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- PDB-3cje: Crystal structure of an osmc-like hydroperoxide resistance protei... -

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Basic information

Entry
Database: PDB / ID: 3cje
TitleCrystal structure of an osmc-like hydroperoxide resistance protein (jann_2040) from jannaschia sp. ccs1 at 1.70 A resolution
ComponentsOsmC-like protein
KeywordsOXIDOREDUCTASE / Structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


OsmC/Ohr family / OsmC/Ohr superfamily / OsmC-like protein / K homology (KH) domain / GMP Synthetase; Chain A, domain 3 / K homology domain-like, alpha/beta / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / OsmC-like protein
Similarity search - Component
Biological speciesJannaschia sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of OsmC-like hydroperoxide resistance protein (YP_509982.1) from Jannaschia sp. CCS1 at 1.70 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionMar 12, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 25, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: 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 30, 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: OsmC-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,24610
Polymers18,4141
Non-polymers8329
Water2,486138
1
A: OsmC-like protein
hetero molecules

A: OsmC-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,49220
Polymers36,8292
Non-polymers1,66318
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_675x-y+1,-y+2,-z+1/31
Buried area6410 Å2
ΔGint-46.3 kcal/mol
Surface area13500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.886, 81.886, 70.633
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-176-

HOH

DetailsAUTHORS STATE THAT THE CRYSTAL PACKING ANALYSIS SUPPORTS THE ASSIGNMENT OF A DIMER AS THE SIGNIFICANT OLIGOMERIZATION STATE.

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Components

#1: Protein OsmC-like protein


Mass: 18414.389 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Jannaschia sp. (bacteria) / Strain: CCS1 / Gene: YP_509982.1, Jann_2040 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q28QQ5
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 138 / 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: 1

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Sample preparation

CrystalDensity Matthews: 3.71 Å3/Da / Density % sol: 66.87 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.57
Details: NANODROP, 1.545M Ammonium dihydrogen phosphate, 0.1M Tris-HCl pH 8.57, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL1-5 / Wavelength: 0.978835 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 10, 2008
Details: 1m long Rh coated bent cylindrical mirror for horizontal and vertical focusing
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978835 Å / Relative weight: 1
ReflectionResolution: 1.7→26.803 Å / Num. obs: 30482 / % possible obs: 100 % / Redundancy: 10.4 % / Biso Wilson estimate: 19.728 Å2 / Rmerge(I) obs: 0.097 / Rsym value: 0.097 / Net I/σ(I): 5.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.7-1.747.60.8120.91622521490.812100
1.74-1.7910.80.6681.12320121560.668100
1.79-1.8410.80.5261.42279321080.526100
1.84-1.910.80.4011.82257820950.401100
1.9-1.9610.80.2892.52132819800.289100
1.96-2.0310.80.2153.52083619360.215100
2.03-2.1110.80.17842013618690.178100
2.11-2.1910.70.1494.81917717870.149100
2.19-2.2910.70.1374.81856517390.137100
2.29-2.410.70.1185.91780316670.118100
2.4-2.5310.60.1086.31660815660.108100
2.53-2.6910.50.0947.21575814940.094100
2.69-2.8710.50.0857.81482614060.085100
2.87-3.110.30.0768.71362213190.076100
3.1-3.410.10.0669.81238612320.066100
3.4-3.89.20.06110.21011410960.06199.9
3.8-4.3910.50.0669.4102969810.066100
4.39-5.3810.70.05910.390378430.059100
5.38-7.610.30.0669.569146710.066100
7.6-26.8039.50.05510.836723880.05598

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
SCALAdata scaling
PDB_EXTRACT3data extraction
ADSCQuantumdata collection
MOSFLMdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 1.7→26.803 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.966 / SU B: 2.334 / SU ML: 0.038 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.062 / ESU R Free: 0.063
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN 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 RECORDS CONTAIN 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. RESIDUES A51-A56 WERE DISORDERED AND NOT VISIBLE IN THE ELECTRON DENSITY MAPS. THEY WERE NOT BUILT. 5. PHOSPHATE (PO4) ION FROM CRYSTALLIZATION AND GLYCEROL (GOL) FROM CRYO SOLUTION WERE MODELED. 6. UNEXPLAINED ELECTRON DENSITY NEAR RESIDUE 103 AND 118 WAS NOT MODELED.
RfactorNum. reflection% reflectionSelection details
Rfree0.164 1538 5.1 %RANDOM
Rwork0.144 ---
obs0.145 30438 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.065 Å2
Baniso -1Baniso -2Baniso -3
1-0.5 Å20.25 Å20 Å2
2--0.5 Å20 Å2
3----0.74 Å2
Refinement stepCycle: LAST / Resolution: 1.7→26.803 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1145 0 53 138 1336
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0221311
X-RAY DIFFRACTIONr_bond_other_d0.0020.02902
X-RAY DIFFRACTIONr_angle_refined_deg1.591.9971777
X-RAY DIFFRACTIONr_angle_other_deg0.93232217
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0395169
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.51824.90653
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.48915221
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.965157
X-RAY DIFFRACTIONr_chiral_restr0.0850.2197
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021458
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02247
X-RAY DIFFRACTIONr_nbd_refined0.2640.2212
X-RAY DIFFRACTIONr_nbd_other0.2060.2914
X-RAY DIFFRACTIONr_nbtor_refined0.1730.2624
X-RAY DIFFRACTIONr_nbtor_other0.0860.2718
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2320.2101
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1930.226
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2350.2104
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1860.223
X-RAY DIFFRACTIONr_mcbond_it2.6583875
X-RAY DIFFRACTIONr_mcbond_other0.5183323
X-RAY DIFFRACTIONr_mcangle_it3.23651321
X-RAY DIFFRACTIONr_scbond_it5.8328533
X-RAY DIFFRACTIONr_scangle_it8.06811456
LS refinement shellResolution: 1.7→1.745 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.269 111 -
Rwork0.221 2116 -
all-2227 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: -0.0888 Å / Origin y: 67.2756 Å / Origin z: 6.8212 Å
111213212223313233
T-0.0378 Å2-0.0071 Å2-0.0013 Å2--0.0225 Å2-0.0034 Å2---0.0308 Å2
L0.1806 °2-0.0356 °2-0.0352 °2-0.76 °20.2396 °2--0.4667 °2
S0.0198 Å °0.0029 Å °0.018 Å °-0.0235 Å °-0.0083 Å °-0.0524 Å °-0.0065 Å °-0.0092 Å °-0.0115 Å °

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