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- PDB-4jgl: Crystal structure of a streptavidin-like protein (BACEGG_01519) f... -

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Basic information

Entry
Database: PDB / ID: 4jgl
TitleCrystal structure of a streptavidin-like protein (BACEGG_01519) from Bacteroides eggerthii DSM 20697 at 1.25 A resolution
Componentshypothetical protein
KeywordsStructural Genomics / Unknown Function / an orphan / streptavidin-like fold with two extra alpha helices / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homologyLipocalin - #530 / Lipocalin / Beta Barrel / Mainly Beta / Unknown ligand / :
Function and homology information
Biological speciesBacteroides eggerthii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.25 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a hypothetical protein (BACEGG_01519) from Bacteroides eggerthii DSM 20697 at 1.25 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionMar 1, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 3, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 24, 2014Group: Structure summary
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.4Feb 1, 2023Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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 6, 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

Downloads & links

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Assembly

Deposited unit
A: hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,1645
Polymers19,0211
Non-polymers1424
Water4,197233
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)79.322, 79.322, 50.113
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61
DetailsCRYSTAL PACKING ANALYSIS SUGGESTS THE ASSIGNMENT OF A MONOMER AS THE SIGNIFICANT OLIGOMERIZATION STATE.

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Components

#1: Protein hypothetical protein


Mass: 19021.312 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides eggerthii (bacteria) / Strain: DSM 20697 / Gene: BACEGG_01519, ZP_03458740.1 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): PB1 / References: UniProt: B7AGJ1
#2: Chemical ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 1 / Source method: obtained synthetically
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 233 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHIS CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THIS CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY RESIDUES 24-191 OF 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: 2.39 Å3/Da / Density % sol: 48.59 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.2M calcium acetate, 20.0% polyethylene glycol 3350, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.918401, 0.979338, 0.979108
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 20, 2012 / Details: KOHZU: Double Crystal Si(111)
RadiationMonochromator: Double Crystal Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9184011
20.9793381
30.9791081
ReflectionResolution: 1.25→28.331 Å / Num. all: 49718 / Num. obs: 49718 / % possible obs: 100 % / Redundancy: 11 % / Rsym value: 0.097 / Net I/σ(I): 12.6
Reflection shell

Rmerge(I) obs: 0.014 / Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.25-1.2810.90.53980536451.371100
1.28-1.32110.73930735841.081100
1.32-1.36110.83791934570.914100
1.36-1.41113690133580.752100
1.4-1.44111.23616132930.599100
1.44-1.49111.63452831310.442100
1.49-1.55112.23372830550.335100
1.55-1.6111.12.93267829560.251100
1.61-1.69113.73106628140.198100
1.69-1.77114.52988827060.161100
1.77-1.86115.52813725490.128100
1.86-1.98116.52702524550.104100
1.98-2.1110.972484122710.095100
2.11-2.2810.87.92333821580.083100
2.28-2.510.682077119550.079100
2.5-2.810.28.41813317820.074100
2.8-3.2311.28.81762715740.068100
3.23-3.9511.6111550213400.055100
3.95-5.5911.511.51200510450.052100
5.59-28.33110.99.164305900.06499.1

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
SHELXphasing
SHARPphasing
SCALA3.3.20data scaling
REFMAC5.5.0110refinement
MOSFLMdata reduction
SHELXDphasing
RefinementMethod to determine structure: MAD / Resolution: 1.25→28.331 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.976 / Occupancy max: 1 / Occupancy min: 0.1 / SU B: 1.104 / SU ML: 0.021 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.037 / ESU R Free: 0.035
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. CALCIUM IONS (CA) AND 1,2-ETHANEDIOL (EDO) MOLECULES FROM THE CRYSTALLIZATION/CRYOPROTECTION SOLUTION ARE MODELED. 4. AN UNKNOWN LIAGAND (UNL) HAS BEEN MODELED AT THE SURFACE OF THE PROTEIN BASED ON THE ELECTRON DENSITY. THE DENSITY RESEMBLES NITROBENZENE (NBZ), BENZOIC ACID (BEZ) AND NICOTINIC ACID (NIO). THE EXACT CHEMICAL SPECIES COULD NOT BE DETERMINED WITH THE AVAILABLE DATA.
RfactorNum. reflection% reflectionSelection details
Rfree0.153 2515 5.1 %RANDOM
Rwork0.134 ---
obs0.135 49663 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 54.62 Å2 / Biso mean: 18.7919 Å2 / Biso min: 8.36 Å2
Baniso -1Baniso -2Baniso -3
1-0.29 Å20.14 Å20 Å2
2--0.29 Å20 Å2
3----0.43 Å2
Refinement stepCycle: LAST / Resolution: 1.25→28.331 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1189 0 15 233 1437
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0221334
X-RAY DIFFRACTIONr_bond_other_d0.0010.02903
X-RAY DIFFRACTIONr_angle_refined_deg1.4071.981825
X-RAY DIFFRACTIONr_angle_other_deg0.7963.0022221
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7575179
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.86624.83962
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.78415224
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.91154
X-RAY DIFFRACTIONr_chiral_restr0.0790.2189
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211541
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02278
X-RAY DIFFRACTIONr_mcbond_it2.253809
X-RAY DIFFRACTIONr_mcbond_other1.3493326
X-RAY DIFFRACTIONr_mcangle_it3.43751320
X-RAY DIFFRACTIONr_scbond_it4.0568525
X-RAY DIFFRACTIONr_scangle_it5.76711493
X-RAY DIFFRACTIONr_rigid_bond_restr1.72832237
X-RAY DIFFRACTIONr_sphericity_free7.0093247
X-RAY DIFFRACTIONr_sphericity_bonded3.52932190
LS refinement shellResolution: 1.25→1.282 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.261 207 -
Rwork0.239 3420 -
all-3627 -
obs--99.83 %

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