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- PDB-2ooj: CRYSTAL STRUCTURE OF A PROTEIN WITH UNKNOWN FUNCTION FROM DUF3224... -

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Basic information

Entry
Database: PDB / ID: 2ooj
TitleCRYSTAL STRUCTURE OF A PROTEIN WITH UNKNOWN FUNCTION FROM DUF3224 FAMILY (SO_1590) FROM SHEWANELLA ONEIDENSIS MR-1 AT 1.84 A RESOLUTION
ComponentsHypothetical protein
KeywordsUNKNOWN FUNCTION / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-2
Function / homologySO1590-like / Protein of unknown function DUF3224 / SO1590-like superfamily / Protein of unknown function (DUF3224) / AOC barrel-like / Beta Barrel / Mainly Beta / ACETATE ION / DUF3224 domain-containing protein
Function and homology information
Biological speciesShewanella oneidensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.84 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of hypothetical protein (NP_717203.1) from Shewanella oneidensis at 1.84 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJan 25, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 6, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Oct 18, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / 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 20, 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 999 SEQUENCE 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.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hypothetical protein
B: Hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,9874
Polymers30,8692
Non-polymers1182
Water3,513195
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4020 Å2
ΔGint-32 kcal/mol
Surface area12270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.211, 55.254, 106.086
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

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / End auth comp-ID: PRO / End label comp-ID: PRO / Refine code: 4 / Auth seq-ID: 2 - 134 / Label seq-ID: 3 - 135

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Hypothetical protein


Mass: 15434.351 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shewanella oneidensis (bacteria) / Strain: MR-1 / Gene: NP_717203.1, SO_1590 / Plasmid: speedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q8EGL1
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 195 / 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: 2.24 Å3/Da / Density % sol: 45.11 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: NANODROP, 0.2M Li2SO4, 2.5M NaCl, 0.1M Acetate pH 4.5, 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: 0.97883 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jan 18, 2007 / Details: Flat mirror (vertical focusing)
RadiationMonochromator: Single crystal Si(111) bent (horizontal focusing)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97883 Å / Relative weight: 1
ReflectionResolution: 1.84→29.79 Å / Num. obs: 24865 / % possible obs: 99.9 % / Redundancy: 4.7 % / Biso Wilson estimate: 26.88 Å2 / Rmerge(I) obs: 0.11 / Rsym value: 0.11 / Net I/σ(I): 10.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.84-1.893.60.6921.4646518050.692100
1.89-1.943.60.5251.4619517400.525100
1.94-23.60.4091.8618017220.409100
2-2.063.60.3492.1602416870.349100
2.06-2.123.60.2812.5570715980.281100
2.12-2.23.60.2313562815730.231100
2.2-2.283.60.2043.4543015270.204100
2.28-2.383.60.183.9521714620.18100
2.38-2.483.60.1694.1503914060.169100
2.48-2.63.60.1424.7479413480.142100
2.6-2.744.90.1743.6617912720.174100
2.74-2.917.10.173.8881812390.17100
2.91-3.117.10.1354.6807211380.135100
3.11-3.367.10.115.8754810700.11100
3.36-3.6870.0956.7706910080.095100
3.68-4.116.90.0867.162719030.086100
4.11-4.756.80.0857.255588170.08599.9
4.75-5.826.70.0837.146106870.08399.8
5.82-8.236.50.085735315450.08599.1
8.23-29.835.60.0787.717943180.07895.6

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
SHELXphasing
REFMAC5.2.0019refinement
SCALAdata scaling
PDB_EXTRACT2data extraction
MAR345CCDdata collection
MOSFLMdata reduction
CCP4(SCALA)data scaling
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 1.84→29.788 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.956 / SU B: 3.012 / SU ML: 0.091 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.13 / ESU R Free: 0.118
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. ACETATE IONS (ACT) ARE MODELED BASED ON THE CRYSTALLIZATION CONDITIONS. 4. THE SE POSITION FOR RESIDUE MSE B1 WAS ASSIGNED BASED ON THE ANOMALOUS DIFFERENCE FOURIER MAPS AND HEAVY ATOM SUB-STRUCTURE USED FOR PHASING. THE CA, CB AND CG ATOMS WERE NOT MODELED DUE TO DISORDER AT THE N-TERMINUS.
RfactorNum. reflection% reflectionSelection details
Rfree0.206 1258 5.1 %RANDOM
Rwork0.178 ---
all0.18 ---
obs0.18 24752 99.89 %-
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: 27.276 Å2
Baniso -1Baniso -2Baniso -3
1-0.88 Å20 Å20 Å2
2--0.56 Å20 Å2
3----1.44 Å2
Refinement stepCycle: LAST / Resolution: 1.84→29.788 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1965 0 8 195 2168
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0222053
X-RAY DIFFRACTIONr_bond_other_d0.0010.021345
X-RAY DIFFRACTIONr_angle_refined_deg1.5251.9592769
X-RAY DIFFRACTIONr_angle_other_deg0.81333302
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.865276
X-RAY DIFFRACTIONr_dihedral_angle_2_deg43.93824.69181
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.06715342
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.332155
X-RAY DIFFRACTIONr_chiral_restr0.0960.2307
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022343
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02418
X-RAY DIFFRACTIONr_nbd_refined0.1930.2337
X-RAY DIFFRACTIONr_nbd_other0.2010.21328
X-RAY DIFFRACTIONr_nbtor_refined0.1810.2950
X-RAY DIFFRACTIONr_nbtor_other0.0860.21250
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1740.2125
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2320.218
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1820.241
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1770.215
X-RAY DIFFRACTIONr_mcbond_it2.43331356
X-RAY DIFFRACTIONr_mcbond_other0.8293569
X-RAY DIFFRACTIONr_mcangle_it3.17652099
X-RAY DIFFRACTIONr_scbond_it5.6158774
X-RAY DIFFRACTIONr_scangle_it7.68511665
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 1535 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
MEDIUM POSITIONAL0.540.5
MEDIUM THERMAL1.512
LS refinement shellResolution: 1.84→1.888 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.293 98 -
Rwork0.253 1692 -
obs-1790 100 %

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