.1 Å / Num. obs: 39549 / % possible obs: 98.3 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.066 / Rsym value: 0.066 / Net I/σ(I): 6.15
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.3-1.3340.4421.8949823740.44281.9
1.33-1.374.60.36921244127010.36994.7
1.37-1.415.40.3282.31489427810.328100
1.41-1.455.40.282.61442526950.28100
1.45-1.55.40.2393.11408026270.239100
1.5-1.555.40.1933.71378125570.193100
1.55-1.615.40.1684.21312624380.168100
1.61-1.685.40.1514.61279823780.151100
1.68-1.755.40.1255.31253323240.125100
1.75-1.845.40.1046.21151021260.104100
1.84-1.945.40.09271141520990.092100
1.94-2.065.80.0837.61144819660.083100
2.06-2.26.60.0787.71208518440.078100
2.2-2.377.50.0777.91304917480.077100
2.37-2.69.30.078.71493916110.07100
2.6-2.9110.70.0659.41544314450.065100
2.91-3.3610.60.05710.91397613160.057100
3.36-4.1110.50.05111.71164711140.051100
4.11-5.81100.05211.787778810.052100
5.81-26.18.80.0621045885240.06297.5

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0053refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
SCALA3.2.5data scaling
PDB_EXTRACT3.006data extraction
MAR345CCDdata collection
MOSFLMdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 1.3→26.1 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.976 / Occupancy max: 1 / Occupancy min: 0.1 / SU B: 1.008 / SU ML: 0.019 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.036 / ESU R Free: 0.035
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. U VALUES: REFINED INDIVIDUALLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. U VALUES: REFINED INDIVIDUALLY. 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. A CALCIUM ION (CA) FROM THE CRYSTALLIZATION SOLUTIONS HAS BEEN MODELED INTO THE STRUCTURE BASED ON ANOMALOUS DIFFERENCE FOURIERS AND COORDINATION GEOMETRY. 5. ACETATE (ACT) AND (4S)-2-METHYL-2,4-PENTANEDIOL (MPD) FROM THE CRYSTALLIZATION SOLUTIONS HAVE BEEN MODELED INTO THE STRUCTURE.
RfactorNum. reflection% reflectionSelection details
Rfree0.143 1969 5 %RANDOM
Rwork0.12 ---
obs0.121 39502 98.25 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 61.33 Å2 / Biso mean: 17.837 Å2 / Biso min: 4.55 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å20.04 Å20 Å2
2--0.07 Å20 Å2
3----0.11 Å2
Refinement stepCycle: LAST / Resolution: 1.3→26.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1009 0 41 181 1231
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0211149
X-RAY DIFFRACTIONr_bond_other_d0.0010.02741
X-RAY DIFFRACTIONr_angle_refined_deg1.8071.9651589
X-RAY DIFFRACTIONr_angle_other_deg0.99931824
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6885155
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.56624.57659
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.13215182
X-RAY DIFFRACTIONr_dihedral_angle_4_deg6.511158
X-RAY DIFFRACTIONr_chiral_restr0.1120.2178
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0211307
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02223
X-RAY DIFFRACTIONr_mcbond_it3.0813693
X-RAY DIFFRACTIONr_mcbond_other2.5083271
X-RAY DIFFRACTIONr_mcangle_it4.11251136
X-RAY DIFFRACTIONr_scbond_it4.8458456
X-RAY DIFFRACTIONr_scangle_it6.57111439
X-RAY DIFFRACTIONr_rigid_bond_restr2.37331890
X-RAY DIFFRACTIONr_sphericity_free13.3343184
X-RAY DIFFRACTIONr_sphericity_bonded6.45831858
LS refinement shellResolution: 1.3→1.334 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.295 101 -
Rwork0.239 2289 -
all-2390 -
obs--81.77 %

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