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- PDB-2ql8: Crystal structure of a putative redox protein (lsei_0423) from la... -

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Basic information

Entry
Database: PDB / ID: 2ql8
TitleCrystal structure of a putative redox protein (lsei_0423) from lactobacillus casei atcc 334 at 1.50 A resolution
ComponentsPutative redox protein
KeywordsOXIDOREDUCTASE / Structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


response to oxidative stress
Similarity search - Function
Organic hydroperoxide resistance protein famiy / 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
BENZOIC ACID / Predicted redox protein, regulator of disulfide bond formation
Similarity search - Component
Biological speciesLactobacillus casei (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.5 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of putative redox protein (YP_805721.1) from Lactobacillus casei ATCC 334 at 1.50 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJul 12, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 24, 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: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Oct 25, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.5Jul 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 1.6Jan 25, 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 1.7Oct 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
Remark 300 BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAINS. ... BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAINS. SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). SIZE EXCLUSION CHROMATOGRAPHY SUGGESTS THE ASSIGNMENT OF A DIMER AS THE SIGNIFICANT OLIGOMERIZATION STATE.
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 PARTIALLY 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: Putative redox protein
B: Putative redox protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,63413
Polymers31,8312
Non-polymers80311
Water7,764431
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8610 Å2
ΔGint-25 kcal/mol
Surface area12580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.990, 81.990, 129.880
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
DetailsSIZE EXCLUSION CHROMATOGRAPHY SUGGESTS THE ASSIGNMENT OF A DIMER AS THE SIGNIFICANT OLIGOMERIZATION STATE.

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Components

#1: Protein Putative redox protein


Mass: 15915.334 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus casei (bacteria) / Strain: ATCC 334 / Gene: YP_805721.1, LSEI_0423 / Plasmid: speedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q03BZ3
#2: Chemical ChemComp-BEZ / BENZOIC ACID


Mass: 122.121 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H6O2
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 431 / 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: 3.43 Å3/Da / Density % sol: 64.11 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: NANODROP, 2.0M (NH4)2SO4, 0.1M Tris-HCl pH 8.5, 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: 0.91837, 0.97917, 0.97891
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 1, 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
20.979171
30.978911
ReflectionResolution: 1.5→29.761 Å / Num. obs: 71427 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 24.94 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 18.13
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.5-1.550.5172.54644812464197.4
1.55-1.620.3913.357472152011100
1.62-1.690.2974.448686128231100
1.69-1.780.2096.252186137051100
1.78-1.890.1399.15097813337199.9
1.89-2.040.08514.353269138851100
2.04-2.240.05421.550781131841100
2.24-2.560.0428.25200713475199.9
2.56-3.230.02739.25284613677199.9
3.23-29.7610.02152.85158513480198.8

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3data extraction
MAR345CCDdata collection
XDSdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.5→29.761 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.97 / SU B: 1.698 / SU ML: 0.029 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.052 / ESU R Free: 0.049
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. ETHYLENE GLYCOL IS MODELED BASED ON CRYO CONDITIONS. 4. THE BENZOIC ACID (BEZ) MOLECULE IS ASSIGNED BASED ON THE ELECTRON DENSITY AND ITS INTERACTION WITH THE PROTEIN. IT COULD BE SOME RELATED COMPOUND WITH A SIMILAR STRUCTURE. 5. RESIDUES A0 AND B0-1 ARE DISORDERED AND WERE NOT MODELED.
RfactorNum. reflection% reflectionSelection details
Rfree0.159 3613 5.1 %RANDOM
Rwork0.135 ---
obs0.136 71338 99.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.81 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å20 Å2
2---0.03 Å20 Å2
3---0.05 Å2
Refinement stepCycle: LAST / Resolution: 1.5→29.761 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2162 0 54 431 2647
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0212353
X-RAY DIFFRACTIONr_bond_other_d0.0040.021561
X-RAY DIFFRACTIONr_angle_refined_deg1.5381.9663209
X-RAY DIFFRACTIONr_angle_other_deg0.9733845
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7245314
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.79525.14107
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.05615382
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.5921510
X-RAY DIFFRACTIONr_chiral_restr0.0910.2365
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022662
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02440
X-RAY DIFFRACTIONr_nbd_refined0.2220.2428
X-RAY DIFFRACTIONr_nbd_other0.1960.21655
X-RAY DIFFRACTIONr_nbtor_refined0.1720.21134
X-RAY DIFFRACTIONr_nbtor_other0.0890.21142
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1760.2249
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1460.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2260.210
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2720.240
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2080.224
X-RAY DIFFRACTIONr_mcbond_it2.92431537
X-RAY DIFFRACTIONr_mcbond_other2.0433589
X-RAY DIFFRACTIONr_mcangle_it3.66952378
X-RAY DIFFRACTIONr_scbond_it4.8588942
X-RAY DIFFRACTIONr_scangle_it6.45311814
X-RAY DIFFRACTIONr_rigid_bond_restr2.5534286
X-RAY DIFFRACTIONr_sphericity_free8.8283431
X-RAY DIFFRACTIONr_sphericity_bonded5.32633859
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.245 230 -
Rwork0.16 4922 -
obs-5152 98.81 %

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