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- PDB-4yok: Crystal structure of a DUF3823 family protein (PARMER_04126) from... -

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Basic information

Entry
Database: PDB / ID: 4yok
TitleCrystal structure of a DUF3823 family protein (PARMER_04126) from Parabacteroides merdae ATCC 43184 at 1.80 A resolution
ComponentsPutative flagellar protein FliS
KeywordsUNKNOWN FUNCTION / Prealbumin-like fold / DUF3823 / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homology
Function and homology information


DUF3823, N-terminal / Domain of unknown function DUF3823_C / Protein of unknown function (DUF3823) N-terminal domain / Domain of unknown function (DUF3823_C) / Immunoglobulin-like - #2060 / Carboxypeptidase-like, regulatory domain / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Putative flagellar protein FliS
Similarity search - Component
Biological speciesParabacteroides merdae ATCC 43184 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a DUF3823 family protein (PARMER_04126) from Parabacteroides merdae ATCC 43184 at 1.80 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionMar 11, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 25, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Derived calculations / Refinement description / Source and taxonomy
Category: entity_src_gen / pdbx_struct_oper_list / software
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.2Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.3Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_conn_type
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_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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_conn_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative flagellar protein FliS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,6915
Polymers22,5041
Non-polymers1874
Water3,135174
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)41.866, 66.212, 68.593
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Putative flagellar protein FliS


Mass: 22503.545 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Parabacteroides merdae ATCC 43184 (bacteria)
Gene: PARMER_04126 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): PB1 / References: UniProt: A7AL02
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 174 / 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: 2.11 Å3/Da / Density % sol: 41.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.33
Details: 0.2M magnesium chloride, 32.0% polyethylene glycol 1000, 0.01M GSH (L-Glutathione reduced), GSSG (L-Glutathione oxidized), 0.1M sodium cacodylate pH 6.33

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 0.97947 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Dec 7, 2014
Details: Vertical focusing mirror; double crystal Si(111) monochromator
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97947 Å / Relative weight: 1
ReflectionResolution: 1.8→26.531 Å / Num. obs: 18276 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 2.58 % / Biso Wilson estimate: 22.698 Å2 / Rmerge F obs: 0.998 / Rmerge(I) obs: 0.062 / Rrim(I) all: 0.078 / Net I/σ(I): 11.04 / Num. measured all: 87402
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) allDiffraction-ID% possible all
1.8-1.860.5650.6491.57957321631610.821198.3
1.86-1.940.7570.4582.29272364236240.57899.5
1.94-2.030.8690.2913.58848346034450.36799.6
2.03-2.130.9310.2034.98299322632140.25699.6
2.13-2.270.9610.156.59240359435830.18999.7
2.27-2.440.9740.1198.38619333533120.1599.3
2.44-2.690.9870.08311.48874344934150.10599
2.69-3.070.9940.05615.88591334433100.07199
3.07-3.870.9970.034258937347734170.04398.3
3.870.9980.02631.38765345233610.03397.4

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassification
PDB_EXTRACT3.1data extraction
SHELXphasing
SHARPphasing
XDSNovember 3, 2014 BUILT=20141118data scaling
XSCALEdata scaling
BUSTER-TNT2.10.2refinement
SHELXDphasing
BUSTER2.10.2refinement
XDSdata reduction
RefinementMethod to determine structure: SAD / Resolution: 1.8→26.531 Å / Cor.coef. Fo:Fc: 0.9504 / Cor.coef. Fo:Fc free: 0.9404 / Occupancy max: 1 / Occupancy min: 0.4 / Cross valid method: THROUGHOUT / σ(F): 0
Details: 1. 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 ...Details: 1. 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. 2. THE MAD PHASES WERE USED AS RESTRAINTS DURING REFINEMENT. 3. MG, CL, AND GOL ARE PRESENT IN CRYSTALLIZATION/CRYO CONDITIONS. 4. ELECTRON DENSITY FOR LOOP 61-65 IS WEAK.
RfactorNum. reflection% reflectionSelection details
Rfree0.2141 925 5.08 %RANDOM
Rwork0.1733 ---
obs0.1753 18214 99.78 %-
Displacement parametersBiso max: 94.69 Å2 / Biso mean: 29.4735 Å2 / Biso min: 13.95 Å2
Baniso -1Baniso -2Baniso -3
1--0.0591 Å20 Å20 Å2
2---4.7125 Å20 Å2
3---4.7716 Å2
Refine analyzeLuzzati coordinate error obs: 0.188 Å
Refinement stepCycle: LAST / Resolution: 1.8→26.531 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1514 0 9 174 1697
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d734SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes46HARMONIC2
X-RAY DIFFRACTIONt_gen_planes234HARMONIC5
X-RAY DIFFRACTIONt_it1575HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion207SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact1853SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d1575HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg2146HARMONIC21.05
X-RAY DIFFRACTIONt_omega_torsion4.08
X-RAY DIFFRACTIONt_other_torsion2.54
LS refinement shellResolution: 1.8→1.91 Å / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.2541 165 5.71 %
Rwork0.2035 2727 -
all0.2064 2892 -
obs--99.78 %
Refinement TLS params.Method: refined / Origin x: 37.5799 Å / Origin y: 65.1055 Å / Origin z: 8.1515 Å
111213212223313233
T-0.0506 Å20.0041 Å20.0136 Å2--0.047 Å20.0034 Å2---0.0292 Å2
L0.7917 °20.0157 °20.5062 °2-0.4181 °20.1161 °2--1.8339 °2
S0.0369 Å °-0.0513 Å °-0.0168 Å °0.0269 Å °0.0431 Å °-0.0169 Å °0.0109 Å °0.1021 Å °-0.0799 Å °
Refinement TLS groupSelection details: {A|28 - 226}

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