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- PDB-2oyo: Crystal structure of Uncharacterized peroxidase-related protein (... -

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Basic information

Entry
Database: PDB / ID: 2oyo
TitleCrystal structure of Uncharacterized peroxidase-related protein (YP_604910.1) from Deinococcus geothermalis DSM 11300 at 1.51 A resolution
ComponentsUncharacterized peroxidase-related protein
KeywordsOXIDOREDUCTASE / YP_604910.1 / Uncharacterised peroxidase-related / Uncharacterized peroxidase-related / Carboxymuconolactone decarboxylase family / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


peroxiredoxin activity
Similarity search - Function
AhpD-like / Uncharacterised peroxidase-related / Alkylhydroperoxidase AhpD core / AhpD-like / Carboxymuconolactone decarboxylase-like / AhpD-like / Carboxymuconolactone decarboxylase family / AhpD-like / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Uncharacterized peroxidase-related protein
Similarity search - Component
Biological speciesDeinococcus geothermalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.51 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of Uncharacterized peroxidase-related protein (YP_604910.1) from Deinococcus geothermalis DSM 11300 at 1.51 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionFeb 22, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 20, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / 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 20, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
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 (0) 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: Uncharacterized peroxidase-related protein
B: Uncharacterized peroxidase-related protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,1795
Polymers43,8252
Non-polymers3553
Water7,782432
1
A: Uncharacterized peroxidase-related protein
B: Uncharacterized peroxidase-related protein
hetero molecules

A: Uncharacterized peroxidase-related protein
B: Uncharacterized peroxidase-related protein
hetero molecules

A: Uncharacterized peroxidase-related protein
B: Uncharacterized peroxidase-related protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,53715
Polymers131,4746
Non-polymers1,0649
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area21420 Å2
ΔGint-197 kcal/mol
Surface area39060 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)135.649, 135.649, 118.084
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-242-

HOH

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Components

#1: Protein Uncharacterized peroxidase-related protein


Mass: 21912.307 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Deinococcus geothermalis (bacteria) / Strain: DSM 11300 / Gene: YP_604910.1, Dgeo_1446 / Plasmid: speedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q1IYE3
#2: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 432 / 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: 2.38 Å3/Da / Density % sol: 48.41 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 9
Details: NANODROP, 40.0% MPD, 0.1M Bicine pH 9.0, 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, 0.97916, 0.97886
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jan 7, 2007 / Details: Flat mirror (vertical focusing)
RadiationMonochromator: Single crystal Si(111) bent (horizontal focusing)
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.979161
30.978861
ReflectionResolution: 1.51→39.163 Å / Num. obs: 64521 / % possible obs: 96.5 % / Biso Wilson estimate: 17.262 Å2 / Rmerge(I) obs: 0.138 / Net I/σ(I): 9.57
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique all% possible all
1.51-1.560.6661.817282506384.3
1.56-1.630.6622.229862664191.7
1.63-1.70.6162.732841588796.7
1.7-1.790.5183.235604636697.4
1.79-1.90.41434912624097.9
1.9-2.050.2736.136780656798.6
2.05-2.250.1848.935076627299
2.25-2.580.12212.737000658899.1
2.580.08118.736724656199.7

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
REFMAC5.2.0019refinement
XSCALEdata scaling
PDB_EXTRACT2data extraction
MAR345CCDdata collection
XDSdata reduction
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.51→39.163 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.948 / SU B: 1.97 / SU ML: 0.068 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.075 / ESU R Free: 0.078
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 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. THE 2-METHYL-2,4-PENTANEDIOL MOLECULES FROM THE CRYSTALLIZATION WERE MODELED INTO THE STRUCTURE. 4. UNEXPLAINED ELECTRON DENSITIES OBSERVED NEAR RESIDUES 189 AND 192 OF THE B SUBUNIT WERE NOT MODELED.
RfactorNum. reflection% reflectionSelection details
Rfree0.215 3275 5.1 %RANDOM
Rwork0.182 ---
all0.184 ---
obs0.184 64519 98.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.894 Å2
Baniso -1Baniso -2Baniso -3
1--0.81 Å2-0.4 Å20 Å2
2---0.81 Å20 Å2
3---1.21 Å2
Refinement stepCycle: LAST / Resolution: 1.51→39.163 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2904 0 24 432 3360
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0223013
X-RAY DIFFRACTIONr_bond_other_d0.0020.021987
X-RAY DIFFRACTIONr_angle_refined_deg1.4971.954114
X-RAY DIFFRACTIONr_angle_other_deg1.03434816
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9245374
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.92223.919148
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.91415462
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.0811524
X-RAY DIFFRACTIONr_chiral_restr0.0960.2457
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023414
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02626
X-RAY DIFFRACTIONr_nbd_refined0.2340.2638
X-RAY DIFFRACTIONr_nbd_other0.1980.22096
X-RAY DIFFRACTIONr_nbtor_refined0.1840.21509
X-RAY DIFFRACTIONr_nbtor_other0.0860.21485
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1750.2281
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1710.210
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3140.277
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1680.227
X-RAY DIFFRACTIONr_mcbond_it1.2041.52264
X-RAY DIFFRACTIONr_mcbond_other0.2781.5748
X-RAY DIFFRACTIONr_mcangle_it1.40822996
X-RAY DIFFRACTIONr_scbond_it2.65931285
X-RAY DIFFRACTIONr_scangle_it3.9174.51118
LS refinement shellResolution: 1.51→1.549 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.373 194 -
Rwork0.347 4187 -
obs-4381 91.84 %

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